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patterninstitute · Aug 6, 2024 · 8916d1c · 8916d1c
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -10,3 +10,4 @@
 ^pkgdown$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+^vignettes/articles$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,8 +11,7 @@ Authors@R: c(
     role = "ctb", comment = c(ORCID = "0000-0001-6884-2886")),
     person("Pattern Institute",
     role = c("cph", "fnd")),
-    person("CCMAR",
-    role = "fnd")
+    person("CCMAR", role = "fnd")
     )
 Description: The EUNIS habitat classification is a comprehensive pan-European
     system for habitat identification
@@ -32,5 +31,5 @@ Depends:
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/patterninstitute/eunis.habitats, https://www.pattern.institute/eunis.habitats/, http://www.pattern.institute/eunis.habitats/
 BugReports: https://github.com/patterninstitute/eunis.habitats/issues
-Config/Needs/website: patterninstitute/chic
+Config/Needs/website: patterninstitute/chic, rmarkdown
 License: CC0
diff --git a/README.Rmd b/README.Rmd
@@ -20,8 +20,10 @@ library(eunis.habitats)
 [![CRAN status](https://www.r-pkg.org/badges/version/eunis.habitats)](https://CRAN.R-project.org/package=eunis.habitats)
 <!-- badges: end -->
 
-`{eunis.habitats}` is an R data package that provides the [EUNIS Habitat
-Classification](https://www.eea.europa.eu/data-and-maps/data/eunis-habitat-classification-1) in tidy format.
+`{eunis.habitats}` is an R data package that provides the EUNIS habitat
+classification in tidy format.
+
+Use the helper `crosswalk()` to map habitat codes across classification systems.
 
 ## Installation
 
@@ -33,67 +35,19 @@ install.packages("eunis.habitats")
 
 ## EUNIS classifications
 
-There are four EUNIS classifications included in the one single data set `eunis_habitats`, namely:
+The data set `eunis_habitats` provides the four EUNIS classifications:
 
 1. EUNIS classification from 2007, revised in 2012.
 2. EUNIS marine classification from 2019
 3. EUNIS marine classification from 2022
 4. EUNIS terrestrial classification from 2021
 
-For example, to access the marine habitats classified according to EUNIS revision of 2022:
-
-```{r}
-subset(eunis_habitats, classification == "EUNIS_M_2022")
-```
-
-Check the documentation for more details: `?eunis_habitats`.
-
-## Crosswalks (mapping of habitat codes)
-
-From EUNIS 2012 to EUNIS Marine 2022:
-
-```{r}
-crosswalk(
-  code = c("A3.4", "A3.5"),
-  from = "EUNIS_2012",
-  to = "EUNIS_M_2022",
-  unnest = TRUE
-)
-```
-
-From EUNIS Marine 2019 to EUNIS 2012:
+See `vignette("eunis-classification")` to learn more. In addition, we also
+provide a helper for converting habitat codes across:
 
-```{r}
-crosswalk(
-code = c("MH152", "MH2331"),
-from = "EUNIS_M_2019",
-to = "EUNIS_2012",
-unnest = TRUE
-)
-```
-
-From EUNIS Marine 2022 to the European Red List of Habitats:
-
-```{r}
-crosswalk(
-code = c("MH152", "MH2331", "MA146", "MD55"),
-from = "EUNIS_M_2022",
-to = "RL",
-unnest = TRUE
-)
-```
-
-From EUNIS Marine 2019 to Habitats Directive Annex I:
-
-```{r}
-crosswalk(
-code = c("M", "MA1", "MA11", "MA12"),
-from = "EUNIS_M_2019",
-to = "Annex_I", unnest = TRUE
-)
-```
+- EUNIS habitat classifications
+- European Red List of Habitats
+- Habitats Directive Annex I
 
-## Original data source
+See `vignette("crosswalks")` for more details.
 
-The original data is by [EUNIS Habitat
-Classification](https://www.eea.europa.eu/data-and-maps/data/eunis-habitat-classification-1).
diff --git a/README.md b/README.md
@@ -9,9 +9,11 @@
 status](https://www.r-pkg.org/badges/version/eunis.habitats)](https://CRAN.R-project.org/package=eunis.habitats)
 <!-- badges: end -->
 
-`{eunis.habitats}` is an R data package that provides the [EUNIS Habitat
-Classification](https://www.eea.europa.eu/data-and-maps/data/eunis-habitat-classification-1)
-in tidy format.
+`{eunis.habitats}` is an R data package that provides the EUNIS habitat
+classification in tidy format.
+
+Use the helper `crosswalk()` to map habitat codes across classification
+systems.
 
