diff --git a/DESCRIPTION b/DESCRIPTION
index be92b784..e41fec5c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: fbi
 Title: Finnish Biodiversity Indicators
-Version: 0.11.5
+Version: 0.11.5.9000
 Authors@R: c(
     person(given = "Finnish Museum of Natural History - Luomus",
            role = "cph"),
diff --git a/docs/authors.html b/docs/authors.html
index 7b808a3f..694e9bb8 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -92,13 +92,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Morris W (2024).
 <em>fbi: Finnish Biodiversity Indicators</em>.
-R package version 0.11.5, https://indicators.laji.fi, <a href="https://github.com/luomus/fin-biodiv-indicators" class="external-link">https://github.com/luomus/fin-biodiv-indicators</a>. 
+R package version 0.11.5.9000, https://indicators.laji.fi, <a href="https://github.com/luomus/fin-biodiv-indicators" class="external-link">https://github.com/luomus/fin-biodiv-indicators</a>. 
 </p>
       <pre>@Manual{,
   title = {fbi: Finnish Biodiversity Indicators},
   author = {William K. Morris},
   year = {2024},
-  note = {R package version 0.11.5, https://indicators.laji.fi},
+  note = {R package version 0.11.5.9000, https://indicators.laji.fi},
   url = {https://github.com/luomus/fin-biodiv-indicators},
 }</pre>
     </div>
diff --git a/docs/dev/CODE_OF_CONDUCT.html b/docs/dev/CODE_OF_CONDUCT.html
index 3906f105..8f0caf64 100644
--- a/docs/dev/CODE_OF_CONDUCT.html
+++ b/docs/dev/CODE_OF_CONDUCT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/CONTRIBUTING.html b/docs/dev/CONTRIBUTING.html
index 0139895f..ae80ead6 100644
--- a/docs/dev/CONTRIBUTING.html
+++ b/docs/dev/CONTRIBUTING.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/LICENSE-text.html b/docs/dev/LICENSE-text.html
index 8f00e84f..9a077fec 100644
--- a/docs/dev/LICENSE-text.html
+++ b/docs/dev/LICENSE-text.html
@@ -10,7 +10,7 @@
     
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-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/LICENSE.html b/docs/dev/LICENSE.html
index 1d9248fc..743cc0f9 100644
--- a/docs/dev/LICENSE.html
+++ b/docs/dev/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/api.html b/docs/dev/api.html
index 965ad6e1..228feb8a 100644
--- a/docs/dev/api.html
+++ b/docs/dev/api.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/alpine-birds.html b/docs/dev/articles/alpine-birds.html
index 58a9beee..6a6c202e 100644
--- a/docs/dev/articles/alpine-birds.html
+++ b/docs/dev/articles/alpine-birds.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/butterfly-abundance.html b/docs/dev/articles/butterfly-abundance.html
index 6714d32c..6bb25e00 100644
--- a/docs/dev/articles/butterfly-abundance.html
+++ b/docs/dev/articles/butterfly-abundance.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/community-temperature-index.html b/docs/dev/articles/community-temperature-index.html
index cd7ddb6a..7771f34a 100644
--- a/docs/dev/articles/community-temperature-index.html
+++ b/docs/dev/articles/community-temperature-index.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/community-temperature-indices.html b/docs/dev/articles/community-temperature-indices.html
index 14642d6a..0781c5f8 100644
--- a/docs/dev/articles/community-temperature-indices.html
+++ b/docs/dev/articles/community-temperature-indices.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/configuration.html b/docs/dev/articles/configuration.html
index e1a9d0b5..56f299ab 100644
--- a/docs/dev/articles/configuration.html
+++ b/docs/dev/articles/configuration.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/farmland-birds.html b/docs/dev/articles/farmland-birds.html
index b942cda2..9e6b093a 100644
--- a/docs/dev/articles/farmland-birds.html
+++ b/docs/dev/articles/farmland-birds.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/farmland-butterflies.html b/docs/dev/articles/farmland-butterflies.html
index 20f20ab8..1dde6142 100644
--- a/docs/dev/articles/farmland-butterflies.html
+++ b/docs/dev/articles/farmland-butterflies.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/forest-birds.html b/docs/dev/articles/forest-birds.html
index 057c0239..d881e066 100644
--- a/docs/dev/articles/forest-birds.html
+++ b/docs/dev/articles/forest-birds.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 78924641..eb3b6565 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/mire-birds.html b/docs/dev/articles/mire-birds.html
index ee90c3dc..b5df9294 100644
--- a/docs/dev/articles/mire-birds.html
+++ b/docs/dev/articles/mire-birds.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/moths.html b/docs/dev/articles/moths.html
index a3af2618..3ebbf179 100644
--- a/docs/dev/articles/moths.html
+++ b/docs/dev/articles/moths.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/multi-taxon-indicator-trim.html b/docs/dev/articles/multi-taxon-indicator-trim.html
index a69b7af6..ad46fb26 100644
--- a/docs/dev/articles/multi-taxon-indicator-trim.html
+++ b/docs/dev/articles/multi-taxon-indicator-trim.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/overall-abundance.html b/docs/dev/articles/overall-abundance.html
index 4b152394..e95fd2b8 100644
--- a/docs/dev/articles/overall-abundance.html
+++ b/docs/dev/articles/overall-abundance.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/overview.html b/docs/dev/articles/overview.html
index 80848fe9..743fbb78 100644
--- a/docs/dev/articles/overview.html
+++ b/docs/dev/articles/overview.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/single-taxon-indicator-rbms.html b/docs/dev/articles/single-taxon-indicator-rbms.html
index eb6f9dea..9cd38c31 100644
--- a/docs/dev/articles/single-taxon-indicator-rbms.html
+++ b/docs/dev/articles/single-taxon-indicator-rbms.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/single-taxon-indicator-trim.html b/docs/dev/articles/single-taxon-indicator-trim.html
index 8b798444..9e060dc4 100644
--- a/docs/dev/articles/single-taxon-indicator-trim.html
+++ b/docs/dev/articles/single-taxon-indicator-trim.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/articles/winter-birds.html b/docs/dev/articles/winter-birds.html
index 8ba7fa21..9beef281 100644
--- a/docs/dev/articles/winter-birds.html
+++ b/docs/dev/articles/winter-birds.html
@@ -29,7 +29,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/authors.html b/docs/dev/authors.html
index a2e56d89..33365661 100644
--- a/docs/dev/authors.html
+++ b/docs/dev/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -92,13 +92,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Morris W (2024).
 <em>fbi: Finnish Biodiversity Indicators</em>.
-R package version 0.11.4.9000, https://indicators.laji.fi, <a href="https://github.com/luomus/fin-biodiv-indicators" class="external-link">https://github.com/luomus/fin-biodiv-indicators</a>. 
+R package version 0.11.5.9000, https://indicators.laji.fi, <a href="https://github.com/luomus/fin-biodiv-indicators" class="external-link">https://github.com/luomus/fin-biodiv-indicators</a>. 
 </p>
       <pre>@Manual{,
   title = {fbi: Finnish Biodiversity Indicators},
   author = {William K. Morris},
   year = {2024},
-  note = {R package version 0.11.4.9000, https://indicators.laji.fi},
+  note = {R package version 0.11.5.9000, https://indicators.laji.fi},
   url = {https://github.com/luomus/fin-biodiv-indicators},
 }</pre>
     </div>
diff --git a/docs/dev/index.html b/docs/dev/index.html
index d012cb7e..52dd69f9 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 9046d718..a5628d25 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -18,7 +18,7 @@ articles:
   single-taxon-indicator-rbms: single-taxon-indicator-rbms.html
   single-taxon-indicator-trim: single-taxon-indicator-trim.html
   winter-birds: winter-birds.html
-last_built: 2024-01-22T11:05Z
+last_built: 2024-02-28T07:35Z
 urls:
   reference: https://indicators-dev.laji.fi/docs/dev/reference
   article: https://indicators-dev.laji.fi/docs/dev/articles
diff --git a/docs/dev/reference/check_input.html b/docs/dev/reference/check_input.html
index 415ac978..c8828277 100644
--- a/docs/dev/reference/check_input.html
+++ b/docs/dev/reference/check_input.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">fbi</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.4.9000</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.11.5.9000</small>
 
     
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Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing","text":"Small typos grammatical errors documentation may edited long changes made source file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"Contributing","text":"make substantial pull request, always file issue make sure someone team agrees ’s problem.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"","what":"Pull request process","title":"Contributing","text":"recommend create Git branch pull request (PR). New code follow style used project. user-facing changes, add section top NEWS.Rd current development version header describing changes made followed username, links relevant issue(s)/PR(s).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing","text":"Please note project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021-2024 LUOMUS - Finnish Museum Natural History Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"NA","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indicators provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"indicator-types","dir":"","previous_headings":"Overview","what":"Indicator types","title":"NA","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"single-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Single-taxon indicators","title":"NA","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator (see /taxa-extra). example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"multi-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Multi-taxon indicators","title":"NA","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"supported-operations","dir":"","previous_headings":"Overview","what":"Supported Operations","title":"NA","text":"Get lists available indicators Get configuration indicator Get statistics indicator CSV JSON Get SVG image indicator","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"examples","dir":"","previous_headings":"Overview","what":"Examples","title":"NA","text":"Get list multi-taxon indicators: Get list taxa included Winter Bird indicator: See Winter Bird indicator configured: Get Winter Bird indicator output json: Get single-taxon (Goldcrest) Winter Bird trim index output southern Finland CSV: Get SVG image Farmland Butterflies RBMS index","code":"$ curl \"https://indicators.laji.fi/indices\" $ curl \"https://indicators.laji.fi/taxa/wb\" $ curl \"https://indicators.laji.fi/config/wb\" $ curl \"https://indicators.laji.fi/data/wb\" $ curl \"https://indicators.laji.fi/csv/wb?taxon=MX.33954&model=trim&region=south\" $ curl -o bf.svg \"https://indicators.laji.fi/svg/bf?model=rbms\""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/alpine-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Alpine Bird Indicator","title":"Alpine Bird Indicator","text":"Northern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/butterfly-abundance.html","id":"section","dir":"Articles","previous_headings":"","what":"Butterfly Abundance Indicator","title":"Butterfly Abundance Indicator","text":"Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Community temperature index","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(lme4) library(arm)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Community temperature index","text":"five fields required survey data. filters restrict survey data Dec-Jan “Winter Bird Census” monitoring dataset December 1958 onwards selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data limit site first survey year (year period Dec-Jan).","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Winter Bird Census\",   date_range_ymd = c(\"1958-12-01\", \"\"),   date_range_md= c(\"12-01\", \"01-31\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_winter(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Community temperature index","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa species temperature index values defined. count data taxa can now downloaded FinBIF. count data combined survey data species temperature indices.","code":"select <- c(\"document_id\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select sti <- c(   \"Poecile montanus\" = -7.51,   \"Regulus regulus\" = -4.23,   \"Lophophanes cristatus\" = -5.90,   \"Certhia familiaris\" = -6.89 ) counts <- lapply(   names(sti),   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, combine_with_surveys, surveys)  counts <- mapply(mutate, counts, sp = names(sti), SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts[[\"sti\"]] <- sti[counts[[\"sp\"]]]"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Community temperature index","text":"community temperature index year created fitting linear mixed effects regression model combined data.","code":"cti_data <- summarise(   group_by(counts, location_id, year),   cti = sum(abundance * sti) / sum(abundance), .groups = \"drop\" )  cti <- lmer(cti ~ (1 | location_id) + (1 | year), cti_data)  cti <- data.frame(index = coef(cti)[[\"year\"]], se = se.coef(cti)[[\"year\"]])  cti[[\"time\"]] <- as.integer(row.names(cti))  names(cti) <- c(\"index\", \"se\", \"time\") ggplot(cti) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-indices.html","id":"section","dir":"Articles","previous_headings":"","what":"Community Temperature Indices","title":"Community Temperature Indices","text":"Winter Birds Summer Birds Farmland Butterflies","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"defaults","dir":"Articles","previous_headings":"","what":"Defaults","title":"Configuration","text":"Default parameters apply indicators can specified special object top-level key, default (see ). Defaults can overwritten specifying different parameters value indicator objects.","code":"default:   surveys:     selection:     - document_id     - location_id     - year     - month     - day     has_value:     - document_id     - location_id     - year     - month     - day   counts:     abundance: abundance   use_data_after: \"01-01\""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"sections","dir":"Articles","previous_headings":"","what":"Sections","title":"Configuration","text":"following describes section multi-taxon indicator objects detail.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"name","dir":"Articles","previous_headings":"Sections","what":"Name","title":"Configuration","text":"string giving long-form name multi-taxon indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"taxa","dir":"Articles","previous_headings":"Sections","what":"Taxa","title":"Configuration","text":"array defining taxa included multi-taxon indicator single-taxon indicators calculated. element array must include: code: string indicating FinBIF taxon MX code (e.g, MX.27328). binomial: string indicating scientific taxon name (e.g., Crex crex). optionally include one : extra_codes: array FinBIF taxon MX codes include along nominal taxon declared code. subtaxa: boolean indicating whether include observations child taxa taxa declared code extra_codes. start_year: integer indicating year observation data taxa begin. Observation data year excluded. Note start_year greater base_year (see section Model) base_year taxon set start_year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"extra-taxa","dir":"Articles","previous_headings":"Sections","what":"Extra taxa","title":"Configuration","text":"array defining taxa included parent multi-taxon indicator single-taxon indicators calculated. element array configured way taxa .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"from","dir":"Articles","previous_headings":"Sections","what":"From","title":"Configuration","text":"Multi-taxon indicators can constituent single-taxon indicators. case, section indicates multi-taxon indicator (form short-code) input data comes .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"filters","dir":"Articles","previous_headings":"Sections","what":"Filters","title":"Configuration","text":"filters section object defining list filters apply observation data FinBIF. See finbif R package documentation details.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"surveys","dir":"Articles","previous_headings":"Sections","what":"Surveys","title":"Configuration","text":"surveys section defines fields selected getting survey data FinBIF. Fields selected key selection array (see finbif R package documentation available fields). second key, has_value, array indicates fields must null values filtering records.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"counts","dir":"Articles","previous_headings":"Sections","what":"Counts","title":"Configuration","text":"counts section defines fields selected accessing count data FinBIF. sections uses selection has_value key manner . additional key, abundance, used indicate field used abundance (counts) data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"combine","dir":"Articles","previous_headings":"Sections","what":"Combine","title":"Configuration","text":"section combine defines single-taxon indicator data combined form multi-taxon indicator. Options include: geometric_mean: combines relative abundance geometric mean abundance. cti: combine abundances community temperature index. overall_abundance: combine abundance total abundance taxon group.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"use-data-after","dir":"Articles","previous_headings":"Sections","what":"Use data after","title":"Configuration","text":"section use_data_after defines calendar date (form \"MM-DD\") data collected current year start included indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"model","dir":"Articles","previous_headings":"Sections","what":"Model","title":"Configuration","text":"model section defines single- multi-taxon indicators calculated survey count data sourced FinBIF. section consists one model objects object keys indicate model used. Models include: trim: Trends Indices Monitoring data model (via rtrim) rbms: Generalised abundance indices butterfly monitoring count data ( via rbms) lmer: Linear Mixed Effects Regression (via lme4) element model section must include: surveys_process: array survey data processing functions (see processing ) counts_process array count data processing functions (see processing ) optionally include: base_year: integer indicating base year indicator. args: additional arguments passed modelling function.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/farmland-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Bird Indicator","title":"Farmland Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/farmland-butterflies.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Butterfly Indicator","title":"Farmland Butterfly Indicator","text":"RBMS TRIM","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/forest-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Forest Bird Indicator","title":"Forest Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/mire-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Mire Bird Indicator","title":"Mire Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/moths.html","id":"section","dir":"Articles","previous_headings":"","what":"Moth Indicator","title":"Moth Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Multi-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Multi-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Multi-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing multi-taxon indicator selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select taxa <- c(   \"Vanellus vanellus\", \"Numenius arquata\", \"Alauda arvensis\", \"Hirundo rustica\",   \"Delichon urbicum\", \"Anthus pratensis\", \"Saxicola rubetra\", \"Turdus pilaris\",   \"Sylvia communis\", \"Corvus monedula\", \"Sturnus vulgaris\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = c(\"scientific_name\", \"document_id\", abundance = \"pair_abundance\"),   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, zero_fill, surveys)  counts <- lapply(counts, sum_by_event)  counts <- lapply(counts, remove_all_zero_locations)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"fit-trim-models","dir":"Articles","previous_headings":"","what":"Fit TRIM Models","title":"Multi-taxon indicator (trim)","text":"TRIM model used estimate change abundance time taxon.","code":"model <- lapply(   counts, trim, count_col =\"abundance\", site_col = \"location_id\",   year_col = \"year\" )"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Multi-taxon indicator (trim)","text":"index change relative abundance created taxon setting base year year 2000. indices combined single table geometric mean relative abundance associated uncertainty can calculated via Monte Carlo simulation method (see details).","code":"indices <- lapply(model, index, base = 2000)  indices <- mapply(mutate, indices, sp = taxa, SIMPLIFY = FALSE)  indices <- do.call(rbind, indices) n <- 1000 max_cv <- 3 imputed_min <- .01 truncfac <- 10 base <- 1 nyrs <- 44  indices <- mutate(   indices, cv = ifelse(imputed >= .1 & se_imp > 0, se_imp / imputed, NA_real_) )  indices <- group_by(indices, sp)  indices <- mutate(indices, cv = mean(cv, na.rm = TRUE))  indices <- filter(indices, cv < max_cv)  indices <- mutate(indices, imputed = pmax(imputed, imputed_min))  indices <- mutate(indices, se_imp = if_else(imputed > imputed_min, se_imp, 0))  indices <- mutate(indices, se_imp = se_imp / imputed)  indices <- mutate(indices, imputed = log(imputed))  indices <- group_by(indices, time, sp)  indices <- summarise(   indices, mc = rnorm(n, imputed, se_imp), i = seq(n), .groups = \"keep\" )  indices <- mutate(indices, mc = pmax(mc, log(imputed_min)))  indices <- group_by(indices, sp, i)  indices <- arrange(indices, time)  indices <- mutate(   indices, mcf = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- arrange(indices, -time)  indices <- mutate(   indices, mcb = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- group_by(indices, i, time)  index <- summarise(   indices,   mcf = mean(mcf, na.rm = TRUE), mcb = mean(mcb, na.rm = TRUE),   .groups = \"drop_last\" )  index <- arrange(index, time)  index <- mutate(index, mcf = cumsum(lag(lead(mcf, base - 1), base, 0)))  index <- arrange(index, -time)  index <- mutate(   index, mcb = cumsum(lag(lead(mcb, nyrs - base), nyrs - base + 1, 0)) )  index <- group_by(index, time)  index <- summarise(   index,   index = exp(mean(mcf)) * exp(mean(mcb)),   se = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) ) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Overall abundance","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Overall abundance","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit surveys sites least seven fortnights surveyed limit site’s surveys first survey fortnight.