markdown source builds

Auto-generated via {sandpaper} Source : 988239c Branch : main Author : Claudiu Forgaci <[email protected]> Time : 2024-05-15 14:45:24 +0000 Message : Merge pull request #41 from carpentries-incubator/post-feedback-update-lesson-4 Post feedback update lesson 4
carpentries-incubator · May 15, 2024 · 4508358 · 4508358
1 parent b47841e
commit 4508358
Show file tree

Hide file tree

Showing 17 changed files with 169 additions and 99 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/18-import-and-visualise-osm-data.md b/18-import-and-visualise-osm-data.md
diff --git a/19-basic-gis-with-r-sf.md b/19-basic-gis-with-r-sf.md
@@ -17,7 +17,7 @@ After completing this episode, participants should be able to…
 - Perform geoprocessing operations such as unions, joins and intersections with dedicated functions from the `sf` package
 - Compute the area of spatial polygons
 - Create buffers and centroids 
-- Map the results
+- Map and save the results
 
 ::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -30,6 +30,8 @@ library(sf)
 library(osmdata)
 library(leaflet)
 library(nominatimlite)
+library(lwgeom)
+library(here)
 assign("has_internet_via_proxy", TRUE, environment(curl::has_internet))
 ```
 
@@ -74,7 +76,9 @@ buildings$start_date <- as.numeric(buildings$start_date)
 old_buildings <- buildings %>%
   filter(start_date <= old)
 
- ggplot(data = old_buildings) + geom_sf(colour="red")
+ ggplot(data = old_buildings) + 
+   geom_sf(colour="red") +
+   coord_sf(datum = st_crs(28992))
 ```
 
 <img src="fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-2-1.png" style="display: block; margin: auto;" />
@@ -153,7 +157,9 @@ PROJCRS["Amersfoort / RD New",
 buffer_old_buildings <- 
   st_buffer(x = old_buildings, dist = distance)
 
-ggplot(data = buffer_old_buildings) + geom_sf()
+ggplot(data = buffer_old_buildings) + 
+  geom_sf() +   
+  coord_sf(datum = st_crs(28992))
 ```
 
 <img src="fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-4-1.png" style="display: block; margin: auto;" />
@@ -189,7 +195,8 @@ centroids_old <- st_centroid(old_buildings) %>%
 
 ggplot() + 
     geom_sf(data = single_old_buffer, aes(fill=ID)) +
-    geom_sf(data = centroids_old)
+    geom_sf(data = centroids_old) +
+    coord_sf(datum = st_crs(28992))
 ```
 
 <img src="fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-6-1.png" style="display: block; margin: auto;" />
@@ -218,7 +225,8 @@ Now, we would like to distinguish conservation areas based on the number of hist
                         begin = 0.6,
                         end = 1,
                         direction = -1,
-                        option = "B")
+                        option = "B") +
+      coord_sf(datum = st_crs(28992))
 ```
 
 <img src="fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" />
@@ -229,21 +237,29 @@ We aggregate them by ID number (`group_by(ID)`) and sum the variable `n` to know
 
 ### Final output:
 
-Let's map this layer over the initial map of individual buildings.
+Let's map this layer over the initial map of individual buildings, and save the result.
 
 
 ```r
-ggplot() + 
+p <- ggplot() + 
    geom_sf(data = buildings) +
    geom_sf(data = single_buffer, aes(fill=n_buildings), colour = NA) +
    scale_fill_viridis_c(alpha = 0.6,
                         begin = 0.6,
                         end = 1,
                         direction = -1,
-                        option = "B") 
+                        option = "B") +
+    coord_sf(datum = st_crs(28992))
+
+ p 
 ```
 
 <img src="fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" />
+
+```r
+ggsave(filename = "fig/ConservationBrielle.png", 
+       plot = p)
+```
 
 ::::::::::::::::::::::::::::::::::::: challenge 
 
@@ -289,17 +305,26 @@ centroid_by_buffer <- centroids_buffers %>%
 
 single_buffer <- single_old_buffer %>% 
   mutate(n_buildings = centroid_by_buffer$n)
-  ggplot() + 
+
+pnew <- ggplot() + 
     geom_sf(data = buildings) +
     geom_sf(data = single_buffer, aes(fill = n_buildings), colour = NA) +
     scale_fill_viridis_c(alpha = 0.6,
                          begin = 0.6,
                          end = 1,
                          direction = -1,
-                         option = "B")    
+                         option = "B")  +
+    coord_sf(datum = st_crs(28992))
+
+  pnew 
 ```
 
