Merge pull request #100 from NOAA-EDAB/dev_branch

pkgdown fix for ROracle
NOAA-EDAB · Apr 15, 2024 · 10210a9 · 10210a9
2 parents 13d4fa1 + 89123c3
commit 10210a9
Show file tree

Hide file tree

Showing 4 changed files with 114 additions and 105 deletions.
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
@@ -9,48 +9,86 @@ on:
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.3.1'
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: install Oracle instant client
+        run: |
+          sudo apt update
+          sudo apt-get install -y alien libaio1 libaio-dev
+          wget https://download.oracle.com/otn_software/linux/instantclient/2112000/oracle-instantclient-basic-21.12.0.0.0-1.el8.x86_64.rpm
+          wget https://download.oracle.com/otn_software/linux/instantclient/2112000/oracle-instantclient-devel-21.12.0.0.0-1.el8.x86_64.rpm
+          wget https://download.oracle.com/otn_software/linux/instantclient/2112000/oracle-instantclient-odbc-21.12.0.0.0-1.el8.x86_64.rpm
+          wget https://download.oracle.com/otn_software/linux/instantclient/2112000/oracle-instantclient-sqlplus-21.12.0.0.0-1.el8.x86_64.rpm
+          sudo alien -i oracle-instantclient-basic-21.12.0.0.0-1.el8.x86_64.rpm
+          sudo alien -i oracle-instantclient-devel-21.12.0.0.0-1.el8.x86_64.rpm
+          sudo alien -i oracle-instantclient-odbc-21.12.0.0.0-1.el8.x86_64.rpm
+          sudo alien -i oracle-instantclient-sqlplus-21.12.0.0.0-1.el8.x86_64.rpm
+
+
+          echo "export ORACLE_HOME=/usr/lib/oracle/21/client64" | sudo tee -a /etc/profile.d/oracle.sh
+          echo "export TNS_ADMIN=/usr/lib/oracle/21/client64/lib/network/admin" | sudo tee -a /etc/profile.d/oracle.sh
+          echo "export LD_LIBRARY_PATH=/usr/lib/oracle/21/client64/lib:${LD_LIBRARY_PATH}" | sudo tee -a /etc/profile.d/oracle.sh
+          echo "export OCI_LIB=/usr/lib/oracle/21/client64/lib" | sudo tee -a /etc/profile.d/oracle.sh
+          echo "export OCI_INC=/usr/include/oracle/21/client64}" | sudo tee -a /etc/profile.d/oracle.sh
+          echo "export PHP_DTRACE=yes" | sudo tee -a /etc/profile.d/oracle.sh
+          echo "export EXTENSION_DIR=/usr/lib64/php/modules" | sudo tee -a /etc/profile.d/oracle.sh
+          echo "export PATH=\$ORACLE_HOME/bin:\$PATH" | sudo tee -a /etc/profile.d/oracle.sh          sudo chmod +x /etc/profile.d/oracle.sh
+          source /etc/profile.d/oracle.sh
+        shell: bash
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install libudunits2-dev libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev libgdal-dev 
+#          sudo apt-get install  libgdal-dev libcurl4-gnutls-dev libgit2-dev 
+        shell: bash
 
-      - name: Query dependencies
+      - name: Install R packages
         run: |
-          install.packages('remotes')
+          install.packages("remotes")
+          install.packages("DBI")
+          install.packages("ROracle", type = "source", configure.args = "--with-oci-lib=/usr/lib/oracle/21/client64/lib --with-oci-inc=/usr/include/oracle/21/client64")
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-
-      - name: Install binary dependencies
-        if: runner.os != 'Linux'
+      - name: Install package dependencies
+        #if: runner.os |= 'Linux'
         run: |
-          remotes::install_deps(dependencies = TRUE, type="binary")
+          remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
 
       - name: Install pkgdown
         run: |
-          install.packages("pkgdown", type = "binary")
+          install.packages("pkgdown")
         shell: Rscript {0}
 