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- require_seven_fortnights(surveys)  surveys <- pick_first_survey_in_fortnight(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Overall abundance","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing total abundance selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : sum counts survey site sections; combine count survey data together; amd sum counts site-year combination. count data can summed across taxa.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select taxa <- c(   \"Aglais urticae\",   \"Boloria euphrosyne\",   \"Lycaena virgaureae\",   \"Polygonia c-album\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, sum_over_sections)  counts <- lapply(counts, combine_with_surveys, surveys)  counts <- lapply(counts, sum_by_event) counts <- mapply(mutate, counts, sp = taxa, SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts <- group_by(counts, location_id, year)  counts <- summarise(counts, abundance = sum(abundance), .groups = \"drop\")"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Overall abundance","text":"index total abundance year created fitting TRIM model combined data setting base year year 2000.","code":"model <- trim(abundance ~ location_id + year, counts)  index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"api","dir":"Articles","previous_headings":"","what":"API","title":"Overview","text":"HTTP API access indicator data products available developers. API documented .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"updates","dir":"Articles","previous_headings":"","what":"Updates","title":"Overview","text":"Indicators updated nightly 12 8am random order. update process checks FinBIF new input data updates affected indices many possible within 8hr update process window.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"indicator-types","dir":"Articles","previous_headings":"","what":"Indicator types","title":"Overview","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"single-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Single-taxon indicators","title":"Overview","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator. example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"multi-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Multi-taxon indicators","title":"Overview","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (rbms)","text":"following packages required. packages available CRAN apart fbi rbms can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rbms)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (rbms)","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data convert year month day fields single date field.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- format_date(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (rbms)","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). count data Aglais urticae (Small tortoiseshell) can now downloaded FinBIF. Two processing functions applied count data : sum counts survey site sections; combine count survey data together.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Aglais urticae\",   filter = filter,   select = select ,   n = \"all\",   quiet = TRUE ) counts <- sum_over_sections(counts, surveys)  counts <- combine_with_surveys(counts, surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"fit-rbms-model","dir":"Articles","previous_headings":"","what":"Fit RBMS Model","title":"Single-taxon indicator (rbms)","text":"RBMS model used estimate change abundance time (see RBMS documentation details) uncertainty estimated via bootstrapping.","code":"StartMonth <- 4 EndMonth <- 9 StartDay <- 1 EndDay <- 30 Anchor <- TRUE AnchorLength <- 14 AnchorLag <- 14 AnchorTimeUnit <- \"d\" NbrSample <- 500 MinVisit <- 5 MinOccur <- 2 MinNbrSite <- 5 MaxTrial <- 4 GamFamily <- \"nb\" FlightCurveTimeUnit <- \"w\" MultiVisit <- \"mean\" MinFC <- 0.10 boot_n <- 200  surveys <- select(surveys, site_id = location_id, year, date)  init_year <- min(surveys[[\"year\"]])  last_year <- max(surveys[[\"year\"]])  nyears <- last_year - init_year + 1  ts_date <- ts_dwmy_table(InitYear = init_year, LastYear = last_year)  ts_season <- ts_monit_season(   d_series     = ts_date,   StartMonth   = StartMonth,   EndMonth     = EndMonth,   StartDay     = StartDay,   EndDay       = EndDay,   Anchor       = Anchor,   AnchorLength = AnchorLength,   AnchorLag    = AnchorLag,   TimeUnit     = AnchorTimeUnit )  ts_season_visit <- ts_monit_site(m_visit = surveys, ts_season = ts_season)  counts <- mutate(counts, species = 1)  counts <- select(   counts, count = abundance, site_id = location_id, year, date, species )  ts_season_count <- ts_monit_count_site(   m_season_visit = ts_season_visit, m_count = counts )  ts_flight_curve <- flight_curve(   ts_season_count = ts_season_count,   NbrSample       = NbrSample,   MinVisit        = MinVisit,   MinOccur        = MinOccur,   MinNbrSite      = MinNbrSite,   MaxTrial        = MaxTrial,   GamFamily       = GamFamily,   SpeedGam        = FALSE,   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit,   verbose         = FALSE )  impt_counts <- impute_count(   ts_season_count = ts_season_count,   ts_flight_curve = ts_flight_curve[[\"pheno\"]],   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit )  sindex <- site_index(butterfly_count = impt_counts, MinFC = MinFC)  bootsample <- boot_sample(data = sindex, boot_n = boot_n)  index_mc <- mapply(   collated_index,   bootID = seq_len(boot_n),   MoreArgs = list(data = sindex, s_sp = 1, boot_ind = bootsample),   SIMPLIFY = FALSE )"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (rbms)","text":"index change relative abundance uncertainty derived bootstrapped estimates can created setting base year year 2000.","code":"base <- which(sort(unique(surveys[[\"year\"]])) == 2000)  index_mc <- lapply(index_mc, getElement, \"col_index\")  index_mc <- do.call(rbind, index_mc)  index_mc <- mutate(index_mc, mc = log(pmax(1 / 100, COL_INDEX)), time = M_YEAR)  index_mc <- group_by(index_mc, BOOTi)  index_mc <- arrange(index_mc, time)  index_mc <- mutate(index_mc, mcf = lead(mc) - mc)  index_mc <- mutate(index_mc, mcf = lead(mcf, base - 1))  index_mc <- mutate(index_mc, mcf = lag(mcf, base, 0))  index_mc <- mutate(index_mc, mcf = cumsum(mcf))  index_mc <- arrange(index_mc, -time)  index_mc <- mutate(index_mc, mcb = lead(mc) - mc)  index_mc <- mutate(index_mc, mcb = lead(mcb, nyears - base))  index_mc <- mutate(index_mc, mcb = lag(mcb, nyears - base + 1, 0))  index_mc <- mutate(index_mc, mcb = cumsum(mcb))  index_mc <- group_by(index_mc, time)  index <- summarise(   index_mc,   mean = exp(mean(mcf)) * exp(mean(mcb)),   sd = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) )  index <- mutate(index, lower = mean - sd, upper = mean + sd) ggplot(index) + aes(x = parse_date_time(time, \"Y\"), y = mean, ymin = lower, ymax = upper) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). count data Anthus pratensis (Meadow pipit) can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Anthus pratensis\",   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- zero_fill(counts, surveys)  counts <- sum_by_event(counts)  counts <- remove_all_zero_locations(counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"fit-trim-model","dir":"Articles","previous_headings":"","what":"Fit TRIM Model","title":"Single-taxon indicator (trim)","text":"TRIM model used estimate change abundance time.","code":"model <- trim(abundance ~ location_id + year, counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (trim)","text":"index change relative abundance created setting base year year 2000.","code":"index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/winter-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Winter Bird Indicator","title":"Winter Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Finnish Museum Natural History - Luomus. Copyright holder. William K. Morris. Author, maintainer.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Morris W (2024). fbi: Finnish Biodiversity Indicators. R package version 0.11.4.9000, https://indicators.laji.fi, https://github.com/luomus/fin-biodiv-indicators.","code":"@Manual{,   title = {fbi: Finnish Biodiversity Indicators},   author = {William K. Morris},   year = {2024},   note = {R package version 0.11.4.9000, https://indicators.laji.fi},   url = {https://github.com/luomus/fin-biodiv-indicators}, }"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/index.html","id":"finnish-biodiversity-indicators","dir":"","previous_headings":"","what":"Finnish Biodiversity Indicators","title":"Finnish Biodiversity Indicators","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indices provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/check_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Check input — check_input","title":"Check input — check_input","text":"Check indicator inputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/check_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check input — check_input","text":"","code":"check_input(index, model, taxon)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/check_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check input — check_input","text":"index Character. index? model Character. model? taxon Character. taxon?","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/clean_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean cache — clean_cache","title":"Clean cache — clean_cache","text":"Remove unneeded tables rows database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/clean_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean cache — clean_cache","text":"","code":"clean_cache(db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/clean_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean cache — clean_cache","text":"db Connection. Database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine with surveys — combine_with_surveys","title":"Combine with surveys — combine_with_surveys","text":"Combine count data survey data","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine with surveys — combine_with_surveys","text":"","code":"combine_with_surveys(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine with surveys — combine_with_surveys","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Combine with surveys — combine_with_surveys","text":"function combines counts surveys data. performs inner join counts surveys document_id. function assumes counts surveys data include document_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":null,"dir":"Reference","previous_headings":"","what":"Format date — format_date","title":"Format date — format_date","text":"Combine year, month, day survey single date string","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format date — format_date","text":"","code":"format_date(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format date — format_date","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format date — format_date","text":"function combines survey year, month day character string - separator. function assumes survey data includes year, month day.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get indices — get_indices","title":"Get indices — get_indices","text":"Get indices configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get indices — get_indices","text":"","code":"get_indices(file = Sys.getenv(\"R_CONFIG_FILE\"))"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get indices — get_indices","text":"file Configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Get output — get_output","title":"Get output — get_output","text":"Get serialized indicator outputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get output — get_output","text":"","code":"get_output(output, index, model, taxon, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get output — get_output","text":"output Character. type output? index Character. Update index? model Character. model use? taxon Character. taxon? region Character. region? db Connection. Database get output.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in fortnight — pick_first_survey_in_fortnight","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"Pick first survey fortnight discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"","code":"pick_first_survey_in_fortnight(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"function groups surveys location_id, year fortnightthen orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, year (integers) location_id, processed function require_seven_fortnights.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in winter — pick_first_survey_in_winter","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"Pick first winter survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"","code":"pick_first_survey_in_winter(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"function moves surveys occurring December ahead one year. enables December surveys grouped subsequent surveys occurring January winter. Surveys grouped location_id year ordered date. first survey group removed. two surveys share date location_id one picked random rest removed. function works assumption surveys winter December January surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in year — pick_first_survey_in_year","title":"Pick first survey in year — pick_first_survey_in_year","text":"Pick first survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in year — pick_first_survey_in_year","text":"","code":"pick_first_survey_in_year(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in year — pick_first_survey_in_year","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in year — pick_first_survey_in_year","text":"function groups surveys location_id year orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/process_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Process functions — process_funs","title":"Process functions — process_funs","text":"Functions process indicator input data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/process_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process functions — process_funs","text":"","code":"process_funs()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove all-zero locations — remove_all_zero_locations","title":"Remove all-zero locations — remove_all_zero_locations","text":"Discard locations taxa always zero abundance","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove all-zero locations — remove_all_zero_locations","text":"","code":"remove_all_zero_locations(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove all-zero locations — remove_all_zero_locations","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove all-zero locations — remove_all_zero_locations","text":"function groups counts location_id removes counts includes location_id abundance.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum gaps — require_minimum_gaps","title":"Require minimum gaps — require_minimum_gaps","text":"Remove survey site-years many large sampling gaps.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum gaps — require_minimum_gaps","text":"","code":"require_minimum_gaps(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum gaps — require_minimum_gaps","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum gaps — require_minimum_gaps","text":"function groups surveys data location_id year. removes groups survey period many large sampling gaps. many defined total gap length year 21 days large single sampling gap 7 days. function expects surveys data least location_id, year, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum weeks — require_minimum_weeks","title":"Require minimum weeks — require_minimum_weeks","text":"Remove survey site-years region covering less minimum number weeks.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum weeks — require_minimum_weeks","text":"","code":"require_minimum_weeks(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum weeks — require_minimum_weeks","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum weeks — require_minimum_weeks","text":"function groups surveys data location_id year. removes groups survey period less minimum number weeks given region. expects surveys data least location_id, year, region, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":null,"dir":"Reference","previous_headings":"","what":"Require seven fortnights — require_seven_fortnights","title":"Require seven fortnights — require_seven_fortnights","text":"Divide year approximate 2 week blocks, selecting blocks 10-16 discarding locations without survey remaining block","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require seven fortnights — require_seven_fortnights","text":"","code":"require_seven_fortnights(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require seven fortnights — require_seven_fortnights","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require seven fortnights — require_seven_fortnights","text":"function assigns survey approximate fortnight. fortnight defined days 16th day month days 15th day month. surveys falling outside date range seven fortnights second fortnight May second fortnight August removed. Surveys grouped location_id year surveys belonging groups least one survey occurring seven remaining fortnights discarded. function assumes surveys data day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":null,"dir":"Reference","previous_headings":"","what":"Require at least two years — require_two_years","title":"Require at least two years — require_two_years","text":"Discard locations less two survey years","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require at least two years — require_two_years","text":"","code":"require_two_years(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require at least two years — require_two_years","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require at least two years — require_two_years","text":"function groups surveys location_id removes surveys locations data one year. function assumes surveys data location_id year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Set start year — set_start_year","title":"Set start year — set_start_year","text":"Discard counts years start year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set start year — set_start_year","text":"","code":"set_start_year(counts, taxon, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set start year — set_start_year","text":"counts Count data. taxon Taxon configuration. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set start year — set_start_year","text":"function sets start year taxon counts. variable start_year configured given taxon count data prior start_year removed.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum by event — sum_by_event","title":"Sum by event — sum_by_event","text":"Sum counts surveys taxa year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum by event — sum_by_event","text":"","code":"sum_by_event(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum by event — sum_by_event","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum by event — sum_by_event","text":"functions groups count data location_id year. multiple taxa counts input data also grouped taxa. Counts summed across survey events locations years.