 <img src="fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-9-1.png" style="display: block; margin: auto;" />
+
+```r
+ggsave(filename = "fig/ConservationBrielle_newrules.png", 
+       plot = pnew)
+```
 ::::::::::::::::::::::::
 
 
@@ -314,21 +339,9 @@ single_buffer <- single_old_buffer %>%
 ```r
 single_buffer$area <- sf::st_area(single_buffer)  %>% 
   units::set_units(., km^2)
-```
 
-```{.error}
-Error in st_area.sfc(st_geometry(x), ...): package lwgeom required, please install it first
-```
-
-```r
 single_buffer$old_buildings_per_km2 <- as.numeric(single_buffer$n_buildings / single_buffer$area)
-```
-
-```{.error}
-Error in `[[<-.data.frame`(`*tmp*`, i, value = numeric(0)): replacement has 0 rows, data has 159
-```
 
-```r
  ggplot() + 
    geom_sf(data = buildings) +
    geom_sf(data = single_buffer, aes(fill=old_buildings_per_km2), colour = NA) +
@@ -339,13 +352,7 @@ Error in `[[<-.data.frame`(`*tmp*`, i, value = numeric(0)): replacement has 0 ro
                         option = "B") 
 ```
 
-```{.error}
-Error in `geom_sf()`:
-! Problem while computing aesthetics.
-ℹ Error occurred in the 2nd layer.
-Caused by error:
-! object 'old_buildings_per_km2' not found
-```
+<img src="fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-10-1.png" style="display: block; margin: auto;" />
 
 
 