 ## Installation
 
@@ -23,119 +25,18 @@ install.packages("eunis.habitats")
 
 ## EUNIS classifications
 
-There are four EUNIS classifications included in the one single data set
-`eunis_habitats`, namely:
+The data set `eunis_habitats` provides the four EUNIS classifications:
 
 1.  EUNIS classification from 2007, revised in 2012.
 2.  EUNIS marine classification from 2019
 3.  EUNIS marine classification from 2022
 4.  EUNIS terrestrial classification from 2021
 
-For example, to access the marine habitats classified according to EUNIS
-revision of 2022:
-
-``` r
-subset(eunis_habitats, classification == "EUNIS_M_2022")
-#> # A tibble: 1,942 × 8
-#>    classification section version group   level code    name         description
-#>    <chr>          <chr>   <chr>   <chr>   <int> <chr>   <chr>        <chr>      
-#>  1 EUNIS_M_2022   marine  2022    benthic     1 M       Marine bent… "Marine be…
-#>  2 EUNIS_M_2022   marine  2022    benthic     2 MA1     Littoral ro… "Littoral …
-#>  3 EUNIS_M_2022   marine  2022    benthic     3 MA11    Arctic litt… "Arctic li…
-#>  4 EUNIS_M_2022   marine  2022    benthic     3 MA12    Atlantic li… "Atlantic …
-#>  5 EUNIS_M_2022   marine  2022    benthic     4 MA121   Lichens or … "Lichen co…
-#>  6 EUNIS_M_2022   marine  2022    benthic     5 MA1211  Yellow and … "Vertical …
-#>  7 EUNIS_M_2022   marine  2022    benthic     5 MA1212  Prasiola st… "Exposed t…
-#>  8 EUNIS_M_2022   marine  2022    benthic     5 MA1213  Verrucaria … "Bedrock o…
-#>  9 EUNIS_M_2022   marine  2022    benthic     6 MA12131 Verrucaria … "The litto…
-#> 10 EUNIS_M_2022   marine  2022    benthic     6 MA12132 Verrucaria … "Upper lit…
-#> # ℹ 1,932 more rows
-```
-
-Check the documentation for more details: `?eunis_habitats`.
-
-## Crosswalks (mapping of habitat codes)
-
-From EUNIS 2012 to EUNIS Marine 2022:
-
-``` r
-crosswalk(
-  code = c("A3.4", "A3.5"),
-  from = "EUNIS_2012",
-  to = "EUNIS_M_2022",
-  unnest = TRUE
-)
-#> # A tibble: 64 × 2
-#>    eunis_2012_code eunis_m_2022_code
-#>    <chr>           <chr>            
-#>  1 A3.4            MA133            
-#>  2 A3.4            MA134            
-#>  3 A3.4            MA135            
-#>  4 A3.4            MA136            
-#>  5 A3.4            MA137            
-#>  6 A3.4            MB13             
-#>  7 A3.4            MB131            
-#>  8 A3.4            MB1311           
-#>  9 A3.4            MB1312           
-#> 10 A3.4            MB1313           
-#> # ℹ 54 more rows
-```
-
-From EUNIS Marine 2019 to EUNIS 2012:
-
-``` r
-crosswalk(
-code = c("MH152", "MH2331"),
-from = "EUNIS_M_2019",
-to = "EUNIS_2012",
-unnest = TRUE
-)
-#> # A tibble: 2 × 2
-#>   eunis_m_2019_code eunis_2012_code
-#>   <chr>             <chr>          
-#> 1 MH152             A7.12          
-#> 2 MH2331            A7.231
-```
-
-From EUNIS Marine 2022 to the European Red List of Habitats:
-
-``` r
-crosswalk(
-code = c("MH152", "MH2331", "MA146", "MD55"),
-from = "EUNIS_M_2022",
-to = "RL",
-unnest = TRUE
-)
-#> # A tibble: 4 × 2
-#>   eunis_m_2022_code rl_code
-#>   <chr>             <chr>  
-#> 1 MH152             <NA>   
-#> 2 MH2331            <NA>   
-#> 3 MA146             A1.1xx 
-#> 4 MD55              A5.27
-```
-
-From EUNIS Marine 2019 to Habitats Directive Annex I:
-
-``` r
-crosswalk(
-code = c("M", "MA1", "MA11", "MA12"),
-from = "EUNIS_M_2019",
-to = "Annex_I", unnest = TRUE
-)
-#> # A tibble: 7 × 2
-#>   eunis_m_2019_code annex_i_code
-#>   <chr>             <chr>       
-#> 1 M                 <NA>        
-#> 2 MA1               <NA>        
-#> 3 MA11              <NA>        
-#> 4 MA12              8330        
-#> 5 MA12              1160        
-#> 6 MA12              1170        
-#> 7 MA12              1130
-```
+See `vignette("eunis-classification")` to learn more. In addition, we
+also provide a helper for converting habitat codes across:
 