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum over sections — sum_over_sections","title":"Sum over sections — sum_over_sections","text":"Sum counts sections surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum over sections — sum_over_sections","text":"","code":"sum_over_sections(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum over sections — sum_over_sections","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum over sections — sum_over_sections","text":"functions groups count data document_id (IDs individual surveys). multiple taxa counts input data also grouped taxa. Counts summed across survey sections count data provided surveys split parts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Update data — update_data","title":"Update data — update_data","text":"Update input data FinBIF.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update data — update_data","text":"","code":"update_data(type, index, taxon, db, do_update = FALSE)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update data — update_data","text":"type Character. type input data (e.g., surveys counts) index Character. Update data index? taxon Character. Update data taxon? Ignored type = \"surveys\" db Connection. Database update data FinBIF. do_update Logical. Update data regardless need.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update index — update_index","title":"Update index — update_index","text":"Update index output data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update index — update_index","text":"","code":"update_index(index, model, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update index — update_index","text":"index Character. Update index? model Character. model use? region Character. region? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_taxon_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update taxon index — update_taxon_index","title":"Update taxon index — update_taxon_index","text":"Update relative abundance index taxon.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_taxon_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update taxon index — update_taxon_index","text":"","code":"update_taxon_index(index, model, taxon, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_taxon_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update taxon index — update_taxon_index","text":"index Character. Update index? model Character. model use? taxon Character. Update data taxa? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":null,"dir":"Reference","previous_headings":"","what":"Zero fill — zero_fill","title":"Zero fill — zero_fill","text":"Combine count data survey data filling missing surveys count data zero counts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zero fill — zero_fill","text":"","code":"zero_fill(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Zero fill — zero_fill","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Zero fill — zero_fill","text":"function combines counts surveys data. performs right outer join counts surveys document_id. surveys corresponding data abundance filled zero. function assumes counts surveys data include document_id counts data includes abundance.","code":""}]
+[{"path":[]},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement helpdesk@laji.fi. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing","text":"Small typos grammatical errors documentation may edited long changes made source file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"Contributing","text":"make substantial pull request, always file issue make sure someone team agrees ’s problem.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"","what":"Pull request process","title":"Contributing","text":"recommend create Git branch pull request (PR). New code follow style used project. user-facing changes, add section top NEWS.Rd current development version header describing changes made followed username, links relevant issue(s)/PR(s).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing","text":"Please note project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021-2024 LUOMUS - Finnish Museum Natural History Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"NA","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indicators provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"indicator-types","dir":"","previous_headings":"Overview","what":"Indicator types","title":"NA","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"single-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Single-taxon indicators","title":"NA","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator (see /taxa-extra). example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"multi-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Multi-taxon indicators","title":"NA","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"supported-operations","dir":"","previous_headings":"Overview","what":"Supported Operations","title":"NA","text":"Get lists available indicators Get configuration indicator Get statistics indicator CSV JSON Get SVG image indicator","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/api.html","id":"examples","dir":"","previous_headings":"Overview","what":"Examples","title":"NA","text":"Get list multi-taxon indicators: Get list taxa included Winter Bird indicator: See Winter Bird indicator configured: Get Winter Bird indicator output json: Get single-taxon (Goldcrest) Winter Bird trim index output southern Finland CSV: Get SVG image Farmland Butterflies RBMS index","code":"$ curl \"https://indicators.laji.fi/indices\" $ curl \"https://indicators.laji.fi/taxa/wb\" $ curl \"https://indicators.laji.fi/config/wb\" $ curl \"https://indicators.laji.fi/data/wb\" $ curl \"https://indicators.laji.fi/csv/wb?taxon=MX.33954&model=trim&region=south\" $ curl -o bf.svg \"https://indicators.laji.fi/svg/bf?model=rbms\""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/alpine-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Alpine Bird Indicator","title":"Alpine Bird Indicator","text":"Northern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/butterfly-abundance.html","id":"section","dir":"Articles","previous_headings":"","what":"Butterfly Abundance Indicator","title":"Butterfly Abundance Indicator","text":"Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Community temperature index","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(lme4) library(arm)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Community temperature index","text":"five fields required survey data. filters restrict survey data Dec-Jan “Winter Bird Census” monitoring dataset December 1958 onwards selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data limit site first survey year (year period Dec-Jan).","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Winter Bird Census\",   date_range_ymd = c(\"1958-12-01\", \"\"),   date_range_md= c(\"12-01\", \"01-31\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_winter(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Community temperature index","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa species temperature index values defined. count data taxa can now downloaded FinBIF. count data combined survey data species temperature indices.","code":"select <- c(\"document_id\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select sti <- c(   \"Poecile montanus\" = -7.51,   \"Regulus regulus\" = -4.23,   \"Lophophanes cristatus\" = -5.90,   \"Certhia familiaris\" = -6.89 ) counts <- lapply(   names(sti),   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, combine_with_surveys, surveys)  counts <- mapply(mutate, counts, sp = names(sti), SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts[[\"sti\"]] <- sti[counts[[\"sp\"]]]"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-index.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Community temperature index","text":"community temperature index year created fitting linear mixed effects regression model combined data.","code":"cti_data <- summarise(   group_by(counts, location_id, year),   cti = sum(abundance * sti) / sum(abundance), .groups = \"drop\" )  cti <- lmer(cti ~ (1 | location_id) + (1 | year), cti_data)  cti <- data.frame(index = coef(cti)[[\"year\"]], se = se.coef(cti)[[\"year\"]])  cti[[\"time\"]] <- as.integer(row.names(cti))  names(cti) <- c(\"index\", \"se\", \"time\") ggplot(cti) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/community-temperature-indices.html","id":"section","dir":"Articles","previous_headings":"","what":"Community Temperature Indices","title":"Community Temperature Indices","text":"Winter Birds Summer Birds Farmland Butterflies","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"defaults","dir":"Articles","previous_headings":"","what":"Defaults","title":"Configuration","text":"Default parameters apply indicators can specified special object top-level key, default (see ). Defaults can overwritten specifying different parameters value indicator objects.","code":"default:   surveys:     selection:     - document_id     - location_id     - year     - month     - day     has_value:     - document_id     - location_id     - year     - month     - day   counts:     abundance: abundance   use_data_after: \"01-01\""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"sections","dir":"Articles","previous_headings":"","what":"Sections","title":"Configuration","text":"following describes section multi-taxon indicator objects detail.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"name","dir":"Articles","previous_headings":"Sections","what":"Name","title":"Configuration","text":"string giving long-form name multi-taxon indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"taxa","dir":"Articles","previous_headings":"Sections","what":"Taxa","title":"Configuration","text":"array defining taxa included multi-taxon indicator single-taxon indicators calculated. element array must include: code: string indicating FinBIF taxon MX code (e.g, MX.27328). binomial: string indicating scientific taxon name (e.g., Crex crex). optionally include one : extra_codes: array FinBIF taxon MX codes include along nominal taxon declared code. subtaxa: boolean indicating whether include observations child taxa taxa declared code extra_codes. start_year: integer indicating year observation data taxa begin. Observation data year excluded. Note start_year greater base_year (see section Model) base_year taxon set start_year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"extra-taxa","dir":"Articles","previous_headings":"Sections","what":"Extra taxa","title":"Configuration","text":"array defining taxa included parent multi-taxon indicator single-taxon indicators calculated. element array configured way taxa .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"from","dir":"Articles","previous_headings":"Sections","what":"From","title":"Configuration","text":"Multi-taxon indicators can constituent single-taxon indicators. case, section indicates multi-taxon indicator (form short-code) input data comes .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"filters","dir":"Articles","previous_headings":"Sections","what":"Filters","title":"Configuration","text":"filters section object defining list filters apply observation data FinBIF. See finbif R package documentation details.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"surveys","dir":"Articles","previous_headings":"Sections","what":"Surveys","title":"Configuration","text":"surveys section defines fields selected getting survey data FinBIF. Fields selected key selection array (see finbif R package documentation available fields). second key, has_value, array indicates fields must null values filtering records.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"counts","dir":"Articles","previous_headings":"Sections","what":"Counts","title":"Configuration","text":"counts section defines fields selected accessing count data FinBIF. sections uses selection has_value key manner . additional key, abundance, used indicate field used abundance (counts) data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"combine","dir":"Articles","previous_headings":"Sections","what":"Combine","title":"Configuration","text":"section combine defines single-taxon indicator data combined form multi-taxon indicator. Options include: geometric_mean: combines relative abundance geometric mean abundance. cti: combine abundances community temperature index. overall_abundance: combine abundance total abundance taxon group.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"use-data-after","dir":"Articles","previous_headings":"Sections","what":"Use data after","title":"Configuration","text":"section use_data_after defines calendar date (form \"MM-DD\") data collected current year start included indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/configuration.html","id":"model","dir":"Articles","previous_headings":"Sections","what":"Model","title":"Configuration","text":"model section defines single- multi-taxon indicators calculated survey count data sourced FinBIF. section consists one model objects object keys indicate model used. Models include: trim: Trends Indices Monitoring data model (via rtrim) rbms: Generalised abundance indices butterfly monitoring count data ( via rbms) lmer: Linear Mixed Effects Regression (via lme4) element model section must include: surveys_process: array survey data processing functions (see processing ) counts_process array count data processing functions (see processing ) optionally include: base_year: integer indicating base year indicator. args: additional arguments passed modelling function.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/farmland-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Bird Indicator","title":"Farmland Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/farmland-butterflies.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Butterfly Indicator","title":"Farmland Butterfly Indicator","text":"RBMS TRIM","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/forest-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Forest Bird Indicator","title":"Forest Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/mire-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Mire Bird Indicator","title":"Mire Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/moths.html","id":"section","dir":"Articles","previous_headings":"","what":"Moth Indicator","title":"Moth Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Multi-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Multi-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Multi-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing multi-taxon indicator selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select taxa <- c(   \"Vanellus vanellus\", \"Numenius arquata\", \"Alauda arvensis\", \"Hirundo rustica\",   \"Delichon urbicum\", \"Anthus pratensis\", \"Saxicola rubetra\", \"Turdus pilaris\",   \"Sylvia communis\", \"Corvus monedula\", \"Sturnus vulgaris\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = c(\"scientific_name\", \"document_id\", abundance = \"pair_abundance\"),   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, zero_fill, surveys)  counts <- lapply(counts, sum_by_event)  counts <- lapply(counts, remove_all_zero_locations)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"fit-trim-models","dir":"Articles","previous_headings":"","what":"Fit TRIM Models","title":"Multi-taxon indicator (trim)","text":"TRIM model used estimate change abundance time taxon.","code":"model <- lapply(   counts, trim, count_col =\"abundance\", site_col = \"location_id\",   year_col = \"year\" )"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/multi-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Multi-taxon indicator (trim)","text":"index change relative abundance created taxon setting base year year 2000. indices combined single table geometric mean relative abundance associated uncertainty can calculated via Monte Carlo simulation method (see details).","code":"indices <- lapply(model, index, base = 2000)  indices <- mapply(mutate, indices, sp = taxa, SIMPLIFY = FALSE)  indices <- do.call(rbind, indices) n <- 1000 max_cv <- 3 imputed_min <- .01 truncfac <- 10 base <- 1 nyrs <- 44  indices <- mutate(   indices, cv = ifelse(imputed >= .1 & se_imp > 0, se_imp / imputed, NA_real_) )  indices <- group_by(indices, sp)  indices <- mutate(indices, cv = mean(cv, na.rm = TRUE))  indices <- filter(indices, cv < max_cv)  indices <- mutate(indices, imputed = pmax(imputed, imputed_min))  indices <- mutate(indices, se_imp = if_else(imputed > imputed_min, se_imp, 0))  indices <- mutate(indices, se_imp = se_imp / imputed)  indices <- mutate(indices, imputed = log(imputed))  indices <- group_by(indices, time, sp)  indices <- summarise(   indices, mc = rnorm(n, imputed, se_imp), i = seq(n), .groups = \"keep\" )  indices <- mutate(indices, mc = pmax(mc, log(imputed_min)))  indices <- group_by(indices, sp, i)  indices <- arrange(indices, time)  indices <- mutate(   indices, mcf = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- arrange(indices, -time)  indices <- mutate(   indices, mcb = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- group_by(indices, i, time)  index <- summarise(   indices,   mcf = mean(mcf, na.rm = TRUE), mcb = mean(mcb, na.rm = TRUE),   .groups = \"drop_last\" )  index <- arrange(index, time)  index <- mutate(index, mcf = cumsum(lag(lead(mcf, base - 1), base, 0)))  index <- arrange(index, -time)  index <- mutate(   index, mcb = cumsum(lag(lead(mcb, nyrs - base), nyrs - base + 1, 0)) )  index <- group_by(index, time)  index <- summarise(   index,   index = exp(mean(mcf)) * exp(mean(mcb)),   se = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) ) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Overall abundance","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Overall abundance","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit surveys sites least seven fortnights surveyed limit site’s surveys first survey fortnight.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- require_seven_fortnights(surveys)  surveys <- pick_first_survey_in_fortnight(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Overall abundance","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing total abundance selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : sum counts survey site sections; combine count survey data together; amd sum counts site-year combination. count data can summed across taxa.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select taxa <- c(   \"Aglais urticae\",   \"Boloria euphrosyne\",   \"Lycaena virgaureae\",   \"Polygonia c-album\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, sum_over_sections)  counts <- lapply(counts, combine_with_surveys, surveys)  counts <- lapply(counts, sum_by_event) counts <- mapply(mutate, counts, sp = taxa, SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts <- group_by(counts, location_id, year)  counts <- summarise(counts, abundance = sum(abundance), .groups = \"drop\")"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overall-abundance.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Overall abundance","text":"index total abundance year created fitting TRIM model combined data setting base year year 2000.","code":"model <- trim(abundance ~ location_id + year, counts)  index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"api","dir":"Articles","previous_headings":"","what":"API","title":"Overview","text":"HTTP API access indicator data products available developers. API documented .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"updates","dir":"Articles","previous_headings":"","what":"Updates","title":"Overview","text":"Indicators updated nightly 12 8am random order. update process checks FinBIF new input data updates affected indices many possible within 8hr update process window.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"indicator-types","dir":"Articles","previous_headings":"","what":"Indicator types","title":"Overview","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"single-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Single-taxon indicators","title":"Overview","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator. example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/overview.html","id":"multi-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Multi-taxon indicators","title":"Overview","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (rbms)","text":"following packages required. packages available CRAN apart fbi rbms can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rbms)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (rbms)","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data convert year month day fields single date field.