       - name: Install package
         run: R CMD INSTALL .
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -27,7 +27,7 @@ Remotes:
   NOAA-EDAB/survdat,
   NOAA-EDAB/ecodata,
   r4atlantis/atlantisom,
-  NEFSC/NEFSC-spatial
+  NEFSC/NEFSC-Spatial
 VignetteBuilder: knitr
 Suggests:
   NEFSCspatial,
@@ -55,7 +55,6 @@ Suggests:
   dplyr,
   here,
   data.table,
-  rgdal,
   ggthemes,
   FSA,
   ecodata,

diff --git a/vignettes/GBSurveySet.Rmd b/vignettes/GBSurveySet.Rmd
@@ -1,18 +1,19 @@
 ---
 title: "MS Keyrun - GB survey footprint"
-author: "Sean Lucey"
-date: "`r format(Sys.time(), '%d %B, %Y')`"
 output:
-  html_document:
-    code_fold: hide
+  bookdown::html_document2:
+    number_sections: false
+link-citations: yes
+pkgdown:
+  as_is: true
 ---
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE, 
                       message = FALSE,
                       warning = FALSE)
 
-library(data.table); library(here); library(rgdal); library(survdat); library(sf) 
+library(data.table); library(here); library(survdat); library(sf) 
 
 ```
 
@@ -27,113 +28,84 @@ While work is ongoing towards segregating the fisheries dependent data, there is
 ### Option 1 - use survey design {#opt1}
 The NEFSC bottom trawl survey uses a stratified random design.  The rationale behind a stratified random design is to minimize variance. The figure below shows the full range of strata with the Georges Bank EPU overlaid in red. As you will notice, some of the survey strata extend beyond the EPU boundary.  There are several ways that this can be accounted for.  The simplest option is to include all strata that are partially within the EPU boundary.
 
-```{r shapefile load}
-coast <- readOGR(dsn=here::here("data-raw/gis"), layer='NES_LME_coast', verbose = F)
-coast <- spTransform(coast, CRS('+init=epsg:4326'))
 
-strata <- readOGR(dsn=here::here("data-raw/gis"), layer='strata', verbose = F)
-strata <- spTransform(strata, CRS('+init=epsg:4326'))
+```{r Survey_map, fig.cap="Survey strata overlaid with Georges Bank EPU", fig.align='center'}
+# load in shape files and plot
+coast <- sf::st_read(dsn=here::here("data-raw/gis"), layer='NES_LME_coast', quiet=T) |> 
+  sf::st_transform(.,crs=4326)
 
-epu <- readOGR(here::here("data-raw/gis"), 'EPU_extended', verbose = F)
-epu <- spTransform(epu, CRS('+init=epsg:4326'))
+strata <- sf::st_read(dsn=here::here("data-raw/gis"), layer='strata', quiet=T) |> 
+  sf::st_transform(.,crs=4326)
+
+epu <- sf::st_read(here::here("data-raw/gis"), 'EPU_extended', quiet=T) |> 
+  sf::st_transform(.,crs=4326)
+
+GB.strata <- sf::st_read(here::here("data-raw/gis"), 'EPU_strata', quiet=T)  |> 
+  sf::st_transform(.,crs=4326) |> 
+  dplyr::mutate(Strata=as.factor(Strata))
 
-GB.strata <- readOGR(here::here("data-raw/gis"), 'EPU_strata', verbose = F)
-GB.strata <- spTransform(GB.strata, CRS('+init=epsg:4326'))
 
 MAB <- c(1010:1080, 1100:1120, 1600:1750, 3010:3450, 3470, 3500, 3510)
 GB  <- c(1090, 1130:1210, 1230, 1250, 3460, 3480, 3490, 3520:3550)
 GOM <- c(1220, 1240, 1260:1290, 1360:1400, 3560:3830)
 SS  <- c(1300:1352, 3840:3990)
-```
-
-```{r Survey_map}
-opar <- par(mar = c(3, 3.5, 2, 2))
-plot(0, 0, xlim = c(-77, -65), ylim = c(35, 45), xlab = '', ylab = '', axes = F,
-     typ = 'n')
-box()
-axis(1, at = c(-75, -70, -65), labels = c(expression('75'* degree * ' W'), 
-                                          expression('70'* degree * ' W'),
-                                          expression('65'* degree * ' W')))
-
-axis(2, at = c(35, 40, 45), labels = c(expression(35 * degree * ' N'),
-                                       expression(40 * degree * ' N'),
-                                       expression(45 * degree * ' N')), las = T)
 
-plot(strata, add = T)
-plot(epu[which(epu@data$EPU == 'GB'), ], add = T, border = 'red', lwd = 2)
+epus <- data.frame(EPU = as.factor(c(rep("MAB",length(MAB)), rep("GB",length(GB)), rep("GOM",length(GOM)), rep("SS",length(SS)))),STRATA = c(MAB,GB,GOM,SS))
 
-plot(coast, col = 'grey', add = T)
+strata <- strata |> 
+  dplyr::left_join(epus,by="STRATA") |> 
+  dplyr::filter(!is.na(EPU))
 
-legend('bottomright', legend = c('Survey Strata', 'Georges Bank EPU'), 
-       col = c('black', 'red'), lty = 1, lwd = 3)
+ggplot2::ggplot() +
+  ggplot2::geom_sf(data = coast,color = "Grey") +
+  ggplot2::geom_sf(data = strata, fill = "white")+
+  ggplot2::geom_sf(data = epu |> dplyr::filter(EPU == "GB"), color = "red", fill = "white", alpha = 0) + 
+  ggplot2::coord_sf(xlim = c(-77,-65), ylim = c(35,45)) + 
+  ggplot2::theme_classic()
 
