diff --git a/.Rbuildignore b/.Rbuildignore index 2601df3..1600f14 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,4 +8,7 @@ ^\.Rproj.user$ ^docs$ ^pkgdown$ +^\.github$ +other ^vignettes/articles$ + diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..b6cac5a --- /dev/null +++ b/.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"' diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 3491027..7e43b39 100644 --- a/.github/workflows/pkgdown.yml +++ b/.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" diff --git a/.github/workflows/update_mdeb_data.yaml b/.github/workflows/update_mdeb_data.yaml new file mode 100644 index 0000000..dc07a84 --- /dev/null +++ b/.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} diff --git a/.gitignore b/.gitignore index d26f767..2edf6a9 100644 --- a/.gitignore +++ b/.gitignore @@ -7,5 +7,6 @@ # exclude folders data-raw/temp inst/doc +other # docs folder, generated by local pkgdown build docs diff --git a/DESCRIPTION b/DESCRIPTION index 30b80c1..3e362ca 100644 --- a/DESCRIPTION +++ b/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 diff --git a/NAMESPACE b/NAMESPACE index 6ae9268..c19e7db 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,2 +1,3 @@ # Generated by roxygen2: do not edit by hand +importFrom(lifecycle,deprecated) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..a894f64 --- /dev/null +++ b/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 diff --git a/R/NEFSCspatial-package.R b/R/NEFSCspatial-package.R new file mode 100644 index 0000000..425b3c1 --- /dev/null +++ b/R/NEFSCspatial-package.R @@ -0,0 +1,7 @@ +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +#' @importFrom lifecycle deprecated +## usethis namespace: end +NULL diff --git a/R/data-coastspan_strata.R b/R/data-coastspan_strata.R new file mode 100644 index 0000000..ea6b339 --- /dev/null +++ b/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 diff --git a/R/data-csbll_stations.R b/R/data-csbll_stations.R new file mode 100644 index 0000000..dee7bfd --- /dev/null +++ b/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 diff --git a/R/data-csbll_strata.R b/R/data-csbll_strata.R new file mode 100644 index 0000000..ab3113b --- /dev/null +++ b/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 diff --git a/R/data-edna_stations.R b/R/data-edna_stations.R new file mode 100644 index 0000000..2b7c6e4 --- /dev/null +++ b/R/data-edna_stations.R @@ -0,0 +1,28 @@ +#' eDNA Survey +#' +#' @description An \code{sf} object containing spatial data for the eDNA Survey. Sampling stations for the eDNA Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POINT} +#' \item{Dimension}{NA} +#' \item{Bounding box}{xmin: -75.5 ymin: 36 xmax: -65.4 ymax: 44.5} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{35 x 13} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name edna_stations +#' @usage data('edna_stations') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(edna_stations) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(edna_stations)) +#' } +NULL diff --git a/R/data-edna_strata.R b/R/data-edna_strata.R new file mode 100644 index 0000000..8148c57 --- /dev/null +++ b/R/data-edna_strata.R @@ -0,0 +1,28 @@ +#' eDNA Survey +#' +#' @description An \code{sf} object containing spatial data for the eDNA Survey. Scientific survey strata for the eDNA Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{MULTIPOLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -76 ymin: 35.1 xmax: -65.2 ymax: 44.5} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{48 x 11} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name edna_strata +#' @usage data('edna_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(edna_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(edna_strata)) +#' } +NULL diff --git a/R/data-gombll_strata.R b/R/data-gombll_strata.R new file mode 100644 index 0000000..66491ef --- /dev/null +++ b/R/data-gombll_strata.R @@ -0,0 +1,28 @@ +#' Gulf of Maine Bottom Longline Survey +#' +#' @description An \code{sf} object containing spatial data for the Gulf of Maine Bottom Longline Survey. Scientific survey strata for the Gulf of Maine Bottom Longline Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -70.7 ymin: 42 xmax: -67.4 ymax: 43.4} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{6 x 9} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name gombll_strata +#' @usage data('gombll_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(gombll_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(gombll_strata)) +#' } +NULL diff --git a/R/data-gombll_substrata.R b/R/data-gombll_substrata.R new file mode 100644 index 0000000..32f94b1 --- /dev/null +++ b/R/data-gombll_substrata.R @@ -0,0 +1,28 @@ +#' Gulf of Maine Bottom Longline Survey +#' +#' @description An \code{sf} object containing spatial data for the Gulf of Maine Bottom Longline Survey. Scientific survey substrata for the Gulf of Maine Bottom Longline Survey. The survey substrata give further details on bottom-type (smooth or rough bottom) encountered in the survey area. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{MULTIPOLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -70.7 ymin: 42 xmax: -67.4 ymax: 43.4} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{12 x 14} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name gombll_substrata +#' @usage data('gombll_substrata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(gombll_substrata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(gombll_substrata)) +#' } +NULL diff --git a/R/data-hl_strata.R b/R/data-hl_strata.R new file mode 100644 index 0000000..b7e736b --- /dev/null +++ b/R/data-hl_strata.R @@ -0,0 +1,28 @@ +#' Hook and Line Survey +#' +#' @description An \code{sf} object containing spatial data for the Hook and Line Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -75.9 ymin: 35.3 xmax: -68.6 ymax: 41.8} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{1 x 6} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name hl_strata +#' @usage data('hl_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(hl_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(hl_strata)) +#' } +NULL diff --git a/R/data-mass_inshore_strata.R b/R/data-mass_inshore_strata.R new file mode 100644 index 0000000..473485f --- /dev/null +++ b/R/data-mass_inshore_strata.R @@ -0,0 +1,29 @@ +#' Massachusetts Inshore State Survey +#' +#' @description An \code{sf} object containing spatial data for the Massachusetts Inshore State Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{MULTIPOLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: 231326.1 ymin: 772098.2 xmax: 336448.2 ymax: 958709} +#' \item{Projected CRS}{NAD83 / Massachusetts Mainland} +#' \item{Features}{42 x 8} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name mass_inshore_strata +#' @usage data('mass_inshore_strata') +#' @keywords {datasets} +#' @source {https://www.mass.gov/info-details/review-trawl-survey-updates. Division of Marine Fisheries - New Bedford Office. For more info contact the +#' [Resource Assessment Project Leader](https://www.mass.gov/info-details/dmf-staff-directory#fisheries-biology-recreational-fishing-survey-and-assessment). } +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(mass_inshore_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(mass_inshore_strata)) +#' } +NULL diff --git a/R/data-mmst_strata.R b/R/data-mmst_strata.R new file mode 100644 index 0000000..22c9f97 --- /dev/null +++ b/R/data-mmst_strata.R @@ -0,0 +1,28 @@ +#' Marine Mammal and Sea Turtle Survey +#' +#' @description An \code{sf} object containing spatial data for the Marine Mammal and Sea Turtle Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -82.1 ymin: 24.2 xmax: -61.8 ymax: 45.2} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{7 x 6} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name mmst_strata +#' @usage data('mmst_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(mmst_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(mmst_strata)) +#' } +NULL diff --git a/R/data-narw_lines.R b/R/data-narw_lines.R new file mode 100644 index 0000000..215c109 --- /dev/null +++ b/R/data-narw_lines.R @@ -0,0 +1,28 @@ +#' North Atlantic Right Whale Aerial Survey +#' +#' @description An \code{sf} object containing spatial data for the North Atlantic Right Whale Aerial Survey. Aerial survey lines for the North Atlantic Right Whale Aerial Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{MULTILINESTRING} +#' \item{Dimension}{NA} +#' \item{Bounding box}{xmin: -76 ymin: 36.7 xmax: -66.9 ymax: 44.8} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{80 x 6} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name narw_lines +#' @usage data('narw_lines') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(narw_lines) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(narw_lines)) +#' } +NULL diff --git a/R/data-narw_strata.R b/R/data-narw_strata.R new file mode 100644 index 0000000..ddf4cc9 --- /dev/null +++ b/R/data-narw_strata.R @@ -0,0 +1,28 @@ +#' North Atlantic Right Whale Aerial Survey +#' +#' @description An \code{sf} object containing spatial data for the North Atlantic Right Whale Aerial Survey. Scientific survey strata for the North Atlantic Right Whale Aerial Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{MULTIPOLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -76 ymin: 36.7 xmax: -66.9 ymax: 44.8} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{1 x 5} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name narw_strata +#' @usage data('narw_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(narw_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(narw_strata)) +#' } +NULL diff --git a/R/data-oq_strata.R b/R/data-oq_strata.R new file mode 100644 index 0000000..2ecaa8b --- /dev/null +++ b/R/data-oq_strata.R @@ -0,0 +1,28 @@ +#' Atlantic Surfclam and Ocean Quahog Survey +#' +#' @description An \code{sf} object containing spatial data for the Atlantic Surfclam and Ocean Quahog Survey. Scientific survey strata for Ocean Quahog Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{MULTIPOLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -74.9 ymin: 36.5 xmax: -66.5 ymax: 42.1} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{12 x 20} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name oq_strata +#' @usage data('oq_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(oq_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(oq_strata)) +#' } +NULL diff --git a/R/data-pam_deployments.R b/R/data-pam_deployments.R new file mode 100644 index 0000000..b63fbef --- /dev/null +++ b/R/data-pam_deployments.R @@ -0,0 +1,28 @@ +#' Passive Acoustic Monitoring Survey +#' +#' @description An \code{sf} object containing spatial data for the Passive Acoustic Monitoring Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POINT} +#' \item{Dimension}{NA} +#' \item{Bounding box}{xmin: -75.7 ymin: 36.5 xmax: -66.9 ymax: 44.8} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{82 x 23} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name pam_deployments +#' @usage data('pam_deployments') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(pam_deployments) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(pam_deployments)) +#' } +NULL diff --git a/R/data-sc_strata.R b/R/data-sc_strata.R new file mode 100644 index 0000000..16c5814 --- /dev/null +++ b/R/data-sc_strata.R @@ -0,0 +1,28 @@ +#' Atlantic Surfclam and Ocean Quahog Survey +#' +#' @description An \code{sf} object containing spatial data for the Atlantic Surfclam and Ocean Quahog Survey. Scientific survey strata for the Atlantic Surfclam Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{MULTIPOLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -76 ymin: 36.5 xmax: -66.9 ymax: 42.1} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{12 x 7} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name sc_strata +#' @usage data('sc_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(sc_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(sc_strata)) +#' } +NULL diff --git a/R/data-scallop_strata.R b/R/data-scallop_strata.R new file mode 100644 index 0000000..da2d7f3 --- /dev/null +++ b/R/data-scallop_strata.R @@ -0,0 +1,28 @@ +#' Sea Scallop Survey +#' +#' @description An \code{sf} object containing spatial data for the Sea Scallop Survey. The current (as of 2025) NEFSC Scallop Strata (SAMS). Starting in 2025, a spatially balanced form of stratified random sampling called Generalized Random Tessellation Stratified (GRTS) was implemented, along with a switch to using Scallop Area Management Simulator (SAMS) areas as survey strata. While still a form of stratified random sampling, this method prevents random stations from being placed very close together. Use of the SAMS areas as strata ensures that sampling is more useful to management.