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- format_date(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (rbms)","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). count data Aglais urticae (Small tortoiseshell) can now downloaded FinBIF. Two processing functions applied count data : sum counts survey site sections; combine count survey data together.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Aglais urticae\",   filter = filter,   select = select ,   n = \"all\",   quiet = TRUE ) counts <- sum_over_sections(counts, surveys)  counts <- combine_with_surveys(counts, surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"fit-rbms-model","dir":"Articles","previous_headings":"","what":"Fit RBMS Model","title":"Single-taxon indicator (rbms)","text":"RBMS model used estimate change abundance time (see RBMS documentation details) uncertainty estimated via bootstrapping.","code":"StartMonth <- 4 EndMonth <- 9 StartDay <- 1 EndDay <- 30 Anchor <- TRUE AnchorLength <- 14 AnchorLag <- 14 AnchorTimeUnit <- \"d\" NbrSample <- 500 MinVisit <- 5 MinOccur <- 2 MinNbrSite <- 5 MaxTrial <- 4 GamFamily <- \"nb\" FlightCurveTimeUnit <- \"w\" MultiVisit <- \"mean\" MinFC <- 0.10 boot_n <- 200  surveys <- select(surveys, site_id = location_id, year, date)  init_year <- min(surveys[[\"year\"]])  last_year <- max(surveys[[\"year\"]])  nyears <- last_year - init_year + 1  ts_date <- ts_dwmy_table(InitYear = init_year, LastYear = last_year)  ts_season <- ts_monit_season(   d_series     = ts_date,   StartMonth   = StartMonth,   EndMonth     = EndMonth,   StartDay     = StartDay,   EndDay       = EndDay,   Anchor       = Anchor,   AnchorLength = AnchorLength,   AnchorLag    = AnchorLag,   TimeUnit     = AnchorTimeUnit )  ts_season_visit <- ts_monit_site(m_visit = surveys, ts_season = ts_season)  counts <- mutate(counts, species = 1)  counts <- select(   counts, count = abundance, site_id = location_id, year, date, species )  ts_season_count <- ts_monit_count_site(   m_season_visit = ts_season_visit, m_count = counts )  ts_flight_curve <- flight_curve(   ts_season_count = ts_season_count,   NbrSample       = NbrSample,   MinVisit        = MinVisit,   MinOccur        = MinOccur,   MinNbrSite      = MinNbrSite,   MaxTrial        = MaxTrial,   GamFamily       = GamFamily,   SpeedGam        = FALSE,   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit,   verbose         = FALSE )  impt_counts <- impute_count(   ts_season_count = ts_season_count,   ts_flight_curve = ts_flight_curve[[\"pheno\"]],   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit )  sindex <- site_index(butterfly_count = impt_counts, MinFC = MinFC)  bootsample <- boot_sample(data = sindex, boot_n = boot_n)  index_mc <- mapply(   collated_index,   bootID = seq_len(boot_n),   MoreArgs = list(data = sindex, s_sp = 1, boot_ind = bootsample),   SIMPLIFY = FALSE )"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-rbms.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (rbms)","text":"index change relative abundance uncertainty derived bootstrapped estimates can created setting base year year 2000.","code":"base <- which(sort(unique(surveys[[\"year\"]])) == 2000)  index_mc <- lapply(index_mc, getElement, \"col_index\")  index_mc <- do.call(rbind, index_mc)  index_mc <- mutate(index_mc, mc = log(pmax(1 / 100, COL_INDEX)), time = M_YEAR)  index_mc <- group_by(index_mc, BOOTi)  index_mc <- arrange(index_mc, time)  index_mc <- mutate(index_mc, mcf = lead(mc) - mc)  index_mc <- mutate(index_mc, mcf = lead(mcf, base - 1))  index_mc <- mutate(index_mc, mcf = lag(mcf, base, 0))  index_mc <- mutate(index_mc, mcf = cumsum(mcf))  index_mc <- arrange(index_mc, -time)  index_mc <- mutate(index_mc, mcb = lead(mc) - mc)  index_mc <- mutate(index_mc, mcb = lead(mcb, nyears - base))  index_mc <- mutate(index_mc, mcb = lag(mcb, nyears - base + 1, 0))  index_mc <- mutate(index_mc, mcb = cumsum(mcb))  index_mc <- group_by(index_mc, time)  index <- summarise(   index_mc,   mean = exp(mean(mcf)) * exp(mean(mcb)),   sd = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) )  index <- mutate(index, lower = mean - sd, upper = mean + sd) ggplot(index) + aes(x = parse_date_time(time, \"Y\"), y = mean, ymin = lower, ymax = upper) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). count data Anthus pratensis (Meadow pipit) can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Anthus pratensis\",   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- zero_fill(counts, surveys)  counts <- sum_by_event(counts)  counts <- remove_all_zero_locations(counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"fit-trim-model","dir":"Articles","previous_headings":"","what":"Fit TRIM Model","title":"Single-taxon indicator (trim)","text":"TRIM model used estimate change abundance time.","code":"model <- trim(abundance ~ location_id + year, counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/single-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (trim)","text":"index change relative abundance created setting base year year 2000.","code":"index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/articles/winter-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Winter Bird Indicator","title":"Winter Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Finnish Museum Natural History - Luomus. Copyright holder. William K. Morris. Author, maintainer.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Morris W (2024). fbi: Finnish Biodiversity Indicators. R package version 0.11.5.9000, https://indicators.laji.fi, https://github.com/luomus/fin-biodiv-indicators.","code":"@Manual{,   title = {fbi: Finnish Biodiversity Indicators},   author = {William K. Morris},   year = {2024},   note = {R package version 0.11.5.9000, https://indicators.laji.fi},   url = {https://github.com/luomus/fin-biodiv-indicators}, }"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/index.html","id":"finnish-biodiversity-indicators","dir":"","previous_headings":"","what":"Finnish Biodiversity Indicators","title":"Finnish Biodiversity Indicators","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indices provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/check_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Check input — check_input","title":"Check input — check_input","text":"Check indicator inputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/check_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check input — check_input","text":"","code":"check_input(index, model, taxon)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/check_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check input — check_input","text":"index Character. index? model Character. model? taxon Character. taxon?","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/clean_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean cache — clean_cache","title":"Clean cache — clean_cache","text":"Remove unneeded tables rows database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/clean_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean cache — clean_cache","text":"","code":"clean_cache(db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/clean_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean cache — clean_cache","text":"db Connection. Database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine with surveys — combine_with_surveys","title":"Combine with surveys — combine_with_surveys","text":"Combine count data survey data","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine with surveys — combine_with_surveys","text":"","code":"combine_with_surveys(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine with surveys — combine_with_surveys","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/combine_with_surveys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Combine with surveys — combine_with_surveys","text":"function combines counts surveys data. performs inner join counts surveys document_id. function assumes counts surveys data include document_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":null,"dir":"Reference","previous_headings":"","what":"Format date — format_date","title":"Format date — format_date","text":"Combine year, month, day survey single date string","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format date — format_date","text":"","code":"format_date(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format date — format_date","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/format_date.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format date — format_date","text":"function combines survey year, month day character string - separator. function assumes survey data includes year, month day.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get indices — get_indices","title":"Get indices — get_indices","text":"Get indices configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get indices — get_indices","text":"","code":"get_indices(file = Sys.getenv(\"R_CONFIG_FILE\"))"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get indices — get_indices","text":"file Configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Get output — get_output","title":"Get output — get_output","text":"Get serialized indicator outputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get output — get_output","text":"","code":"get_output(output, index, model, taxon, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/get_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get output — get_output","text":"output Character. type output? index Character. Update index? model Character. model use? taxon Character. taxon? region Character. region? db Connection. Database get output.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in fortnight — pick_first_survey_in_fortnight","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"Pick first survey fortnight discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"","code":"pick_first_survey_in_fortnight(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_fortnight.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"function groups surveys location_id, year fortnightthen orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, year (integers) location_id, processed function require_seven_fortnights.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in winter — pick_first_survey_in_winter","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"Pick first winter survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"","code":"pick_first_survey_in_winter(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_winter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"function moves surveys occurring December ahead one year. enables December surveys grouped subsequent surveys occurring January winter. Surveys grouped location_id year ordered date. first survey group removed. two surveys share date location_id one picked random rest removed. function works assumption surveys winter December January surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in year — pick_first_survey_in_year","title":"Pick first survey in year — pick_first_survey_in_year","text":"Pick first survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in year — pick_first_survey_in_year","text":"","code":"pick_first_survey_in_year(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in year — pick_first_survey_in_year","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/pick_first_survey_in_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in year — pick_first_survey_in_year","text":"function groups surveys location_id year orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/process_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Process functions — process_funs","title":"Process functions — process_funs","text":"Functions process indicator input data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/process_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process functions — process_funs","text":"","code":"process_funs()"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove all-zero locations — remove_all_zero_locations","title":"Remove all-zero locations — remove_all_zero_locations","text":"Discard locations taxa always zero abundance","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove all-zero locations — remove_all_zero_locations","text":"","code":"remove_all_zero_locations(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove all-zero locations — remove_all_zero_locations","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/remove_all_zero_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove all-zero locations — remove_all_zero_locations","text":"function groups counts location_id removes counts includes location_id abundance.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum gaps — require_minimum_gaps","title":"Require minimum gaps — require_minimum_gaps","text":"Remove survey site-years many large sampling gaps.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum gaps — require_minimum_gaps","text":"","code":"require_minimum_gaps(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum gaps — require_minimum_gaps","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_gaps.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum gaps — require_minimum_gaps","text":"function groups surveys data location_id year. removes groups survey period many large sampling gaps. many defined total gap length year 21 days large single sampling gap 7 days. function expects surveys data least location_id, year, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum weeks — require_minimum_weeks","title":"Require minimum weeks — require_minimum_weeks","text":"Remove survey site-years region covering less minimum number weeks.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum weeks — require_minimum_weeks","text":"","code":"require_minimum_weeks(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum weeks — require_minimum_weeks","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_minimum_weeks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum weeks — require_minimum_weeks","text":"function groups surveys data location_id year. removes groups survey period less minimum number weeks given region. expects surveys data least location_id, year, region, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":null,"dir":"Reference","previous_headings":"","what":"Require seven fortnights — require_seven_fortnights","title":"Require seven fortnights — require_seven_fortnights","text":"Divide year approximate 2 week blocks, selecting blocks 10-16 discarding locations without survey remaining block","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require seven fortnights — require_seven_fortnights","text":"","code":"require_seven_fortnights(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require seven fortnights — require_seven_fortnights","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_seven_fortnights.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require seven fortnights — require_seven_fortnights","text":"function assigns survey approximate fortnight. fortnight defined days 16th day month days 15th day month. surveys falling outside date range seven fortnights second fortnight May second fortnight August removed. Surveys grouped location_id year surveys belonging groups least one survey occurring seven remaining fortnights discarded. function assumes surveys data day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":null,"dir":"Reference","previous_headings":"","what":"Require at least two years — require_two_years","title":"Require at least two years — require_two_years","text":"Discard locations less two survey years","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require at least two years — require_two_years","text":"","code":"require_two_years(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require at least two years — require_two_years","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/require_two_years.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require at least two years — require_two_years","text":"function groups surveys location_id removes surveys locations data one year. function assumes surveys data location_id year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Set start year — set_start_year","title":"Set start year — set_start_year","text":"Discard counts years start year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set start year — set_start_year","text":"","code":"set_start_year(counts, taxon, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set start year — set_start_year","text":"counts Count data. taxon Taxon configuration. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/set_start_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set start year — set_start_year","text":"function sets start year taxon counts. variable start_year configured given taxon count data prior start_year removed.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum by event — sum_by_event","title":"Sum by event — sum_by_event","text":"Sum counts surveys taxa year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum by event — sum_by_event","text":"","code":"sum_by_event(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum by event — sum_by_event","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_by_event.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum by event — sum_by_event","text":"functions groups count data location_id year. multiple taxa counts input data also grouped taxa. Counts summed across survey events locations years.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum over sections — sum_over_sections","title":"Sum over sections — sum_over_sections","text":"Sum counts sections surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum over sections — sum_over_sections","text":"","code":"sum_over_sections(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum over sections — sum_over_sections","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/sum_over_sections.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum over sections — sum_over_sections","text":"functions groups count data document_id (IDs individual surveys). multiple taxa counts input data also grouped taxa. Counts summed across survey sections count data provided surveys split parts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Update data — update_data","title":"Update data — update_data","text":"Update input data FinBIF.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update data — update_data","text":"","code":"update_data(type, index, taxon, db, do_update = FALSE)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update data — update_data","text":"type Character. type input data (e.g., surveys counts) index Character. Update data index? taxon Character. Update data taxon? Ignored type = \"surveys\" db Connection. Database update data FinBIF. do_update Logical. Update data regardless need.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update index — update_index","title":"Update index — update_index","text":"Update index output data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update index — update_index","text":"","code":"update_index(index, model, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update index — update_index","text":"index Character. Update index? model Character. model use? region Character. region? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_taxon_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update taxon index — update_taxon_index","title":"Update taxon index — update_taxon_index","text":"Update relative abundance index taxon.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_taxon_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update taxon index — update_taxon_index","text":"","code":"update_taxon_index(index, model, taxon, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/update_taxon_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update taxon index — update_taxon_index","text":"index Character. Update index? model Character. model use? taxon Character. Update data taxa? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":null,"dir":"Reference","previous_headings":"","what":"Zero fill — zero_fill","title":"Zero fill — zero_fill","text":"Combine count data survey data filling missing surveys count data zero counts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zero fill — zero_fill","text":"","code":"zero_fill(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Zero fill — zero_fill","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/dev/reference/zero_fill.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Zero fill — zero_fill","text":"function combines counts surveys data. performs right outer join counts surveys document_id. surveys corresponding data abundance filled zero. function assumes counts surveys data include document_id counts data includes abundance.","code":""}]