-## Original data source
+- EUNIS habitat classifications
+- European Red List of Habitats
+- Habitats Directive Annex I
 
-The original data is by [EUNIS Habitat
-Classification](https://www.eea.europa.eu/data-and-maps/data/eunis-habitat-classification-1).
+See `vignette("crosswalks")` for more details.
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -6,6 +6,9 @@ template:
 home:
   title: EUNIS Habitat Classification
   description: EUNIS Habitats and crosswalks
+  links:
+  - text: EUNIS habitat classification
+    href: https://www.eea.europa.eu/data-and-maps/data/eunis-habitat-classification-1/
 
 authors:
   Ramiro Magno:
@@ -29,3 +32,15 @@ reference:
   desc: "Convert habitat codes across EUNIS, European Red List and Habitats Directive Annex I"
   contents:
   - crosswalk
+
+navbar:
+  structure:
+    left:  [eunis, crosswalks, reference, news]
+    right: [search, github]
+  components:
+    eunis:
+      text: EUNIS Classification
+      href: articles/eunis-classification.html
+    crosswalks:
+      text: Crosswalks
+      href: articles/crosswalks.html
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/articles/crosswalks.Rmd b/vignettes/articles/crosswalks.Rmd
@@ -0,0 +1,74 @@
+---
+title: "Crosswalk of Habitat Codes"
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+library(eunis.habitats)
+```
+
+The function `crosswalk()` provides an easy mapping from habitat codes in
+one classification system to another.
+
+### From EUNIS 2012 to EUNIS Marine 2022
+
+```{r}
+crosswalk(
+  code = c("A3.4", "A3.5"),
+  from = "EUNIS_2012",
+  to = "EUNIS_M_2022",
+  unnest = TRUE
+)
+```
+
+### From EUNIS Marine 2019 to EUNIS 2012
+
+```{r}
+crosswalk(
+  code = c("MH152", "MH2331"),
+  from = "EUNIS_M_2019",
+  to = "EUNIS_2012",
+  unnest = TRUE
+)
+```
+
+### From EUNIS Marine 2022 to the European Red List of Habitats
+
+```{r}
+crosswalk(
+  code = c("MH152", "MH2331", "MA146", "MD55"),
+  from = "EUNIS_M_2022",
+  to = "RL",
+  unnest = TRUE
+)
+```
+
+### One to many mappings
+
+Note that some mappings are one to many, e.g. `"MA12"` in EUNIS Marine 2019 maps
+to the following _Habitats Directive Annex I_ habitat codes: `"8330"`, `"1160"`,
+`"1170"` and `"1130"`. That is why, by default, the _to_ column is a
+list-column.
+
+```{r}
+crosswalk(
+  code = c("M", "MA1", "MA11", "MA12"),
+  from = "EUNIS_M_2019",
+  to = "Annex_I"
+)
+```
+
+You need to use `unnest = TRUE` to flatten out the table of mappings and
+convert the _to_ list-column to a character vector column.
+
+```{r}
+crosswalk(
+  code = c("M", "MA1", "MA11", "MA12"),
+  from = "EUNIS_M_2019",
+  to = "Annex_I",
+  unnest = TRUE
+)
+```