For release v.0.1.0

.Rbuildignore

@@ -8,4 +8,7 @@
 ^\.Rproj.user$
 ^docs$
 ^pkgdown$
+^\.github$
+other
 ^vignettes/articles$
+

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'

.github/workflows/pkgdown.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - main
-      - master
 
 jobs:
   pkgdown:
@@ -40,15 +39,10 @@ jobs:
         run: |
           install.packages(c("pkgdown", "yaml"), type = "binary")
         shell: Rscript {0}
-        
+
       - name: Install package
         run: R CMD INSTALL .
-
-      - name: Create leaflet maps
-        run: |
-          source("./data-raw/create_leaflet_maps.R", echo = TRUE)
-        shell: Rscript {0}
-
+
       - name: Deploy package
         run: |
           git config --local user.email "actions@github.com"

.github/workflows/update_mdeb_data.yaml

@@ -0,0 +1,121 @@
+name: pull data from MDEB data hub
+
+on:
+  push:
+    branches:
+      - main2
+  pull_request:
+    branches:
+      - main2
+  #schedule:
+    # uses UTC/GMT time (+ 5 hrs)
+    ## put on HOLD temporarily
+    #- cron: "0 17 * * 3" # Every Wednesday at 1200 hrs = 1700 UTC
+
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GH_RELEASE }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install command line packages
+        run: |
+          sudo apt update
+          sudo apt-get install libcurl4-openssl-dev libgit2-dev
+#          sudo apt-get install  libgdal-dev libcurl4-gnutls-dev libgit2-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
+        shell: bash
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.2.0'
+
+      - name: Install packages
+        run: |
+          install.packages(c("remotes","jsonlite", "dplyr", "httr2", "here", "sf","rmarkdown"))
+          remotes::install_github("NEFSC/NEFSC-Spatial")
+        shell: Rscript {0}
+
+      - name: Pull MDEB data and save to repo
+        run: |
+          options(timeout = 60 * 60 * 6)
+          source(here::here("data-raw/get_mdeb_for_package.R"))
+          get_mdeb_for_package()
+        shell: Rscript {0}
+
+   - name: Make Comparisons for commit
+      # check for new data added or data omitted. Not concerned with data fixes
+      # update NEWS.md, DESCRIPTION with version/notes
+      # increments package version in description
+        run: |
+          options(timeout = 60 * 60 * 6)
+          source(here::here("data-raw/compare_data.r"))
+          source(here::here("data-raw/update_description.R"))
+          source(here::here("data-raw/update_news.R"))
+          diffs <- compare_data()
+          version <- update_description(diffs, digit=3)
+          update_news(version, diffs)
+          rmarkdown::render(here::here("data-raw/sendAsEmail.Rmd"),
+                    params = diffs)
+
+          saveRDS(version,here::here("data-raw/version.rds"))
+        shell: Rscript {0}
+
+      - name: render readme.rmd
+        run: |
+          options(timeout = 60 * 60 * 6)
+          rmarkdown::render(here::here("README.Rmd"))
+        shell: Rscript {0}
+
+      # Send email indicating if anything has changed
+      # - name: Send email
+      #   uses: dawidd6/action-send-mail@v3
+      #
+      #   with:
+      #     server_address: smtp.gmail.com
+      #     server_port: 465
+      #
+      #     username: ${{ secrets.MAIL_USERNAME }}
+      #     password: ${{ secrets.MAIL_PASSWORD }}
+      #
+      #     subject: Github Actions job result
+      #     to: andrew.beet@noaa.gov
+      #
+      #     from: NEFSCspatial GitHub
+      #
+      #     #body: file://${{github.workspace}}/data-raw/datapull.txt
+      #
+      #     html_body: file://${{github.workspace}}/data-raw/sendAsEmail.html
+      #
+      #     #attachments: ./data-raw/sendAsEmail.html
+      #
+      # - name: commit data files
+      #   run: |
+      #     git config user.name github-actions
+      #     git config user.email github-actions@github.com
+      #     git add data/*
+      #     git add README.md
+      #     git add NEWS.md
+      #     git add DESCRIPTION
+      #     git commit -m "automated mdeb pull from update_mdeb_data yml"
+      #     git push
+      #
+      # - name: create gh-release
+      #   run: |
+      #       version <- readRDS(here::here("data-raw/version.rds"))
+      #       if(!is.null(version)){
+      #       usethis::use_github_release(publish = TRUE)
+      #       }
+      #   shell: Rscript {0}

.gitignore

@@ -7,5 +7,6 @@
 # exclude folders
 data-raw/temp
 inst/doc
+other
 # docs folder, generated by local pkgdown build
 docs

DESCRIPTION

@@ -1,17 +1,20 @@
 Package: NEFSCspatial
-Title: Spatial data package
-Version: 0.0.1
-Authors@R: c(person("Andy", "Beet", , "andrew.beet@noaa.gov", role = c("aut", "cre")), person("Kimberly", "Bastille", , "kimberly.bastille@noaa.gov", role = "aut"), person("Joshua", "Hatch", , "joshua.hatch@noaa.gov", role = "aut"))
-URL: https://github.com/NEFSC/NEFSC-Spatial
+Title: Spatial data package for regions in the northeast atlantic
+Version: 0.1.0
+Authors@R: c(person("Andy", "Beet", email = "andrew.beet@noaa.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8270-7090")),
+             person("Joshua", "Hatch", email = "joshua.hatch@noaa.gov", role = "aut"),
+             person("Kimberly", "Bastille", email = "kimberly.bastille@noaa.gov", role = "aut"))
+URL: https://github.com/NEFSC/NEFSC-Spatial/, https://nefsc.github.io/NEFSC-Spatial/
 BugReports: https://github.com/NEFSC/NEFSC-Spatial/issues
-Description: Provides spatial data as sf objects
+Description: Provides spatial data as sf or raster objects for the Northeast Fisheries Science Center
 License: file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends: 
-    R (>= 3.5.0)
+    R (>= 4.0)
 Imports:
+    lifecycle,
     sf
 Suggests: 
     curl,
@@ -26,6 +29,10 @@ Suggests:
     hexSticker,
     ggimage,
     dplyr,
-    leaflet
+    ggplot2,
+    jsonlite,
+    httr2, 
+    gt
 LazyData: true
+LazyDataCompression: bzip2
 VignetteBuilder: knitr