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 182933c9..d76757b3 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -18,7 +18,7 @@ articles:
   single-taxon-indicator-rbms: single-taxon-indicator-rbms.html
   single-taxon-indicator-trim: single-taxon-indicator-trim.html
   winter-birds: winter-birds.html
-last_built: 2024-02-28T07:32Z
+last_built: 2024-02-28T07:34Z
 urls:
   reference: https://indicators-dev.laji.fi/docs/dev/reference
   article: https://indicators-dev.laji.fi/docs/dev/articles
diff --git a/docs/search.json b/docs/search.json
index 369a2c86..8faa6285 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement helpdesk@laji.fi. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing","text":"Small typos grammatical errors documentation may edited long changes made source file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"Contributing","text":"make substantial pull request, always file issue make sure someone team agrees ’s problem.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"","what":"Pull request process","title":"Contributing","text":"recommend create Git branch pull request (PR). New code follow style used project. user-facing changes, add section top NEWS.Rd current development version header describing changes made followed username, links relevant issue(s)/PR(s).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing","text":"Please note project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021-2024 LUOMUS - Finnish Museum Natural History Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"NA","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indicators provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"indicator-types","dir":"","previous_headings":"Overview","what":"Indicator types","title":"NA","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"single-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Single-taxon indicators","title":"NA","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator (see /taxa-extra). example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"multi-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Multi-taxon indicators","title":"NA","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"supported-operations","dir":"","previous_headings":"Overview","what":"Supported Operations","title":"NA","text":"Get lists available indicators Get configuration indicator Get statistics indicator CSV JSON Get SVG image indicator","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"examples","dir":"","previous_headings":"Overview","what":"Examples","title":"NA","text":"Get list multi-taxon indicators: Get list taxa included Winter Bird indicator: See Winter Bird indicator configured: Get Winter Bird indicator output json: Get single-taxon (Goldcrest) Winter Bird trim index output southern Finland CSV: Get SVG image Farmland Butterflies RBMS index","code":"$ curl \"https://indicators.laji.fi/indices\" $ curl \"https://indicators.laji.fi/taxa/wb\" $ curl \"https://indicators.laji.fi/config/wb\" $ curl \"https://indicators.laji.fi/data/wb\" $ curl \"https://indicators.laji.fi/csv/wb?taxon=MX.33954&model=trim&region=south\" $ curl -o bf.svg \"https://indicators.laji.fi/svg/bf?model=rbms\""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/alpine-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Alpine Bird Indicator","title":"Alpine Bird Indicator","text":"Northern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/butterfly-abundance.html","id":"section","dir":"Articles","previous_headings":"","what":"Butterfly Abundance Indicator","title":"Butterfly Abundance Indicator","text":"Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Community temperature index","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(lme4) library(arm)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Community temperature index","text":"five fields required survey data. filters restrict survey data Dec-Jan “Winter Bird Census” monitoring dataset December 1958 onwards selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data limit site first survey year (year period Dec-Jan).","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Winter Bird Census\",   date_range_ymd = c(\"1958-12-01\", \"\"),   date_range_md= c(\"12-01\", \"01-31\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_winter(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Community temperature index","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa species temperature index values defined. count data taxa can now downloaded FinBIF. count data combined survey data species temperature indices.","code":"select <- c(\"document_id\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select sti <- c(   \"Poecile montanus\" = -7.51,   \"Regulus regulus\" = -4.23,   \"Lophophanes cristatus\" = -5.90,   \"Certhia familiaris\" = -6.89 ) counts <- lapply(   names(sti),   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, combine_with_surveys, surveys)  counts <- mapply(mutate, counts, sp = names(sti), SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts[[\"sti\"]] <- sti[counts[[\"sp\"]]]"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Community temperature index","text":"community temperature index year created fitting linear mixed effects regression model combined data.","code":"cti_data <- summarise(   group_by(counts, location_id, year),   cti = sum(abundance * sti) / sum(abundance), .groups = \"drop\" )  cti <- lmer(cti ~ (1 | location_id) + (1 | year), cti_data)  cti <- data.frame(index = coef(cti)[[\"year\"]], se = se.coef(cti)[[\"year\"]])  cti[[\"time\"]] <- as.integer(row.names(cti))  names(cti) <- c(\"index\", \"se\", \"time\") ggplot(cti) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-indices.html","id":"section","dir":"Articles","previous_headings":"","what":"Community Temperature Indices","title":"Community Temperature Indices","text":"Winter Birds Summer Birds Farmland Butterflies","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"defaults","dir":"Articles","previous_headings":"","what":"Defaults","title":"Configuration","text":"Default parameters apply indicators can specified special object top-level key, default (see ). Defaults can overwritten specifying different parameters value indicator objects.","code":"default:   surveys:     selection:     - document_id     - location_id     - year     - month     - day     has_value:     - document_id     - location_id     - year     - month     - day   counts:     abundance: abundance   use_data_after: \"01-01\""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"sections","dir":"Articles","previous_headings":"","what":"Sections","title":"Configuration","text":"following describes section multi-taxon indicator objects detail.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"name","dir":"Articles","previous_headings":"Sections","what":"Name","title":"Configuration","text":"string giving long-form name multi-taxon indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"taxa","dir":"Articles","previous_headings":"Sections","what":"Taxa","title":"Configuration","text":"array defining taxa included multi-taxon indicator single-taxon indicators calculated. element array must include: code: string indicating FinBIF taxon MX code (e.g, MX.27328). binomial: string indicating scientific taxon name (e.g., Crex crex). optionally include one : extra_codes: array FinBIF taxon MX codes include along nominal taxon declared code. subtaxa: boolean indicating whether include observations child taxa taxa declared code extra_codes. start_year: integer indicating year observation data taxa begin. Observation data year excluded. Note start_year greater base_year (see section Model) base_year taxon set start_year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"extra-taxa","dir":"Articles","previous_headings":"Sections","what":"Extra taxa","title":"Configuration","text":"array defining taxa included parent multi-taxon indicator single-taxon indicators calculated. element array configured way taxa .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"from","dir":"Articles","previous_headings":"Sections","what":"From","title":"Configuration","text":"Multi-taxon indicators can constituent single-taxon indicators. case, section indicates multi-taxon indicator (form short-code) input data comes .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"filters","dir":"Articles","previous_headings":"Sections","what":"Filters","title":"Configuration","text":"filters section object defining list filters apply observation data FinBIF. See finbif R package documentation details.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"surveys","dir":"Articles","previous_headings":"Sections","what":"Surveys","title":"Configuration","text":"surveys section defines fields selected getting survey data FinBIF. Fields selected key selection array (see finbif R package documentation available fields). second key, has_value, array indicates fields must null values filtering records.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"counts","dir":"Articles","previous_headings":"Sections","what":"Counts","title":"Configuration","text":"counts section defines fields selected accessing count data FinBIF. sections uses selection has_value key manner . additional key, abundance, used indicate field used abundance (counts) data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"combine","dir":"Articles","previous_headings":"Sections","what":"Combine","title":"Configuration","text":"section combine defines single-taxon indicator data combined form multi-taxon indicator. Options include: geometric_mean: combines relative abundance geometric mean abundance. cti: combine abundances community temperature index. overall_abundance: combine abundance total abundance taxon group.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"use-data-after","dir":"Articles","previous_headings":"Sections","what":"Use data after","title":"Configuration","text":"section use_data_after defines calendar date (form \"MM-DD\") data collected current year start included indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"model","dir":"Articles","previous_headings":"Sections","what":"Model","title":"Configuration","text":"model section defines single- multi-taxon indicators calculated survey count data sourced FinBIF. section consists one model objects object keys indicate model used. Models include: trim: Trends Indices Monitoring data model (via rtrim) rbms: Generalised abundance indices butterfly monitoring count data ( via rbms) lmer: Linear Mixed Effects Regression (via lme4) element model section must include: surveys_process: array survey data processing functions (see processing ) counts_process array count data processing functions (see processing ) optionally include: base_year: integer indicating base year indicator. args: additional arguments passed modelling function.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/farmland-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Bird Indicator","title":"Farmland Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/farmland-butterflies.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Butterfly Indicator","title":"Farmland Butterfly Indicator","text":"RBMS TRIM","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/forest-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Forest Bird Indicator","title":"Forest Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/mire-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Mire Bird Indicator","title":"Mire Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/moths.html","id":"section","dir":"Articles","previous_headings":"","what":"Moth Indicator","title":"Moth Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Multi-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Multi-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Multi-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing multi-taxon indicator selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select taxa <- c(   \"Vanellus vanellus\", \"Numenius arquata\", \"Alauda arvensis\", \"Hirundo rustica\",   \"Delichon urbicum\", \"Anthus pratensis\", \"Saxicola rubetra\", \"Turdus pilaris\",   \"Sylvia communis\", \"Corvus monedula\", \"Sturnus vulgaris\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = c(\"scientific_name\", \"document_id\", abundance = \"pair_abundance\"),   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, zero_fill, surveys)  counts <- lapply(counts, sum_by_event)  counts <- lapply(counts, remove_all_zero_locations)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"fit-trim-models","dir":"Articles","previous_headings":"","what":"Fit TRIM Models","title":"Multi-taxon indicator (trim)","text":"TRIM model used estimate change abundance time taxon.","code":"model <- lapply(   counts, trim, count_col =\"abundance\", site_col = \"location_id\",   year_col = \"year\" )"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Multi-taxon indicator (trim)","text":"index change relative abundance created taxon setting base year year 2000. indices combined single table geometric mean relative abundance associated uncertainty can calculated via Monte Carlo simulation method (see details).","code":"indices <- lapply(model, index, base = 2000)  indices <- mapply(mutate, indices, sp = taxa, SIMPLIFY = FALSE)  indices <- do.call(rbind, indices) n <- 1000 max_cv <- 3 imputed_min <- .01 truncfac <- 10 base <- 1 nyrs <- 44  indices <- mutate(   indices, cv = ifelse(imputed >= .1 & se_imp > 0, se_imp / imputed, NA_real_) )  indices <- group_by(indices, sp)  indices <- mutate(indices, cv = mean(cv, na.rm = TRUE))  indices <- filter(indices, cv < max_cv)  indices <- mutate(indices, imputed = pmax(imputed, imputed_min))  indices <- mutate(indices, se_imp = if_else(imputed > imputed_min, se_imp, 0))  indices <- mutate(indices, se_imp = se_imp / imputed)  indices <- mutate(indices, imputed = log(imputed))  indices <- group_by(indices, time, sp)  indices <- summarise(   indices, mc = rnorm(n, imputed, se_imp), i = seq(n), .groups = \"keep\" )  indices <- mutate(indices, mc = pmax(mc, log(imputed_min)))  indices <- group_by(indices, sp, i)  indices <- arrange(indices, time)  indices <- mutate(   indices, mcf = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- arrange(indices, -time)  indices <- mutate(   indices, mcb = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- group_by(indices, i, time)  index <- summarise(   indices,   mcf = mean(mcf, na.rm = TRUE), mcb = mean(mcb, na.rm = TRUE),   .groups = \"drop_last\" )  index <- arrange(index, time)  index <- mutate(index, mcf = cumsum(lag(lead(mcf, base - 1), base, 0)))  index <- arrange(index, -time)  index <- mutate(   index, mcb = cumsum(lag(lead(mcb, nyrs - base), nyrs - base + 1, 0)) )  index <- group_by(index, time)  index <- summarise(   index,   index = exp(mean(mcf)) * exp(mean(mcb)),   se = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) ) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Overall abundance","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Overall abundance","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit surveys sites least seven fortnights surveyed limit site’s surveys first survey fortnight.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- require_seven_fortnights(surveys)  surveys <- pick_first_survey_in_fortnight(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Overall abundance","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing total abundance selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : sum counts survey site sections; combine count survey data together; amd sum counts site-year combination. count data can summed across taxa.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select taxa <- c(   \"Aglais urticae\",   \"Boloria euphrosyne\",   \"Lycaena virgaureae\",   \"Polygonia c-album\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, sum_over_sections)  counts <- lapply(counts, combine_with_surveys, surveys)  counts <- lapply(counts, sum_by_event) counts <- mapply(mutate, counts, sp = taxa, SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts <- group_by(counts, location_id, year)  counts <- summarise(counts, abundance = sum(abundance), .groups = \"drop\")"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Overall abundance","text":"index total abundance year created fitting TRIM model combined data setting base year year 2000.","code":"model <- trim(abundance ~ location_id + year, counts)  index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"api","dir":"Articles","previous_headings":"","what":"API","title":"Overview","text":"HTTP API access indicator data products available developers. API documented .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"updates","dir":"Articles","previous_headings":"","what":"Updates","title":"Overview","text":"Indicators updated nightly 12 8am random order. update process checks FinBIF new input data updates affected indices many possible within 8hr update process window.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"indicator-types","dir":"Articles","previous_headings":"","what":"Indicator types","title":"Overview","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"single-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Single-taxon indicators","title":"Overview","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator. example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"multi-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Multi-taxon indicators","title":"Overview","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (rbms)","text":"following packages required. packages available CRAN apart fbi rbms can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rbms)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (rbms)","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data convert year month day fields single date field.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- format_date(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (rbms)","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). count data Aglais urticae (Small tortoiseshell) can now downloaded FinBIF. Two processing functions applied count data : sum counts survey site sections; combine count survey data together.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Aglais urticae\",   filter = filter,   select = select ,   n = \"all\",   quiet = TRUE ) counts <- sum_over_sections(counts, surveys)  counts <- combine_with_surveys(counts, surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"fit-rbms-model","dir":"Articles","previous_headings":"","what":"Fit RBMS Model","title":"Single-taxon indicator (rbms)","text":"RBMS model used estimate change abundance time (see RBMS documentation details) uncertainty estimated via bootstrapping.","code":"StartMonth <- 4 EndMonth <- 9 StartDay <- 1 EndDay <- 30 Anchor <- TRUE AnchorLength <- 14 AnchorLag <- 14 AnchorTimeUnit <- \"d\" NbrSample <- 500 MinVisit <- 5 MinOccur <- 2 MinNbrSite <- 5 MaxTrial <- 4 GamFamily <- \"nb\" FlightCurveTimeUnit <- \"w\" MultiVisit <- \"mean\" MinFC <- 0.10 boot_n <- 200  surveys <- select(surveys, site_id = location_id, year, date)  init_year <- min(surveys[[\"year\"]])  last_year <- max(surveys[[\"year\"]])  nyears <- last_year - init_year + 1  ts_date <- ts_dwmy_table(InitYear = init_year, LastYear = last_year)  ts_season <- ts_monit_season(   d_series     = ts_date,   StartMonth   = StartMonth,   EndMonth     = EndMonth,   StartDay     = StartDay,   EndDay       = EndDay,   Anchor       = Anchor,   AnchorLength = AnchorLength,   AnchorLag    = AnchorLag,   TimeUnit     = AnchorTimeUnit )  ts_season_visit <- ts_monit_site(m_visit = surveys, ts_season = ts_season)  counts <- mutate(counts, species = 1)  counts <- select(   counts, count = abundance, site_id = location_id, year, date, species )  ts_season_count <- ts_monit_count_site(   m_season_visit = ts_season_visit, m_count = counts )  ts_flight_curve <- flight_curve(   ts_season_count = ts_season_count,   NbrSample       = NbrSample,   MinVisit        = MinVisit,   MinOccur        = MinOccur,   MinNbrSite      = MinNbrSite,   MaxTrial        = MaxTrial,   GamFamily       = GamFamily,   SpeedGam        = FALSE,   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit,   verbose         = FALSE )  impt_counts <- impute_count(   ts_season_count = ts_season_count,   ts_flight_curve = ts_flight_curve[[\"pheno\"]],   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit )  sindex <- site_index(butterfly_count = impt_counts, MinFC = MinFC)  bootsample <- boot_sample(data = sindex, boot_n = boot_n)  index_mc <- mapply(   collated_index,   bootID = seq_len(boot_n),   MoreArgs = list(data = sindex, s_sp = 1, boot_ind = bootsample),   SIMPLIFY = FALSE )"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (rbms)","text":"index change relative abundance uncertainty derived bootstrapped estimates can created setting base year year 2000.","code":"base <- which(sort(unique(surveys[[\"year\"]])) == 2000)  index_mc <- lapply(index_mc, getElement, \"col_index\")  index_mc <- do.call(rbind, index_mc)  index_mc <- mutate(index_mc, mc = log(pmax(1 / 100, COL_INDEX)), time = M_YEAR)  index_mc <- group_by(index_mc, BOOTi)  index_mc <- arrange(index_mc, time)  index_mc <- mutate(index_mc, mcf = lead(mc) - mc)  index_mc <- mutate(index_mc, mcf = lead(mcf, base - 1))  index_mc <- mutate(index_mc, mcf = lag(mcf, base, 0))  index_mc <- mutate(index_mc, mcf = cumsum(mcf))  index_mc <- arrange(index_mc, -time)  index_mc <- mutate(index_mc, mcb = lead(mc) - mc)  index_mc <- mutate(index_mc, mcb = lead(mcb, nyears - base))  index_mc <- mutate(index_mc, mcb = lag(mcb, nyears - base + 1, 0))  index_mc <- mutate(index_mc, mcb = cumsum(mcb))  index_mc <- group_by(index_mc, time)  index <- summarise(   index_mc,   mean = exp(mean(mcf)) * exp(mean(mcb)),   sd = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) )  index <- mutate(index, lower = mean - sd, upper = mean + sd) ggplot(index) + aes(x = parse_date_time(time, \"Y\"), y = mean, ymin = lower, ymax = upper) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). count data Anthus pratensis (Meadow pipit) can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Anthus pratensis\",   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- zero_fill(counts, surveys)  counts <- sum_by_event(counts)  counts <- remove_all_zero_locations(counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"fit-trim-model","dir":"Articles","previous_headings":"","what":"Fit TRIM Model","title":"Single-taxon indicator (trim)","text":"TRIM model used estimate change abundance time.","code":"model <- trim(abundance ~ location_id + year, counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (trim)","text":"index change relative abundance created setting base year year 2000.","code":"index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/winter-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Winter Bird Indicator","title":"Winter Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Finnish Museum Natural History - Luomus. Copyright holder. William K. Morris. Author, maintainer.