Merge pull request #117 from weecology/colony-updates

Redefine Hidden colony [minor] Rename colonies in counts and nests Also correct Paurotis Pond Update shapefiles
weecology · Mar 1, 2024 · 1ff510c · 1ff510c
2 parents a7761b9 + 5fa0626
commit 1ff510c
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Showing 14 changed files with 5,074 additions and 5,064 deletions.
diff --git a/Counts/maxcounts.csv b/Counts/maxcounts.csv
diff --git a/DataCleaningScripts/clean_nest_checks.R b/DataCleaningScripts/clean_nest_checks.R
@@ -220,9 +220,16 @@ for(i in 1:length(tab_names)) {
                     "missed pulled","couldn’t check","too high","can't see","miss","n/a",
                     "c(\"n/a\", \"n/a\")","flagging gone","missed, no record","flag not found","missing",
                     "c(na, \"empty\")","couldn't find","flag on ground"), NA)) %>%
-    dplyr::mutate(date = as.Date(date),
-                  eggs = as.character(eggs),
-                  chicks = as.character(chicks)) %>%
+    dplyr::mutate(dplyr::across(everything(),~ purrr:map_chr(.x, ~ gsub("\"", "", .x)))) %>%
+    dplyr::mutate(year = as.integer(year),
+                  colony = as.character(colony),
+                  nest = as.character(nest),
+                  species = as.character(species),
+                  date = lubridate::ymd(date),
+                  eggs = as.integer(eggs),
+                  chicks = as.integer(chicks),
+                  stage = as.character(stage),
+                  notes = as.character(notes)) %>%
     dplyr::select(year, colony, nest, species, date, eggs, chicks, stage, notes)
 
     if(!all(new_data$colony %in% colonies$colony)| 

diff --git a/DataCleaningScripts/get_counts.R b/DataCleaningScripts/get_counts.R
@@ -3,15 +3,15 @@ species <- read.csv("SiteandMethods/species_list.csv")
 counts <- read.csv("Counts/maxcounts.csv")
 under40 <- read.csv("Counts/maxcounts_under40.csv")
 
-
-
-
+colonies$aka[which(colonies$colony=="hidden")] = "Hidden North, L-28, Hidden, L-28 Hidden, 58, 163"
+counts$group_id[which(counts$colony=="58")] = 57
+counts$colony[which(counts$colony=="58")] = "hidden"
 
 colonies <- colonies %>% dplyr::arrange(colony)
 write.table(colonies, "SiteandMethods/colonies.csv", row.names = FALSE, col.names = TRUE, 
             na = "", sep = ",", quote = c(7,8))
 
-counts <- counts %>% dplyr::arrange()
+counts <- counts %>% dplyr::arrange(colony,year)
 write.table(counts, "Counts/maxcounts.csv", row.names = FALSE, na = "", sep = ",", quote = 9)
 
 under40 <- under40 %>% dplyr::arrange()

diff --git a/DataCleaningScripts/old_nest_checks.R b/DataCleaningScripts/old_nest_checks.R
@@ -168,10 +168,15 @@ nests <- dplyr::bind_rows(old_data,nests) %>%
   dplyr::filter_at(.vars = dplyr::vars(eggs, chicks, stage, notes), 
                    .vars_predicate = dplyr::any_vars(!is.na(.)))
 
-write.csv(nests, "Nesting/nest_checks.csv", row.names = FALSE, na = "", quote = 9)
+nests <- nests %>%
+         dplyr::mutate(dplyr::across(c(colony,nest,species,stage,notes),as.character),
+                       dplyr::across(c(year,eggs,chicks),as.integer),
+                       date = lubridate::ymd(date))
+write.table(nests, "Nesting/nest_checks.csv", row.names = FALSE, na = "", sep = ",", quote = 9)
 
 species <- species %>% dplyr::arrange(species)
-write.csv(species, "SiteandMethods/species_list.csv", row.names = FALSE, na = "", quote = 5:25)
+write.table(species, "SiteandMethods/species_list.csv", row.names = FALSE, na = "", sep = ",", quote = 5:25)
 
 colonies <- colonies %>% dplyr::arrange(colony)
-write.csv(colonies, "SiteandMethods/colonies.csv", row.names = FALSE, na = "", quote = FALSE)
+write.table(colonies, "SiteandMethods/colonies.csv", row.names = FALSE, col.names = TRUE, 
+            na = "", sep = ",", quote = c(7,8))