Update habitatmap_stdized and habitatmap_terr

src/generate_habitatmap_stdized/10_generate_habmap_stdized.Rmd

@@ -2,9 +2,9 @@
 
 ## Data source
 
-The shapefile of the BWK and Natura 2000 habitat map of Flanders can be downloaded [here](https://zenodo.org/record/4428002#.YBqzu-hKigY).
+The shapefile of the BWK and Natura 2000 habitat map of Flanders can be downloaded [here](https://zenodo.org/record/10167695).
 
-To be sure we will use the correct version of the data source (habitatmap_2020), we will derive the md5 file hashes and compare it to the file hashes in the [data source version overview table](https://docs.google.com/spreadsheets/d/1E8ERlfYwP3OjluL8d7_4rR1W34ka4LRCE35JTxf3WMI/edit#gid=2100595853).
+To be sure we will use the correct version of the data source (habitatmap_2023), we will derive the md5 file hashes and compare it to the file hashes in the [data source version overview table](https://docs.google.com/spreadsheets/d/1E8ERlfYwP3OjluL8d7_4rR1W34ka4LRCE35JTxf3WMI/edit#gid=2100595853).
 
 ```{r}
 
@@ -18,15 +18,18 @@ hashes <-
         list.files(path = mypath,
             recursive = TRUE)
       )) %>%
+    filter(!str_detect(filepath, "habitatmap_2020|habitatmap_2018")) %>% 
+    #in case you store an older version in a subfolder 
     mutate(filename = str_match(filepath, "(.+\\/)*(.+)")[,3],
            md5 = map(filepath, function(x) {
                            file(x) %>% md5 %>% str_c(collapse = '')
                          }) %>% as.character,
-           md5_ref = c("f767a12540b2bde435c6709c9c9675ad",
-                      "358ff672c2fae48eba5bd09f8a671675",
+           md5_ref = c("8d436686b2ad4bc9355bf1c403b5ba43",
+                       "358ff672c2fae48eba5bd09f8a671675",
                       "f881f61a6c07741b58cb618d8bbb0b99",
-                      "1da89a5dc267bbd427c8c07fcf63f344",
-                      "79ae8b4b3c6d970a1f10e78f3eca9ef7"),
+                      "8c6999e914d7f95948d84d5221f58e6f",
+                      "8e9c2c1ef888ce085e027d32f7c73b8c",
+                      "7ff6cc0efbd34f4cfef52d73e466df0d"),
            match = md5 == md5_ref) %>%
     select(filename,
            md5,
@@ -175,8 +178,18 @@ In this case we will sum the phab-values and create one record for each type.
 + a certain and an uncertain record of the same type, for example:
 
 ```{r}
+
+example <- habmap_long %>%
+  group_by(polygon_id, type) %>%
+  filter(n() > 1) %>%
+  filter(any(certain) & any(!certain)) %>%
+  ungroup()
+
+polygon_id_example <- (example %>%
+  slice_head(n = 1))$polygon_id
+
 habmap_long %>%
-  filter(polygon_id == "639375_v2014")
+  filter(polygon_id == polygon_id_example)
 ```
 
 We will not aggregate the certain and uncertain record, because we will loose some information used to create `habitatmap_terr`. It is some of the uncertain records (such as `9120, gh`) are eliminated when processing `habitatmap_terr`. 
@@ -202,22 +215,19 @@ habmap_long_aggr <- habmap_long %>%
               certain = all(certain)) %>%
     ungroup() 
 ```
-See below the result of the aggregation for both examples. 
+See below the result of the aggregation for the first example. 
 
 ```{r}
 habmap_long_aggr %>%
   filter(polygon_id == "357179_v2020")
 ```
 
-```{r}
-habmap_long_aggr %>%
-  filter(polygon_id == "639375_v2014")
-```
-
-
 ## Select vegetation types that belong to the standard list of habitat and rbb types  
 
-Table \@ref(tab:selectTypes) shows the records with habitat types that do not belong to the standard list of habitat and rbb types. These records are filtered out. 
+Table \@ref(tab:selectTypes) shows the records with habitat types that do not belong to the standard list of habitat and rbb types.
+
+Good news! 
+The table is empty
 
 ```{r selectTypes}
 
@@ -257,6 +267,24 @@ habmap_types_sf <- habmap_sf %>%
 
 ```
 
+## Let 's have a quick look at the result
+
+The ID of each polygon in the habitatmap contains the year in which the polygon
+was last updated.
+In the table below we show the number of records per type and per update year.
+
+```{r}
+habmap_types %>%
+  mutate(polygon_version = str_sub(polygon_id, start = -4)) %>%
+  group_by(type, polygon_version) %>%
+  summarise(n_records = n()) %>%
+  ungroup() %>%
+  pivot_wider(names_from = "polygon_version", values_from = "n_records", values_fill = 0) %>%
+  kable() %>%
+  kable_styling()
+```
+
+
 ## Write results into a geopackage
 
 ```{r}

src/generate_habitatmap_stdized/index.Rmd

@@ -55,6 +55,10 @@ opts_chunk$set(
   echo = TRUE,
   dpi = 300
 )
+
+conflicted::conflict_prefer("select", "dplyr")
+conflicted::conflict_prefer("filter", "dplyr")
+
 # ISO8601 timestamp to set as fixed value in the GeoPackage 
 # (to be UPDATED to the actual creation date; at least update for each version):
 Sys.setenv(OGR_CURRENT_DATE = "2021-03-11T00:00:00.000Z")