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Morris W (2024). fbi: Finnish Biodiversity Indicators. R package version 0.11.5, https://indicators.laji.fi, https://github.com/luomus/fin-biodiv-indicators.","code":"@Manual{,   title = {fbi: Finnish Biodiversity Indicators},   author = {William K. Morris},   year = {2024},   note = {R package version 0.11.5, https://indicators.laji.fi},   url = {https://github.com/luomus/fin-biodiv-indicators}, }"},{"path":"https://indicators-dev.laji.fi/docs/dev/index.html","id":"finnish-biodiversity-indicators","dir":"","previous_headings":"","what":"Finnish Biodiversity Indicators","title":"Finnish Biodiversity Indicators","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indices provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/check_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Check input — check_input","title":"Check input — check_input","text":"Check indicator inputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/check_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check input — check_input","text":"","code":"check_input(index, model, taxon)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/check_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check input — check_input","text":"index Character. index? model Character. model? taxon Character. taxon?","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/clean_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean cache — clean_cache","title":"Clean cache — clean_cache","text":"Remove unneeded tables rows database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/clean_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean cache — clean_cache","text":"","code":"clean_cache(db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/clean_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean cache — clean_cache","text":"db Connection. Database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine with surveys — combine_with_surveys","title":"Combine with surveys — combine_with_surveys","text":"Combine count data survey data","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine with surveys — combine_with_surveys","text":"","code":"combine_with_surveys(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine with surveys — combine_with_surveys","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Combine with surveys — combine_with_surveys","text":"function combines counts surveys data. performs inner join counts surveys document_id. function assumes counts surveys data include document_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":null,"dir":"Reference","previous_headings":"","what":"Format date — format_date","title":"Format date — format_date","text":"Combine year, month, day survey single date string","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format date — format_date","text":"","code":"format_date(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format date — format_date","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format date — format_date","text":"function combines survey year, month day character string - separator. function assumes survey data includes year, month day.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get indices — get_indices","title":"Get indices — get_indices","text":"Get indices configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get indices — get_indices","text":"","code":"get_indices(file = Sys.getenv(\"R_CONFIG_FILE\"))"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get indices — get_indices","text":"file Configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Get output — get_output","title":"Get output — get_output","text":"Get serialized indicator outputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get output — get_output","text":"","code":"get_output(output, index, model, taxon, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get output — get_output","text":"output Character. type output? index Character. Update index? model Character. model use? taxon Character. taxon? region Character. region? db Connection. Database get output.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in fortnight — pick_first_survey_in_fortnight","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"Pick first survey fortnight discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"","code":"pick_first_survey_in_fortnight(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"function groups surveys location_id, year fortnightthen orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, year (integers) location_id, processed function require_seven_fortnights.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in winter — pick_first_survey_in_winter","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"Pick first winter survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"","code":"pick_first_survey_in_winter(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"function moves surveys occurring December ahead one year. enables December surveys grouped subsequent surveys occurring January winter. Surveys grouped location_id year ordered date. first survey group removed. two surveys share date location_id one picked random rest removed. function works assumption surveys winter December January surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in year — pick_first_survey_in_year","title":"Pick first survey in year — pick_first_survey_in_year","text":"Pick first survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in year — pick_first_survey_in_year","text":"","code":"pick_first_survey_in_year(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in year — pick_first_survey_in_year","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in year — pick_first_survey_in_year","text":"function groups surveys location_id year orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/process_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Process functions — process_funs","title":"Process functions — process_funs","text":"Functions process indicator input data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/process_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process functions — process_funs","text":"","code":"process_funs()"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove all-zero locations — remove_all_zero_locations","title":"Remove all-zero locations — remove_all_zero_locations","text":"Discard locations taxa always zero abundance","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove all-zero locations — remove_all_zero_locations","text":"","code":"remove_all_zero_locations(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove all-zero locations — remove_all_zero_locations","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove all-zero locations — remove_all_zero_locations","text":"function groups counts location_id removes counts includes location_id abundance.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum gaps — require_minimum_gaps","title":"Require minimum gaps — require_minimum_gaps","text":"Remove survey site-years many large sampling gaps.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum gaps — require_minimum_gaps","text":"","code":"require_minimum_gaps(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum gaps — require_minimum_gaps","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum gaps — require_minimum_gaps","text":"function groups surveys data location_id year. removes groups survey period many large sampling gaps. many defined total gap length year 21 days large single sampling gap 7 days. function expects surveys data least location_id, year, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum weeks — require_minimum_weeks","title":"Require minimum weeks — require_minimum_weeks","text":"Remove survey site-years region covering less minimum number weeks.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum weeks — require_minimum_weeks","text":"","code":"require_minimum_weeks(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum weeks — require_minimum_weeks","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum weeks — require_minimum_weeks","text":"function groups surveys data location_id year. removes groups survey period less minimum number weeks given region. expects surveys data least location_id, year, region, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":null,"dir":"Reference","previous_headings":"","what":"Require seven fortnights — require_seven_fortnights","title":"Require seven fortnights — require_seven_fortnights","text":"Divide year approximate 2 week blocks, selecting blocks 10-16 discarding locations without survey remaining block","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require seven fortnights — require_seven_fortnights","text":"","code":"require_seven_fortnights(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require seven fortnights — require_seven_fortnights","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require seven fortnights — require_seven_fortnights","text":"function assigns survey approximate fortnight. fortnight defined days 16th day month days 15th day month. surveys falling outside date range seven fortnights second fortnight May second fortnight August removed. Surveys grouped location_id year surveys belonging groups least one survey occurring seven remaining fortnights discarded. function assumes surveys data day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":null,"dir":"Reference","previous_headings":"","what":"Require at least two years — require_two_years","title":"Require at least two years — require_two_years","text":"Discard locations less two survey years","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require at least two years — require_two_years","text":"","code":"require_two_years(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require at least two years — require_two_years","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require at least two years — require_two_years","text":"function groups surveys location_id removes surveys locations data one year. function assumes surveys data location_id year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Set start year — set_start_year","title":"Set start year — set_start_year","text":"Discard counts years start year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set start year — set_start_year","text":"","code":"set_start_year(counts, taxon, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set start year — set_start_year","text":"counts Count data. taxon Taxon configuration. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set start year — set_start_year","text":"function sets start year taxon counts. variable start_year configured given taxon count data prior start_year removed.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/shift_year_winter.html","id":null,"dir":"Reference","previous_headings":"","what":"Shift year winter — shift_year_winter","title":"Shift year winter — shift_year_winter","text":"Transpose early winter months following calendar year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/shift_year_winter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shift year winter — shift_year_winter","text":"","code":"shift_year_winter(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/shift_year_winter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shift year winter — shift_year_winter","text":"surveys Survey data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum by event — sum_by_event","title":"Sum by event — sum_by_event","text":"Sum counts surveys taxa year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum by event — sum_by_event","text":"","code":"sum_by_event(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum by event — sum_by_event","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum by event — sum_by_event","text":"functions groups count data location_id year. multiple taxa counts input data also grouped taxa. Counts summed across survey events locations years.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum over sections — sum_over_sections","title":"Sum over sections — sum_over_sections","text":"Sum counts sections surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum over sections — sum_over_sections","text":"","code":"sum_over_sections(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum over sections — sum_over_sections","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum over sections — sum_over_sections","text":"functions groups count data document_id (IDs individual surveys). multiple taxa counts input data also grouped taxa. Counts summed across survey sections count data provided surveys split parts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Update data — update_data","title":"Update data — update_data","text":"Update input data FinBIF.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update data — update_data","text":"","code":"update_data(type, index, taxon, db, do_update = FALSE)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update data — update_data","text":"type Character. type input data (e.g., surveys counts) index Character. Update data index? taxon Character. Update data taxon? Ignored type = \"surveys\" db Connection. Database update data FinBIF. do_update Logical. Update data regardless need.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update index — update_index","title":"Update index — update_index","text":"Update index output data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update index — update_index","text":"","code":"update_index(index, model, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update index — update_index","text":"index Character. Update index? model Character. model use? region Character. region? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_taxon_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update taxon index — update_taxon_index","title":"Update taxon index — update_taxon_index","text":"Update relative abundance index taxon.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_taxon_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update taxon index — update_taxon_index","text":"","code":"update_taxon_index(index, model, taxon, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_taxon_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update taxon index — update_taxon_index","text":"index Character. Update index? model Character. model use? taxon Character. Update data taxa? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":null,"dir":"Reference","previous_headings":"","what":"Zero fill — zero_fill","title":"Zero fill — zero_fill","text":"Combine count data survey data filling missing surveys count data zero counts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zero fill — zero_fill","text":"","code":"zero_fill(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Zero fill — zero_fill","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Zero fill — zero_fill","text":"function combines counts surveys data. performs right outer join counts surveys document_id. surveys corresponding data abundance filled zero. function assumes counts surveys data include document_id counts data includes abundance.","code":""}]
+[{"path":[]},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement helpdesk@laji.fi. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing","text":"Small typos grammatical errors documentation may edited long changes made source file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"Contributing","text":"make substantial pull request, always file issue make sure someone team agrees ’s problem.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"","what":"Pull request process","title":"Contributing","text":"recommend create Git branch pull request (PR). New code follow style used project. user-facing changes, add section top NEWS.Rd current development version header describing changes made followed username, links relevant issue(s)/PR(s).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing","text":"Please note project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021-2024 LUOMUS - Finnish Museum Natural History Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"NA","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indicators provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"indicator-types","dir":"","previous_headings":"Overview","what":"Indicator types","title":"NA","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"single-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Single-taxon indicators","title":"NA","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator (see /taxa-extra). example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"multi-taxon-indicators","dir":"","previous_headings":"Overview > Indicator types","what":"Multi-taxon indicators","title":"NA","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"supported-operations","dir":"","previous_headings":"Overview","what":"Supported Operations","title":"NA","text":"Get lists available indicators Get configuration indicator Get statistics indicator CSV JSON Get SVG image indicator","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/api.html","id":"examples","dir":"","previous_headings":"Overview","what":"Examples","title":"NA","text":"Get list multi-taxon indicators: Get list taxa included Winter Bird indicator: See Winter Bird indicator configured: Get Winter Bird indicator output json: Get single-taxon (Goldcrest) Winter Bird trim index output southern Finland CSV: Get SVG image Farmland Butterflies RBMS index","code":"$ curl \"https://indicators.laji.fi/indices\" $ curl \"https://indicators.laji.fi/taxa/wb\" $ curl \"https://indicators.laji.fi/config/wb\" $ curl \"https://indicators.laji.fi/data/wb\" $ curl \"https://indicators.laji.fi/csv/wb?taxon=MX.33954&model=trim&region=south\" $ curl -o bf.svg \"https://indicators.laji.fi/svg/bf?model=rbms\""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/alpine-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Alpine Bird Indicator","title":"Alpine Bird Indicator","text":"Northern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/butterfly-abundance.html","id":"section","dir":"Articles","previous_headings":"","what":"Butterfly Abundance Indicator","title":"Butterfly Abundance Indicator","text":"Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Community temperature index","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(lme4) library(arm)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Community temperature index","text":"five fields required survey data. filters restrict survey data Dec-Jan “Winter Bird Census” monitoring dataset December 1958 onwards selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data limit site first survey year (year period Dec-Jan).","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Winter Bird Census\",   date_range_ymd = c(\"1958-12-01\", \"\"),   date_range_md= c(\"12-01\", \"01-31\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_winter(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Community temperature index","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa species temperature index values defined. count data taxa can now downloaded FinBIF. count data combined survey data species temperature indices.","code":"select <- c(\"document_id\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select sti <- c(   \"Poecile montanus\" = -7.51,   \"Regulus regulus\" = -4.23,   \"Lophophanes cristatus\" = -5.90,   \"Certhia familiaris\" = -6.89 ) counts <- lapply(   names(sti),   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, combine_with_surveys, surveys)  counts <- mapply(mutate, counts, sp = names(sti), SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts[[\"sti\"]] <- sti[counts[[\"sp\"]]]"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-index.