diff --git a/4-gis-slides.html b/4-gis-slides.html
diff --git a/fig/18-import-and-visualise-osm-data-rendered-reproducibility-1.png b/fig/18-import-and-visualise-osm-data-rendered-reproducibility-1.png
diff --git a/fig/18-import-and-visualise-osm-data-rendered-reproducibility-2.png b/fig/18-import-and-visualise-osm-data-rendered-reproducibility-2.png
diff --git a/fig/18-import-and-visualise-osm-data-rendered-unnamed-chunk-8-1.png b/fig/18-import-and-visualise-osm-data-rendered-unnamed-chunk-8-1.png
diff --git a/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-10-1.png b/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-10-1.png
diff --git a/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-2-1.png b/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-2-1.png
diff --git a/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-4-1.png b/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-4-1.png
diff --git a/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-6-1.png b/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-6-1.png
diff --git a/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-7-1.png b/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-7-1.png
diff --git a/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-8-1.png b/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-8-1.png
diff --git a/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-9-1.png b/fig/19-basic-gis-with-r-sf-rendered-unnamed-chunk-9-1.png
diff --git a/fig/ConservationBrielle.png b/fig/ConservationBrielle.png
diff --git a/fig/ConservationBrielle_newrules.png b/fig/ConservationBrielle_newrules.png
diff --git a/md5sum.txt b/md5sum.txt
@@ -1,28 +1,28 @@
 "file" "checksum" "built" "date"
-"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-05-14"
-"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-05-14"
-"config.yaml" "eba2e90f9f89b711e953fb45172634ef" "site/built/config.yaml" "2024-05-14"
-"index.md" "db222f765de8e62e7990ec8ba4328199" "site/built/index.md" "2024-05-14"
-"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-05-14"
-"renv.lock" "faa3e4f5fc92beb7c4044d2633303c4c" "site/built/renv.lock" "2024-05-14"
-"episodes/01-intro-to-r.Rmd" "b13d8b2857351dc5b861e6f3f86f8add" "site/built/01-intro-to-r.md" "2024-05-14"
-"episodes/02-data-structures.Rmd" "2e3bbbc3ff746151b6bfeffdce1d61c9" "site/built/02-data-structures.md" "2024-05-14"
-"episodes/03-explore-data.Rmd" "9e557be2898dfa30ff101cb2717b7deb" "site/built/03-explore-data.md" "2024-05-14"
-"episodes/04-intro-to-visualisation.Rmd" "1837275ff28be449e5dee9fc69d49aa7" "site/built/04-intro-to-visualisation.md" "2024-05-14"
-"episodes/08-intro-to-geospatial-concepts.Rmd" "cea04d6fd3be978d734ddc03483b5d58" "site/built/08-intro-to-geospatial-concepts.md" "2024-05-14"
-"episodes/09-open-and-plot-vector-layers.Rmd" "cb9c1453822a18918067f5cb26a0b951" "site/built/09-open-and-plot-vector-layers.md" "2024-05-14"
-"episodes/10-explore-and-plot-by-vector-layer-attributes.Rmd" "4637f1b2bf993bb4a6cb2688ebd38ea8" "site/built/10-explore-and-plot-by-vector-layer-attributes.md" "2024-05-14"
-"episodes/11-plot-multiple-shape-files.Rmd" "1fa5e6d7bbce5d4bd8b2e1a083b53460" "site/built/11-plot-multiple-shape-files.md" "2024-05-14"
-"episodes/12-handling-spatial-projection-and-crs.Rmd" "a0f6523fa9e0a92bf7f469fed449aa87" "site/built/12-handling-spatial-projection-and-crs.md" "2024-05-14"
-"episodes/13-intro-to-raster-data.Rmd" "eacc90b2e62a4b612715534c3b92e34a" "site/built/13-intro-to-raster-data.md" "2024-05-14"
-"episodes/14-plot-raster-data.Rmd" "e74c1aae5e32478ba386f15a9b7b80d9" "site/built/14-plot-raster-data.md" "2024-05-14"
-"episodes/15-reproject-raster-data.Rmd" "9392077cf50153cc1443b270b904e28b" "site/built/15-reproject-raster-data.md" "2024-05-14"
-"episodes/16-raster-calculations.Rmd" "b5be879fb97fb5aa53184ef3890f3243" "site/built/16-raster-calculations.md" "2024-05-14"