NAMESPACE

@@ -1,2 +1,3 @@
 # Generated by roxygen2: do not edit by hand
 
+importFrom(lifecycle,deprecated)

NEWS.md

@@ -0,0 +1,38 @@
+# NEFSCspatial 0.1.0
+
+## Data set additions/removals
+
+- Data sets from [MDEB](Marine Development GIS Data Hub) data hub (Marine Development GIS Data Hub)
+- Scallop restricted areas
+- Massachusetts inshore survey strata
+- Deprecation warnings for data sets due to be replaced by MDEB data
+- Added bzip2 data set compression
+
+## Minor fixes
+
+- Removed leaflet documentation
+- Standardized data set documentation with added examples
+
+
+# NEFSCspatial 0.0.1
+
+Initial release of sf objects
+
+- BTS_Strata
+- EcoMon_Strata
+- epu_sf
+- final_mass_inshore_stat
+- GillnetClosureAreas_20211021
+- Great_South_Channel_Restricted_Trap_Pot_Area
+- Herring_Management_Areas
+- LMA1_Restricted_Area_FR
+- NAFO_Divisions_2021_line_enclosed
+- NAFO_Divisions_2021_line_not_enclosed
+- NAFO_Divisions_2021_poly_clipped
+- NAFO_Divisions_2021_poly_not_clipped
+- Neus_atlantis
+- Scallop_Rotational_Areas_20230411
+- Shellfish_Strata
+- Shrimp_Strata
+- Statistical_Areas_2010
+- Statistical_Areas_2010_withNames

R/NEFSCspatial-package.R

@@ -0,0 +1,7 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom lifecycle deprecated
+## usethis namespace: end
+NULL

R/data-coastspan_strata.R

@@ -0,0 +1,28 @@
+#' Cooperative Atlantic States Shark Pupping and Nursery Survey
+#'
+#' @description An \code{sf} object containing spatial data for the Cooperative Atlantic States Shark Pupping and Nursery Survey.
+#'
+#' @format An \code{sf} object:
+#' \describe{
+#'   \item{Geometry type}{POLYGON}
+#'   \item{Dimension}{XY}
+#'   \item{Bounding box}{xmin: -81.6 ymin: 27.1 xmax: -74.9 ymax: 39.2}
+#'   \item{Projected CRS}{WGS 84}
+#'   \item{Features}{7 x 5}
+#'   \item{Metadata}{See source}
+#' }
+#'
+#' @docType data
+#' @name coastspan_strata
+#' @usage data('coastspan_strata')
+#' @keywords {datasets}
+#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/}
+#' @examples
+#' \dontrun{
+#' # Load the dataset
+#' data(coastspan_strata)
+#'
+#' # Plot the geometry
+#' plot(sf::st_geometry(coastspan_strata))
+#' }
+NULL

R/data-csbll_stations.R

@@ -0,0 +1,28 @@
+#' Coastal Shark Bottom Longline Survey
+#'
+#' @description An \code{sf} object containing spatial data for the Coastal Shark Bottom Longline Survey. Sampling stations for the Coastal Shark Bottom Longline Survey.
+#'
+#' @format An \code{sf} object:
+#' \describe{
+#'   \item{Geometry type}{POINT}
+#'   \item{Dimension}{NA}
+#'   \item{Bounding box}{xmin: -81.6 ymin: 24.5 xmax: -74.5 ymax: 38.4}
+#'   \item{Projected CRS}{WGS 84}
+#'   \item{Features}{87 x 6}
+#'   \item{Metadata}{See source}
+#' }
+#'
+#' @docType data
+#' @name csbll_stations
+#' @usage data('csbll_stations')
+#' @keywords {datasets}
+#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/}
+#' @examples
+#' \dontrun{
+#' # Load the dataset
+#' data(csbll_stations)
+#'
+#' # Plot the geometry
+#' plot(sf::st_geometry(csbll_stations))
+#' }
+NULL

R/data-csbll_strata.R

@@ -0,0 +1,28 @@
+#' Coastal Shark Bottom Longline Survey
+#'
+#' @description An \code{sf} object containing spatial data for the Coastal Shark Bottom Longline Survey. Scientific survey strata for the Coastal Shark Bottom Longline Survey.
+#'
+#' @format An \code{sf} object:
+#' \describe{
+#'   \item{Geometry type}{MULTIPOLYGON}
+#'   \item{Dimension}{XY}
+#'   \item{Bounding box}{xmin: -81.7 ymin: 24.4 xmax: -74.4 ymax: 38.5}
+#'   \item{Projected CRS}{WGS 84}
+#'   \item{Features}{1 x 5}
+#'   \item{Metadata}{See source}
+#' }
+#'
+#' @docType data
+#' @name csbll_strata
+#' @usage data('csbll_strata')
+#' @keywords {datasets}
+#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/}
+#' @examples
+#' \dontrun{
+#' # Load the dataset
+#' data(csbll_strata)
+#'
+#' # Plot the geometry
+#' plot(sf::st_geometry(csbll_strata))
+#' }
+NULL