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Community temperature index","text":"community temperature index year created fitting linear mixed effects regression model combined data.","code":"cti_data <- summarise(   group_by(counts, location_id, year),   cti = sum(abundance * sti) / sum(abundance), .groups = \"drop\" )  cti <- lmer(cti ~ (1 | location_id) + (1 | year), cti_data)  cti <- data.frame(index = coef(cti)[[\"year\"]], se = se.coef(cti)[[\"year\"]])  cti[[\"time\"]] <- as.integer(row.names(cti))  names(cti) <- c(\"index\", \"se\", \"time\") ggplot(cti) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/community-temperature-indices.html","id":"section","dir":"Articles","previous_headings":"","what":"Community Temperature Indices","title":"Community Temperature Indices","text":"Winter Birds Summer Birds Farmland Butterflies","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"defaults","dir":"Articles","previous_headings":"","what":"Defaults","title":"Configuration","text":"Default parameters apply indicators can specified special object top-level key, default (see ). Defaults can overwritten specifying different parameters value indicator objects.","code":"default:   surveys:     selection:     - document_id     - location_id     - year     - month     - day     has_value:     - document_id     - location_id     - year     - month     - day   counts:     abundance: abundance   use_data_after: \"01-01\""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"sections","dir":"Articles","previous_headings":"","what":"Sections","title":"Configuration","text":"following describes section multi-taxon indicator objects detail.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"name","dir":"Articles","previous_headings":"Sections","what":"Name","title":"Configuration","text":"string giving long-form name multi-taxon indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"taxa","dir":"Articles","previous_headings":"Sections","what":"Taxa","title":"Configuration","text":"array defining taxa included multi-taxon indicator single-taxon indicators calculated. element array must include: code: string indicating FinBIF taxon MX code (e.g, MX.27328). binomial: string indicating scientific taxon name (e.g., Crex crex). optionally include one : extra_codes: array FinBIF taxon MX codes include along nominal taxon declared code. subtaxa: boolean indicating whether include observations child taxa taxa declared code extra_codes. start_year: integer indicating year observation data taxa begin. Observation data year excluded. Note start_year greater base_year (see section Model) base_year taxon set start_year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"extra-taxa","dir":"Articles","previous_headings":"Sections","what":"Extra taxa","title":"Configuration","text":"array defining taxa included parent multi-taxon indicator single-taxon indicators calculated. element array configured way taxa .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"from","dir":"Articles","previous_headings":"Sections","what":"From","title":"Configuration","text":"Multi-taxon indicators can constituent single-taxon indicators. case, section indicates multi-taxon indicator (form short-code) input data comes .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"filters","dir":"Articles","previous_headings":"Sections","what":"Filters","title":"Configuration","text":"filters section object defining list filters apply observation data FinBIF. See finbif R package documentation details.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"surveys","dir":"Articles","previous_headings":"Sections","what":"Surveys","title":"Configuration","text":"surveys section defines fields selected getting survey data FinBIF. Fields selected key selection array (see finbif R package documentation available fields). second key, has_value, array indicates fields must null values filtering records.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"counts","dir":"Articles","previous_headings":"Sections","what":"Counts","title":"Configuration","text":"counts section defines fields selected accessing count data FinBIF. sections uses selection has_value key manner . additional key, abundance, used indicate field used abundance (counts) data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"combine","dir":"Articles","previous_headings":"Sections","what":"Combine","title":"Configuration","text":"section combine defines single-taxon indicator data combined form multi-taxon indicator. Options include: geometric_mean: combines relative abundance geometric mean abundance. cti: combine abundances community temperature index. overall_abundance: combine abundance total abundance taxon group.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"use-data-after","dir":"Articles","previous_headings":"Sections","what":"Use data after","title":"Configuration","text":"section use_data_after defines calendar date (form \"MM-DD\") data collected current year start included indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/configuration.html","id":"model","dir":"Articles","previous_headings":"Sections","what":"Model","title":"Configuration","text":"model section defines single- multi-taxon indicators calculated survey count data sourced FinBIF. section consists one model objects object keys indicate model used. Models include: trim: Trends Indices Monitoring data model (via rtrim) rbms: Generalised abundance indices butterfly monitoring count data ( via rbms) lmer: Linear Mixed Effects Regression (via lme4) element model section must include: surveys_process: array survey data processing functions (see processing ) counts_process array count data processing functions (see processing ) optionally include: base_year: integer indicating base year indicator. args: additional arguments passed modelling function.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/farmland-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Bird Indicator","title":"Farmland Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/farmland-butterflies.html","id":"section","dir":"Articles","previous_headings":"","what":"Farmland Butterfly Indicator","title":"Farmland Butterfly Indicator","text":"RBMS TRIM","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/forest-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Forest Bird Indicator","title":"Forest Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/mire-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Mire Bird Indicator","title":"Mire Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/moths.html","id":"section","dir":"Articles","previous_headings":"","what":"Moth Indicator","title":"Moth Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Multi-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Multi-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Multi-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing multi-taxon indicator selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select taxa <- c(   \"Vanellus vanellus\", \"Numenius arquata\", \"Alauda arvensis\", \"Hirundo rustica\",   \"Delichon urbicum\", \"Anthus pratensis\", \"Saxicola rubetra\", \"Turdus pilaris\",   \"Sylvia communis\", \"Corvus monedula\", \"Sturnus vulgaris\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = c(\"scientific_name\", \"document_id\", abundance = \"pair_abundance\"),   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, zero_fill, surveys)  counts <- lapply(counts, sum_by_event)  counts <- lapply(counts, remove_all_zero_locations)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"fit-trim-models","dir":"Articles","previous_headings":"","what":"Fit TRIM Models","title":"Multi-taxon indicator (trim)","text":"TRIM model used estimate change abundance time taxon.","code":"model <- lapply(   counts, trim, count_col =\"abundance\", site_col = \"location_id\",   year_col = \"year\" )"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/multi-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Multi-taxon indicator (trim)","text":"index change relative abundance created taxon setting base year year 2000. indices combined single table geometric mean relative abundance associated uncertainty can calculated via Monte Carlo simulation method (see details).","code":"indices <- lapply(model, index, base = 2000)  indices <- mapply(mutate, indices, sp = taxa, SIMPLIFY = FALSE)  indices <- do.call(rbind, indices) n <- 1000 max_cv <- 3 imputed_min <- .01 truncfac <- 10 base <- 1 nyrs <- 44  indices <- mutate(   indices, cv = ifelse(imputed >= .1 & se_imp > 0, se_imp / imputed, NA_real_) )  indices <- group_by(indices, sp)  indices <- mutate(indices, cv = mean(cv, na.rm = TRUE))  indices <- filter(indices, cv < max_cv)  indices <- mutate(indices, imputed = pmax(imputed, imputed_min))  indices <- mutate(indices, se_imp = if_else(imputed > imputed_min, se_imp, 0))  indices <- mutate(indices, se_imp = se_imp / imputed)  indices <- mutate(indices, imputed = log(imputed))  indices <- group_by(indices, time, sp)  indices <- summarise(   indices, mc = rnorm(n, imputed, se_imp), i = seq(n), .groups = \"keep\" )  indices <- mutate(indices, mc = pmax(mc, log(imputed_min)))  indices <- group_by(indices, sp, i)  indices <- arrange(indices, time)  indices <- mutate(   indices, mcf = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- arrange(indices, -time)  indices <- mutate(   indices, mcb = pmax(pmin(lead(mc) - mc, log(truncfac)), log(1 / truncfac)) )  indices <- group_by(indices, i, time)  index <- summarise(   indices,   mcf = mean(mcf, na.rm = TRUE), mcb = mean(mcb, na.rm = TRUE),   .groups = \"drop_last\" )  index <- arrange(index, time)  index <- mutate(index, mcf = cumsum(lag(lead(mcf, base - 1), base, 0)))  index <- arrange(index, -time)  index <- mutate(   index, mcb = cumsum(lag(lead(mcb, nyrs - base), nyrs - base + 1, 0)) )  index <- group_by(index, time)  index <- summarise(   index,   index = exp(mean(mcf)) * exp(mean(mcb)),   se = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) ) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"),   y = index,   ymin = index - se,   ymax = index + se ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Overall abundance","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Overall abundance","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit surveys sites least seven fortnights surveyed limit site’s surveys first survey fortnight.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- require_seven_fortnights(surveys)  surveys <- pick_first_survey_in_fortnight(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Overall abundance","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). set taxa contributing total abundance selected. count data taxa can now downloaded FinBIF. Three processing functions applied count data : sum counts survey site sections; combine count survey data together; amd sum counts site-year combination. count data can summed across taxa.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select taxa <- c(   \"Aglais urticae\",   \"Boloria euphrosyne\",   \"Lycaena virgaureae\",   \"Polygonia c-album\" ) counts <- lapply(   taxa,   finbif_occurrence,   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- lapply(counts, sum_over_sections)  counts <- lapply(counts, combine_with_surveys, surveys)  counts <- lapply(counts, sum_by_event) counts <- mapply(mutate, counts, sp = taxa, SIMPLIFY = FALSE)  counts <- do.call(rbind, counts)  counts <- group_by(counts, location_id, year)  counts <- summarise(counts, abundance = sum(abundance), .groups = \"drop\")"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overall-abundance.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Overall abundance","text":"index total abundance year created fitting TRIM model combined data setting base year year 2000.","code":"model <- trim(abundance ~ location_id + year, counts)  index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"api","dir":"Articles","previous_headings":"","what":"API","title":"Overview","text":"HTTP API access indicator data products available developers. API documented .","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"updates","dir":"Articles","previous_headings":"","what":"Updates","title":"Overview","text":"Indicators updated nightly 12 8am random order. update process checks FinBIF new input data updates affected indices many possible within 8hr update process window.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"indicator-types","dir":"Articles","previous_headings":"","what":"Indicator types","title":"Overview","text":"Indicators either single-taxon multi-taxon. indicators calculated whole Finland well separately North (Lappi, Kainuu Pohjois-Pohjanmaa regions) South (regions).","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"single-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Single-taxon indicators","title":"Overview","text":"Single-taxon indicators track average abundance across monitoring sites, relative base year. example, base year 2000 indicator 2003 0.8, average abundance across sites monitored 2003 declined 20 percentage points relative average abundance sites monitored year 2000. Single-taxon indicators can calculated using different models including TRIM RBMS. Single-taxon indicators “belong” multi-taxon indicator individual taxa can constitute one single-taxon indicator “belonging” different multi-taxon indicator. example, Goldcrest (Regulus regulus) , belongs Winter Bird indicator Forest Breeding Bird indicator two corresponding single-taxon indicators species. taxon “belong” multi-taxon indicator contribute given indicator. example, single-taxon indicator Eurasian Sparrowhawk (Accipiter nisus) winter contribute multi-taxon Winter Bird Indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/overview.html","id":"multi-taxon-indicators","dir":"Articles","previous_headings":"Indicator types","what":"Multi-taxon indicators","title":"Overview","text":"Multi-taxon indicators come different forms. include: geometric mean relative abundance across set taxa; community temperature index set taxa; total expected abundance taxon group. multi-taxon indicators single-taxon indicators belong . Instead, multi-taxon indicators without single-taxon indicators can “reuse” input another multi-taxon indicator. example, single-taxon indices “belong” Winter Bird Community Temperature Index, multi-taxon indicator constructed taxa (extra taxa) fall Winter Bird indicator.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (rbms)","text":"following packages required. packages available CRAN apart fbi rbms can installed GitHub.","code":"library(dplyr) library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rbms)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (rbms)","text":"five fields required survey data. filters restrict survey data “Butterflies Finnish agricultural landscapes” dataset selected data fields missing data. survey data can now downloaded FinBIF. single processing function applied survey data convert year month day fields single date field.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   collection = \"Butterflies in Finnish agricultural landscapes\",   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- format_date(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (rbms)","text":"Count data requires three fields selected: survey identifier (document_id) survey site section (section) measure abundance (abundance_interpreted). count data requires filters survey data (though filter has_value needs redefined). count data Aglais urticae (Small tortoiseshell) can now downloaded FinBIF. Two processing functions applied count data : sum counts survey site sections; combine count survey data together.","code":"select <- c(\"document_id\", \"section\", abundance = \"abundance_interpreted\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Aglais urticae\",   filter = filter,   select = select ,   n = \"all\",   quiet = TRUE ) counts <- sum_over_sections(counts, surveys)  counts <- combine_with_surveys(counts, surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"fit-rbms-model","dir":"Articles","previous_headings":"","what":"Fit RBMS Model","title":"Single-taxon indicator (rbms)","text":"RBMS model used estimate change abundance time (see RBMS documentation details) uncertainty estimated via bootstrapping.","code":"StartMonth <- 4 EndMonth <- 9 StartDay <- 1 EndDay <- 30 Anchor <- TRUE AnchorLength <- 14 AnchorLag <- 14 AnchorTimeUnit <- \"d\" NbrSample <- 500 MinVisit <- 5 MinOccur <- 2 MinNbrSite <- 5 MaxTrial <- 4 GamFamily <- \"nb\" FlightCurveTimeUnit <- \"w\" MultiVisit <- \"mean\" MinFC <- 0.10 boot_n <- 200  surveys <- select(surveys, site_id = location_id, year, date)  init_year <- min(surveys[[\"year\"]])  last_year <- max(surveys[[\"year\"]])  nyears <- last_year - init_year + 1  ts_date <- ts_dwmy_table(InitYear = init_year, LastYear = last_year)  ts_season <- ts_monit_season(   d_series     = ts_date,   StartMonth   = StartMonth,   EndMonth     = EndMonth,   StartDay     = StartDay,   EndDay       = EndDay,   Anchor       = Anchor,   AnchorLength = AnchorLength,   AnchorLag    = AnchorLag,   TimeUnit     = AnchorTimeUnit )  ts_season_visit <- ts_monit_site(m_visit = surveys, ts_season = ts_season)  counts <- mutate(counts, species = 1)  counts <- select(   counts, count = abundance, site_id = location_id, year, date, species )  ts_season_count <- ts_monit_count_site(   m_season_visit = ts_season_visit, m_count = counts )  ts_flight_curve <- flight_curve(   ts_season_count = ts_season_count,   NbrSample       = NbrSample,   MinVisit        = MinVisit,   MinOccur        = MinOccur,   MinNbrSite      = MinNbrSite,   MaxTrial        = MaxTrial,   GamFamily       = GamFamily,   SpeedGam        = FALSE,   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit,   verbose         = FALSE )  impt_counts <- impute_count(   ts_season_count = ts_season_count,   ts_flight_curve = ts_flight_curve[[\"pheno\"]],   TimeUnit        = FlightCurveTimeUnit,   MultiVisit      = MultiVisit )  sindex <- site_index(butterfly_count = impt_counts, MinFC = MinFC)  bootsample <- boot_sample(data = sindex, boot_n = boot_n)  index_mc <- mapply(   collated_index,   bootID = seq_len(boot_n),   MoreArgs = list(data = sindex, s_sp = 1, boot_ind = bootsample),   SIMPLIFY = FALSE )"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-rbms.