 ```
 
 Another option is to include only those strata that are at least 50% within the EPU boundary by area.  This was the preferred method of the Northeast IEA program for their State of the Ecosystem report.  The map below shows the strata that were included.  The medium blue color represents Georges Bank.
 
-```{r SOE}
-opar <- par(mar = c(3, 3.5, 2, 2))
-plot(0, 0, xlim = c(-77, -65), ylim = c(35, 45), xlab = '', ylab = '', axes = F,
-     typ = 'n')
-box()
-axis(1, at = c(-75, -70, -65), labels = c(expression('75'* degree * ' W'), 
-                                          expression('70'* degree * ' W'),
-                                          expression('65'* degree * ' W')))
 
-axis(2, at = c(35, 40, 45), labels = c(expression(35 * degree * ' N'),
-                                       expression(40 * degree * ' N'),
-                                       expression(45 * degree * ' N')), las = T)
+```{r SOE, fig.cap="Survey strata by EPU",fig.align='center'}
 
-plot(strata[which(strata@data$STRATA %in% MAB), ], add = T, col = '#0093D0')
-plot(strata[which(strata@data$STRATA %in% GB),  ], add = T, col = '#0055A4')
-plot(strata[which(strata@data$STRATA %in% GOM), ], add = T, col = '#00467F')
-plot(strata[which(strata@data$STRATA %in% SS),  ], add = T, col = '#007078')
-plot(epu[which(epu@data$EPU == 'GB'), ], add = T, border = '#D65f00', lwd = 2)
+ggplot2::ggplot() +
+  ggplot2::geom_sf(data = coast,color = "Grey") +
+  ggplot2::geom_sf(data = strata, ggplot2::aes(fill = EPU),color = "Black")+
+  ggplot2::geom_sf(data = epu |> dplyr::filter(EPU == "GB"), color = "red", fill = "white", alpha = 0) + 
+  ggplot2::coord_sf(xlim = c(-77,-65), ylim = c(35,45)) + 
+  ggplot2::theme_classic() +
+  ggplot2::scale_fill_manual(values=c('#0093D0', '#0055A4','#00467F','#007078'))
 
-plot(coast, col = 'grey', add = T)
+```
 
-legend('bottomright', legend = c('Scotian Shelf', 'Gulf of Maine', 'Georges Bank',
-                                 'Mid-Atlantic', 'EPU'), 
-       fill = c('#007078', '#00467F', '#0055A4', '#0093D0', NA), 
-       border = c(rep('black', 4), NA), 
-       col = c(rep(0, 4), '#D65f00'), lty = c(rep(NA, 4), 1), lwd = 3, 
-       x.intersp = c(rep(-0.5, 4), 1))
 
 
-```
 
 The difference between these two options would be the inclusion of strata 01100, 01110, and 01120 in the southwest corner of the EPU.
 