-"episodes/17-work-with-multi-band-rasters.Rmd" "9f8d16f868ab05241d010bd3d81c641a" "site/built/17-work-with-multi-band-rasters.md" "2024-05-14"
-"episodes/18-import-and-visualise-osm-data.Rmd" "70e7ee3ffe79367612ad50fa97d83f96" "site/built/18-import-and-visualise-osm-data.md" "2024-05-14"
-"episodes/19-basic-gis-with-r-sf.Rmd" "cd4fe4050b67f46536fe61b3b72a43c2" "site/built/19-basic-gis-with-r-sf.md" "2024-05-14"
-"instructors/instructor-notes.md" "55fd6f5f1627ddc05b0d8a25a1fc22bd" "site/built/instructor-notes.md" "2024-05-14"
-"learners/reference.md" "1c7cc4e229304d9806a13f69ca1b8ba4" "site/built/reference.md" "2024-05-14"
-"learners/setup.md" "dea81100282d7460d6534bcb721c6982" "site/built/setup.md" "2024-05-14"
-"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-05-14"
-"renv/profiles/lesson-requirements/renv.lock" "faa3e4f5fc92beb7c4044d2633303c4c" "site/built/renv.lock" "2024-05-14"
+"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-05-15"
+"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-05-15"
+"config.yaml" "eba2e90f9f89b711e953fb45172634ef" "site/built/config.yaml" "2024-05-15"
+"index.md" "db222f765de8e62e7990ec8ba4328199" "site/built/index.md" "2024-05-15"
+"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-05-15"
+"renv.lock" "5234c6582daf3ebb1f126ee9f57c2876" "site/built/renv.lock" "2024-05-15"
+"episodes/01-intro-to-r.Rmd" "b13d8b2857351dc5b861e6f3f86f8add" "site/built/01-intro-to-r.md" "2024-05-15"
+"episodes/02-data-structures.Rmd" "2e3bbbc3ff746151b6bfeffdce1d61c9" "site/built/02-data-structures.md" "2024-05-15"
+"episodes/03-explore-data.Rmd" "9e557be2898dfa30ff101cb2717b7deb" "site/built/03-explore-data.md" "2024-05-15"
+"episodes/04-intro-to-visualisation.Rmd" "1837275ff28be449e5dee9fc69d49aa7" "site/built/04-intro-to-visualisation.md" "2024-05-15"
+"episodes/08-intro-to-geospatial-concepts.Rmd" "cea04d6fd3be978d734ddc03483b5d58" "site/built/08-intro-to-geospatial-concepts.md" "2024-05-15"
+"episodes/09-open-and-plot-vector-layers.Rmd" "cb9c1453822a18918067f5cb26a0b951" "site/built/09-open-and-plot-vector-layers.md" "2024-05-15"
+"episodes/10-explore-and-plot-by-vector-layer-attributes.Rmd" "4637f1b2bf993bb4a6cb2688ebd38ea8" "site/built/10-explore-and-plot-by-vector-layer-attributes.md" "2024-05-15"
+"episodes/11-plot-multiple-shape-files.Rmd" "1fa5e6d7bbce5d4bd8b2e1a083b53460" "site/built/11-plot-multiple-shape-files.md" "2024-05-15"
+"episodes/12-handling-spatial-projection-and-crs.Rmd" "a0f6523fa9e0a92bf7f469fed449aa87" "site/built/12-handling-spatial-projection-and-crs.md" "2024-05-15"
+"episodes/13-intro-to-raster-data.Rmd" "eacc90b2e62a4b612715534c3b92e34a" "site/built/13-intro-to-raster-data.md" "2024-05-15"
+"episodes/14-plot-raster-data.Rmd" "e74c1aae5e32478ba386f15a9b7b80d9" "site/built/14-plot-raster-data.md" "2024-05-15"
+"episodes/15-reproject-raster-data.Rmd" "9392077cf50153cc1443b270b904e28b" "site/built/15-reproject-raster-data.md" "2024-05-15"
+"episodes/16-raster-calculations.Rmd" "b5be879fb97fb5aa53184ef3890f3243" "site/built/16-raster-calculations.md" "2024-05-15"
+"episodes/17-work-with-multi-band-rasters.Rmd" "9f8d16f868ab05241d010bd3d81c641a" "site/built/17-work-with-multi-band-rasters.md" "2024-05-15"
+"episodes/18-import-and-visualise-osm-data.Rmd" "3f152cee5c4ab57d134057a72a44341b" "site/built/18-import-and-visualise-osm-data.md" "2024-05-15"
+"episodes/19-basic-gis-with-r-sf.Rmd" "113bb971333546663f7e61f2f6498693" "site/built/19-basic-gis-with-r-sf.md" "2024-05-15"
+"instructors/instructor-notes.md" "55fd6f5f1627ddc05b0d8a25a1fc22bd" "site/built/instructor-notes.md" "2024-05-15"
+"learners/reference.md" "1c7cc4e229304d9806a13f69ca1b8ba4" "site/built/reference.md" "2024-05-15"
+"learners/setup.md" "dea81100282d7460d6534bcb721c6982" "site/built/setup.md" "2024-05-15"
+"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-05-15"
+"renv/profiles/lesson-requirements/renv.lock" "5234c6582daf3ebb1f126ee9f57c2876" "site/built/renv.lock" "2024-05-15"