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (rbms)","text":"index change relative abundance uncertainty derived bootstrapped estimates can created setting base year year 2000.","code":"base <- which(sort(unique(surveys[[\"year\"]])) == 2000)  index_mc <- lapply(index_mc, getElement, \"col_index\")  index_mc <- do.call(rbind, index_mc)  index_mc <- mutate(index_mc, mc = log(pmax(1 / 100, COL_INDEX)), time = M_YEAR)  index_mc <- group_by(index_mc, BOOTi)  index_mc <- arrange(index_mc, time)  index_mc <- mutate(index_mc, mcf = lead(mc) - mc)  index_mc <- mutate(index_mc, mcf = lead(mcf, base - 1))  index_mc <- mutate(index_mc, mcf = lag(mcf, base, 0))  index_mc <- mutate(index_mc, mcf = cumsum(mcf))  index_mc <- arrange(index_mc, -time)  index_mc <- mutate(index_mc, mcb = lead(mc) - mc)  index_mc <- mutate(index_mc, mcb = lead(mcb, nyears - base))  index_mc <- mutate(index_mc, mcb = lag(mcb, nyears - base + 1, 0))  index_mc <- mutate(index_mc, mcb = cumsum(mcb))  index_mc <- group_by(index_mc, time)  index <- summarise(   index_mc,   mean = exp(mean(mcf)) * exp(mean(mcb)),   sd = sd(mcf) * exp(mean(mcf)) + sd(mcb) * exp(mean(mcb)) )  index <- mutate(index, lower = mean - sd, upper = mean + sd) ggplot(index) + aes(x = parse_date_time(time, \"Y\"), y = mean, ymin = lower, ymax = upper) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"load-packages","dir":"Articles","previous_headings":"","what":"Load packages","title":"Single-taxon indicator (trim)","text":"following packages required. packages available CRAN apart fbi can installed GitHub.","code":"library(fbi) library(finbif) library(ggplot2) library(lubridate) library(rtrim)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"survey-data","dir":"Articles","previous_headings":"","what":"Survey data","title":"Single-taxon indicator (trim)","text":"five fields required survey data. filters restrict survey data “Point count” “Line transect” bird monitoring datasets 1979 onwards sites labelled “farmland” selected data fields missing data. survey data can now downloaded FinBIF. Two processing functions applied survey data first limit site first survey year limit surveys sites least two years surveyed.","code":"select <- c(\"document_id\", \"location_id\", \"year\", \"month\", \"day\") filter <- list(   location_tag = \"farmland\",   collection = c(     \"Point counts of breeding terrestrial birds\",     \"Line transect censuses of breeding birds\"   ),   date_range_ymd = c(\"1979-01-01\", \"\"),   has_value = select ) surveys <- finbif_occurrence(   filter = filter,   select = select,   aggregate = \"events\",   aggregate_counts = FALSE,   n = \"all\",   quiet = TRUE ) surveys <- pick_first_survey_in_year(surveys)  surveys <- require_two_years(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"count-data","dir":"Articles","previous_headings":"","what":"Count data","title":"Single-taxon indicator (trim)","text":"Count data requires two fields selected: survey identifier (document_id) measure abundance (case number breeding pairs: pair_abundance). count data requires filters survey data (though filter has_value needs redefined). count data Anthus pratensis (Meadow pipit) can now downloaded FinBIF. Three processing functions applied count data : infill count data zero occurrences using survey data; sum counts site-year combination; remove sites number breeding pairs zero every occasion.","code":"select <- c(\"document_id\", abundance = \"pair_abundance\") filter[[\"has_value\"]] <- select counts <- finbif_occurrence(   taxa = \"Anthus pratensis\",   filter = filter,   select = select,   n = \"all\",   quiet = TRUE ) counts <- zero_fill(counts, surveys)  counts <- sum_by_event(counts)  counts <- remove_all_zero_locations(counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"fit-trim-model","dir":"Articles","previous_headings":"","what":"Fit TRIM Model","title":"Single-taxon indicator (trim)","text":"TRIM model used estimate change abundance time.","code":"model <- trim(abundance ~ location_id + year, counts)"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/single-taxon-indicator-trim.html","id":"create-index","dir":"Articles","previous_headings":"","what":"Create Index","title":"Single-taxon indicator (trim)","text":"index change relative abundance created setting base year year 2000.","code":"index <- index(model, base = 2000) ggplot(index) + aes(   x = parse_date_time(time, \"Y\"), y = imputed,   ymin = imputed - se_imp, ymax = imputed + se_imp ) + geom_ribbon(alpha = .2) + geom_line() + ylab(NULL) + xlab(NULL) + theme_minimal()"},{"path":"https://indicators-dev.laji.fi/docs/dev/articles/winter-birds.html","id":"section","dir":"Articles","previous_headings":"","what":"Winter Bird Indicator","title":"Winter Bird Indicator","text":"Finland Northern Finland Southern Finland","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Finnish Museum Natural History - Luomus. Copyright holder. William K. Morris. Author, maintainer.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Morris W (2024). fbi: Finnish Biodiversity Indicators. R package version 0.11.5.9000, https://indicators.laji.fi, https://github.com/luomus/fin-biodiv-indicators.","code":"@Manual{,   title = {fbi: Finnish Biodiversity Indicators},   author = {William K. Morris},   year = {2024},   note = {R package version 0.11.5.9000, https://indicators.laji.fi},   url = {https://github.com/luomus/fin-biodiv-indicators}, }"},{"path":"https://indicators-dev.laji.fi/docs/dev/index.html","id":"finnish-biodiversity-indicators","dir":"","previous_headings":"","what":"Finnish Biodiversity Indicators","title":"Finnish Biodiversity Indicators","text":"Finnish biodiversity indicators (FBI) service providing time series abundance indices related metrics Finland. input data indices provided Finnish Biodiversity Information Facility.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/check_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Check input — check_input","title":"Check input — check_input","text":"Check indicator inputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/check_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check input — check_input","text":"","code":"check_input(index, model, taxon)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/check_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check input — check_input","text":"index Character. index? model Character. model? taxon Character. taxon?","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/clean_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean cache — clean_cache","title":"Clean cache — clean_cache","text":"Remove unneeded tables rows database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/clean_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean cache — clean_cache","text":"","code":"clean_cache(db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/clean_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean cache — clean_cache","text":"db Connection. Database cache.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine with surveys — combine_with_surveys","title":"Combine with surveys — combine_with_surveys","text":"Combine count data survey data","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine with surveys — combine_with_surveys","text":"","code":"combine_with_surveys(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine with surveys — combine_with_surveys","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/combine_with_surveys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Combine with surveys — combine_with_surveys","text":"function combines counts surveys data. performs inner join counts surveys document_id. function assumes counts surveys data include document_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":null,"dir":"Reference","previous_headings":"","what":"Format date — format_date","title":"Format date — format_date","text":"Combine year, month, day survey single date string","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format date — format_date","text":"","code":"format_date(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format date — format_date","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/format_date.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format date — format_date","text":"function combines survey year, month day character string - separator. function assumes survey data includes year, month day.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get indices — get_indices","title":"Get indices — get_indices","text":"Get indices configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get indices — get_indices","text":"","code":"get_indices(file = Sys.getenv(\"R_CONFIG_FILE\"))"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get indices — get_indices","text":"file Configuration file.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_output.html","id":null,"dir":"Reference","previous_headings":"","what":"Get output — get_output","title":"Get output — get_output","text":"Get serialized indicator outputs","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_output.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get output — get_output","text":"","code":"get_output(output, index, model, taxon, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/get_output.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get output — get_output","text":"output Character. type output? index Character. Update index? model Character. model use? taxon Character. taxon? region Character. region? db Connection. Database get output.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in fortnight — pick_first_survey_in_fortnight","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"Pick first survey fortnight discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"","code":"pick_first_survey_in_fortnight(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_fortnight.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in fortnight — pick_first_survey_in_fortnight","text":"function groups surveys location_id, year fortnightthen orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, year (integers) location_id, processed function require_seven_fortnights.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in winter — pick_first_survey_in_winter","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"Pick first winter survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"","code":"pick_first_survey_in_winter(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_winter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in winter — pick_first_survey_in_winter","text":"function moves surveys occurring December ahead one year. enables December surveys grouped subsequent surveys occurring January winter. Surveys grouped location_id year ordered date. first survey group removed. two surveys share date location_id one picked random rest removed. function works assumption surveys winter December January surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick first survey in year — pick_first_survey_in_year","title":"Pick first survey in year — pick_first_survey_in_year","text":"Pick first survey year discarding subsequent surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick first survey in year — pick_first_survey_in_year","text":"","code":"pick_first_survey_in_year(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick first survey in year — pick_first_survey_in_year","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/pick_first_survey_in_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Pick first survey in year — pick_first_survey_in_year","text":"function groups surveys location_id year orders date. first survey group removed. two surveys share date location_id one picked random rest removed. function assumes surveys data includes day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/process_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Process functions — process_funs","title":"Process functions — process_funs","text":"Functions process indicator input data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/process_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Process functions — process_funs","text":"","code":"process_funs()"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove all-zero locations — remove_all_zero_locations","title":"Remove all-zero locations — remove_all_zero_locations","text":"Discard locations taxa always zero abundance","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove all-zero locations — remove_all_zero_locations","text":"","code":"remove_all_zero_locations(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove all-zero locations — remove_all_zero_locations","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/remove_all_zero_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove all-zero locations — remove_all_zero_locations","text":"function groups counts location_id removes counts includes location_id abundance.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum gaps — require_minimum_gaps","title":"Require minimum gaps — require_minimum_gaps","text":"Remove survey site-years many large sampling gaps.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum gaps — require_minimum_gaps","text":"","code":"require_minimum_gaps(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum gaps — require_minimum_gaps","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_gaps.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum gaps — require_minimum_gaps","text":"function groups surveys data location_id year. removes groups survey period many large sampling gaps. many defined total gap length year 21 days large single sampling gap 7 days. function expects surveys data least location_id, year, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":null,"dir":"Reference","previous_headings":"","what":"Require minimum weeks — require_minimum_weeks","title":"Require minimum weeks — require_minimum_weeks","text":"Remove survey site-years region covering less minimum number weeks.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require minimum weeks — require_minimum_weeks","text":"","code":"require_minimum_weeks(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require minimum weeks — require_minimum_weeks","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_minimum_weeks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require minimum weeks — require_minimum_weeks","text":"function groups surveys data location_id year. removes groups survey period less minimum number weeks given region. expects surveys data least location_id, year, region, ordinal_day_start ordinal_day_end.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":null,"dir":"Reference","previous_headings":"","what":"Require seven fortnights — require_seven_fortnights","title":"Require seven fortnights — require_seven_fortnights","text":"Divide year approximate 2 week blocks, selecting blocks 10-16 discarding locations without survey remaining block","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require seven fortnights — require_seven_fortnights","text":"","code":"require_seven_fortnights(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require seven fortnights — require_seven_fortnights","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_seven_fortnights.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require seven fortnights — require_seven_fortnights","text":"function assigns survey approximate fortnight. fortnight defined days 16th day month days 15th day month. surveys falling outside date range seven fortnights second fortnight May second fortnight August removed. Surveys grouped location_id year surveys belonging groups least one survey occurring seven remaining fortnights discarded. function assumes surveys data day, month year (integers) location_id.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":null,"dir":"Reference","previous_headings":"","what":"Require at least two years — require_two_years","title":"Require at least two years — require_two_years","text":"Discard locations less two survey years","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require at least two years — require_two_years","text":"","code":"require_two_years(surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require at least two years — require_two_years","text":"surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/require_two_years.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Require at least two years — require_two_years","text":"function groups surveys location_id removes surveys locations data one year. function assumes surveys data location_id year.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":null,"dir":"Reference","previous_headings":"","what":"Set start year — set_start_year","title":"Set start year — set_start_year","text":"Discard counts years start year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set start year — set_start_year","text":"","code":"set_start_year(counts, taxon, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set start year — set_start_year","text":"counts Count data. taxon Taxon configuration. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/set_start_year.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set start year — set_start_year","text":"function sets start year taxon counts. variable start_year configured given taxon count data prior start_year removed.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/shift_year_winter.html","id":null,"dir":"Reference","previous_headings":"","what":"Shift year winter — shift_year_winter","title":"Shift year winter — shift_year_winter","text":"Transpose early winter months following calendar year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/shift_year_winter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shift year winter — shift_year_winter","text":"","code":"shift_year_winter(surveys)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/shift_year_winter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shift year winter — shift_year_winter","text":"surveys Survey data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum by event — sum_by_event","title":"Sum by event — sum_by_event","text":"Sum counts surveys taxa year","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum by event — sum_by_event","text":"","code":"sum_by_event(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum by event — sum_by_event","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_by_event.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum by event — sum_by_event","text":"functions groups count data location_id year. multiple taxa counts input data also grouped taxa. Counts summed across survey events locations years.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum over sections — sum_over_sections","title":"Sum over sections — sum_over_sections","text":"Sum counts sections surveys","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum over sections — sum_over_sections","text":"","code":"sum_over_sections(counts, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum over sections — sum_over_sections","text":"counts Count data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/sum_over_sections.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sum over sections — sum_over_sections","text":"functions groups count data document_id (IDs individual surveys). multiple taxa counts input data also grouped taxa. Counts summed across survey sections count data provided surveys split parts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Update data — update_data","title":"Update data — update_data","text":"Update input data FinBIF.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update data — update_data","text":"","code":"update_data(type, index, taxon, db, do_update = FALSE)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update data — update_data","text":"type Character. type input data (e.g., surveys counts) index Character. Update data index? taxon Character. Update data taxon? Ignored type = \"surveys\" db Connection. Database update data FinBIF. do_update Logical. Update data regardless need.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update index — update_index","title":"Update index — update_index","text":"Update index output data.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update index — update_index","text":"","code":"update_index(index, model, region, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update index — update_index","text":"index Character. Update index? model Character. model use? region Character. region? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_taxon_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Update taxon index — update_taxon_index","title":"Update taxon index — update_taxon_index","text":"Update relative abundance index taxon.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_taxon_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update taxon index — update_taxon_index","text":"","code":"update_taxon_index(index, model, taxon, db)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/update_taxon_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update taxon index — update_taxon_index","text":"index Character. Update index? model Character. model use? taxon Character. Update data taxa? db Connection. Database update index.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":null,"dir":"Reference","previous_headings":"","what":"Zero fill — zero_fill","title":"Zero fill — zero_fill","text":"Combine count data survey data filling missing surveys count data zero counts.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zero fill — zero_fill","text":"","code":"zero_fill(counts, surveys, ...)"},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Zero fill — zero_fill","text":"counts Count data. surveys Survey data. ... Additional arguments.","code":""},{"path":"https://indicators-dev.laji.fi/docs/dev/reference/zero_fill.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Zero fill — zero_fill","text":"function combines counts surveys data. performs right outer join counts surveys document_id. surveys corresponding data abundance filled zero. function assumes counts surveys data include document_id counts data includes abundance.","code":""}]