Start water updates [patch]

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-# Install packages, update data, test, and archive 
+# Install packages, update data, test, and archive
 
 name: CI
 
@@ -17,7 +17,7 @@ on:
 jobs:
   build:
     if: contains(toJson(github.event.commits), '[skip ci]') == false
-    
+
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -26,64 +26,66 @@ jobs:
       matrix:
         config:
           - {os: ubuntu-latest, r: '4.2.2', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          
+
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      
+
     steps:
       - uses: actions/checkout@v3
         with:
             fetch-depth: 3
-            
+
       - uses: r-lib/actions/setup-r@v2
-        
+
       - name: Cache R packages
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: |
             ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-
-            
+
       - name: Install system dependencies
-        run: sudo apt-get install libgit2-dev libcurl4-openssl-dev libudunits2-dev libgdal-dev libnetcdf-dev libgeos-dev libproj-dev
-
+        run: |
+             sudo apt remove libudunits2-dev libgdal-dev libgeos-dev libproj-dev
+             sudo apt-get install libgit2-dev libcurl4-openssl-dev libudunits2-dev libgdal-dev libnetcdf-dev libgeos-dev libproj-dev
+
       - name: Install packages
-        run: Rscript install-packages.R        
-        
+        run: Rscript install-packages.R
+
       - name: Update data
         run: Rscript update-data.R
-          
+
       - name: Test
         run: Rscript testthat.R
-        
+
       - name: Check for new files
         id: check_files
         run: |
-          if [[ -z "$(git status --porcelain)" ]] ; then 
+          if [[ -z "$(git status --porcelain)" ]] ; then
             echo "Git status is empty"
             echo "diff=FALSE" >> $GITHUB_OUTPUT
-          else 
+          else
             echo "diff=TRUE" >> $GITHUB_OUTPUT
           fi
-          
+
       - name: Bump version
         id: version
-        env: 
+        env:
           LOG: ${{ github.event_name == 'pull_request' && '$(git log --no-merges --format=%B -n 1 HEAD^2)' || '$(git log --no-merges --format=%B -n 1 HEAD)' }}
           CRON: ${{ github.event_name == 'schedule' && 'TRUE' || 'FALSE' }}
         run: |
           R -e "source('version_bump.R'); bump_version('${{ env.LOG }}', ${{ env.CRON }}, ${{ steps.check_files.outputs.diff }})"
-          if echo "$(git status --porcelain)" | grep -q version.txt ; then 
+          if echo "$(git status --porcelain)" | grep -q version.txt ; then
             echo "Version changed"
             echo "new_ver=TRUE" >> $GITHUB_OUTPUT
-          else 
+          else
             echo "No version bump"
             echo "new_ver=FALSE" >> $GITHUB_OUTPUT
           fi
-        
+
       - name: Setup Tag
         if: github.event_name != 'pull_request' && steps.version.outputs.new_ver == 'TRUE'
         id: tagging
@@ -92,18 +94,18 @@ jobs:
           echo "tag=$value" >> $GITHUB_OUTPUT
           value="v${value}"
           echo "release=$value" >> $GITHUB_OUTPUT
-      
+
       - name: Tag new version for release
         if: github.event_name != 'pull_request' && steps.version.outputs.new_ver == 'TRUE'
-        env: 
+        env:
           JOB_TAGS: ${{ github.event_name == 'schedule' && '[skip ci] [cron]' || '[skip ci]' }}
         uses: EndBug/add-and-commit@v9
         with:
           author_name: Weecology Deploy Bot
           author_email: [email protected]
           message: "Update data and trigger archive: GitHub Build ${{ github.run_number }} ${{ env.JOB_TAGS }}"
           tag: ${{ steps.tagging.outputs.tag }}
-          
+
       - name: Create Release
         if: github.event_name != 'pull_request' && steps.version.outputs.new_ver == 'TRUE'
         id: create_release

DataCleaningScripts/get_water_data.R

@@ -9,6 +9,7 @@ get_eden_data <- function() {
 
 wader::download_eden_depths()
 
+covariate_data <- read.table("../Water/eden_covariates.csv", header = TRUE, sep = ",")
 new_data <- wader::get_eden_covariates()
 new_data2 <- wader::get_eden_covariates(level="all")
 new_data3 <- wader::get_eden_covariates(level="wcas")
@@ -18,18 +19,26 @@ all_data <- dplyr::bind_rows(new_data,new_data2,new_data3) %>%
   dplyr::select(-geometry) %>%
   tidyr::pivot_wider(names_from="variable", values_from="value") %>%
   dplyr::arrange("year", "region")
+new_covariates <- all_data %>%
+  merge(dplyr::filter(covariate_data, !date %in% all_data$year)) %>%
+  dplyr::arrange("year", "region")
 
-depth_data <- wader::get_eden_depths() %>%
+depth_data <- read.table("../Water/eden_depth.csv", header = TRUE, sep = ",") %>%
+              dplyr::mutate(date=as.Date(date))
+new_depths <- wader::get_eden_depths() %>%
               dplyr::bind_rows(wader::get_eden_depths(level="all")) %>%
               dplyr::bind_rows(wader::get_eden_depths(level="wcas")) %>%
               dplyr::mutate(date=as.Date(date))
+new_depths <- new_depths %>%
+              merge(dplyr::filter(depth_data, !date %in% new_depths$date)) %>%
+              dplyr::arrange("date", "region")
 
 file.remove(dir(path=file.path(get_default_data_path(), 'EvergladesWadingBird/Water'),  pattern="_.*_depth.nc"))
 
 return(list(new_covariates=new_covariates, new_depths=new_depths))
 }
 
-#' Appends new water data
+#' Writes new water data
 #'
 #'
 

install-packages.R

@@ -3,7 +3,7 @@ if ("pacman" %in% rownames(installed.packages()) == FALSE) install.packages("pac
 
 # Install packages required for analysis
 
-pacman::p_load(git2r, httr, semver, testthat, yaml, 
+pacman::p_load(git2r, httr, semver, sf, testthat, yaml,
                dplyr, lubridate, remotes)
 
 remotes::install_github("weecology/wader")

update-data.R

@@ -1,3 +1,3 @@
 message("Updating weather station data")
 source("DataCleaningScripts/get_new_weather.R"); append_weather()
-# source("DataCleaningScripts/get_water_data.R"); update_water()
+source("DataCleaningScripts/get_water_data.R"); update_water()