 ### Option 2 - ignore survey design
 Ignoring the survey design leaves us with two options: a straight mean of the EPU or a post-stratified design.  The first option creates large variances which make it difficult to conduct any kind of statistical testing.  Other previous work by EDAB stratified Georges Bank into large strata based on whether the area was considered open access or withing a closed area, inside or outside of US waters, and the shelf break.  
 
-```{r GB}
-opar <- par(mar = c(3, 3.5, 2, 2))
-plot(0, 0, xlim = c(-72, -65), ylim = c(38, 43), xlab = '', ylab = '', axes = F,
-     typ = 'n')
-box()
-axis(1, at = c(-75, -70, -65), labels = c(expression('75'* degree * ' W'), 
-                                          expression('70'* degree * ' W'),
-                                          expression('65'* degree * ' W')))
-
-axis(2, at = c(35, 40, 45), labels = c(expression(35 * degree * ' N'),
-                                       expression(40 * degree * ' N'),
-                                       expression(45 * degree * ' N')), las = T)
 
 
-plot(GB.strata, add = T, border = '#D65f00', lwd = 2)
+```{r GB,fig.cap="Gearoges Bank EPU defined by survey strata",fig.align='center'}
 
-plot(coast, col = 'grey', add = T)
+ggplot2::ggplot() +
+  ggplot2::geom_sf(data = coast,color = "Grey") +
+  ggplot2::geom_sf(data = GB.strata, ggplot2::aes(fill = Strata),color = "Black") +
+  ggplot2::scale_fill_brewer(palette = "Blues") +
+  ggplot2::coord_sf(xlim = c(-72,-65), ylim = c(38,43)) + 
+  ggplot2::theme_classic() 
 ```
 
 
 ## Testing the options
 To see if there was an noticeable difference between the three options outlined above (All - Any strata that is at least partially within the GB EPU boundary, SOE - strata set used by the State of the Ecosystem report, and EPU - post-stratified EPU) biomass indices were calculated for the top 11 species that will be included in the MS Keyrun project.  
 
-```{r test, results="hide"}
-library(data.table); library(here); library(rgdal)#; library(Survdat);
-library(ggplot2); library(survdat)
 
+```{r test, results="hide"}
 
 #source(here('Survdat.r'))
 #load(here('data-raw/data/Survdat.RData'))
@@ -197,10 +169,10 @@ epu.mean[, subset := 'EPU']
 #Combine data
 combo.data <- rbindlist(list(all.mean, soe.mean, epu.mean))
 
-survey.plot <- ggplot(combo.data,
-                      aes(x = YEAR, y = strat.biomass)) +
-    geom_point(aes(color = subset)) +
-    facet_wrap(~SVSPP, ncol = 2, nrow = 6, scales = 'free_y')
+survey.plot <- ggplot2::ggplot(combo.data,
+                      ggplot2::aes(x = YEAR, y = strat.biomass)) +
+    ggplot2::geom_point(ggplot2::aes(color = subset)) +
+    ggplot2::facet_wrap(~SVSPP, ncol = 2, nrow = 6, scales = 'free_y')
 
 plot(survey.plot)
 

diff --git a/vignettes/allocateLandingsEPU.Rmd b/vignettes/allocateLandingsEPU.Rmd
@@ -1,13 +1,13 @@
 ---
 title: "Allocate landings to Georges Bank EPU"
-author: Andy Beet
-date: "`r format(Sys.time(), '%d %B, %Y')`"
 output:
   bookdown::html_document2:
     number_sections: false
 csl: apa-annotated-bibliography.csl
 bibliography: references.bib
 link-citations: yes
+pkgdown:
+  as_is: true
 ---
 
 ```{r setup, include=FALSE}