+#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -74.9 ymin: 36.6 xmax: -66.3 ymax: 42.2} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{23 x 8} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name scallop_strata +#' @usage data('scallop_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(scallop_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(scallop_strata)) +#' } +NULL diff --git a/R/data-scallop_strata_historic.R b/R/data-scallop_strata_historic.R new file mode 100644 index 0000000..06940c8 --- /dev/null +++ b/R/data-scallop_strata_historic.R @@ -0,0 +1,28 @@ +#' Sea Scallop Survey +#' +#' @description An \code{sf} object containing spatial data for the Sea Scallop Survey. The historic (pre-2025) NEFSC Shellfish Strata. The standardized scallop dredge survey has been conducted since 1975 (annually since 1977) and employs a stratified random sampling design. The original NEFSC Shellfish Strata were based primarily on depth and secondarily by latitude, and locations of sampling stations were randomly selected within each stratum prior to each annual cruise. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -76 ymin: 35.5 xmax: -65.9 ymax: 42.2} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{97 x 13} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name scallop_strata_historic +#' @usage data('scallop_strata_historic') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(scallop_strata_historic) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(scallop_strata_historic)) +#' } +NULL diff --git a/R/data-seal_stations.R b/R/data-seal_stations.R new file mode 100644 index 0000000..51a420d --- /dev/null +++ b/R/data-seal_stations.R @@ -0,0 +1,28 @@ +#' Seal Aerial Survey +#' +#' @description An \code{sf} object containing spatial data for the Seal Aerial Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POINT} +#' \item{Dimension}{NA} +#' \item{Bounding box}{xmin: -70.9 ymin: 41.3 xmax: -67 ymax: 44.9} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{1026 x 14} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name seal_stations +#' @usage data('seal_stations') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(seal_stations) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(seal_stations)) +#' } +NULL diff --git a/R/data-turtle_strata.R b/R/data-turtle_strata.R new file mode 100644 index 0000000..b1baea6 --- /dev/null +++ b/R/data-turtle_strata.R @@ -0,0 +1,28 @@ +#' Turtle Ecology Survey +#' +#' @description An \code{sf} object containing spatial data for the Turtle Ecology Survey. +#' +#' @format An \code{sf} object: +#' \describe{ +#' \item{Geometry type}{POLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -82.1 ymin: 24.2 xmax: -61.8 ymax: 45.2} +#' \item{Projected CRS}{WGS 84} +#' \item{Features}{1 x 5} +#' \item{Metadata}{See source} +#' } +#' +#' @docType data +#' @name turtle_strata +#' @usage data('turtle_strata') +#' @keywords {datasets} +#' @source {https://mdeb-nefsc-noaa.hub.arcgis.com/} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(turtle_strata) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(turtle_strata)) +#' } +NULL diff --git a/R/data_BTS_strata.R b/R/data_BTS_strata.R index de88cf3..5dbc7a9 100644 --- a/R/data_BTS_strata.R +++ b/R/data_BTS_strata.R @@ -1,16 +1,17 @@ -#' @title NEFSC Bottom Trawl Survey Strata +#' `r lifecycle::badge("deprecated")` +#' +#' NEFSC Bottom Trawl Survey Strata #' -#' @description An \code{sf} object containing the boundaries of the NEFSC bottom trawl survey strata. +#' An \code{sf} object containing the boundaries of the NEFSC bottom trawl survey strata. #' This set of strata is considered historical. (Pre 2000). #' -#' #' @format An \code{sf} object: #' \describe{ #' \item{Geometry type}{POLYGON} #' \item{dimension}{XY} #' \item{Bounding box}{xmin: -79.18422 ymin: 32.50221 xmax: -65.16869 ymax: 44.83202} #' \item{Geodetic CRS}{NAD 83} -#' \item{Features}{185 x 9} +#' \item{Features}{185 x 10} #' \item{Metadata}{See source} #' } #' @@ -20,4 +21,5 @@ #' @keywords datasets #' @source \url{https://drive.google.com/drive/folders/15s70lDwezatlNVReDMWRJadtlklMYSnC} #' @source \url{https://www.fisheries.noaa.gov/inport/item/33471} +#' @note Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/datasets/noaa::bottom-trawl-survey/about} instead. NULL diff --git a/R/data_EcoMon_Strata.R b/R/data_EcoMon_Strata.R index ffa9184..ef3c0d5 100644 --- a/R/data_EcoMon_Strata.R +++ b/R/data_EcoMon_Strata.R @@ -1,3 +1,5 @@ +#' `r lifecycle::badge("deprecated")` +#' #' Ecosystem Monitoring Cruise (EcoMon) strata #' #' An sf object containing the EcoMon strata @@ -8,7 +10,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -75.96791 ymin: 35.14219 xmax: -65.16869 ymax: 44.48558} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{47 x 3} +#' \item{Features}{47 x 4} #' \item{Metadata}{See source} #' } #' @@ -18,4 +20,5 @@ #' @usage data("EcoMon_Strata") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/inport/item/33468} +#' @note Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/datasets/noaa::ecosystem-monitoring-survey/about} instead. NULL diff --git a/R/data_GillnetClosureAreas_20211021.R b/R/data_GillnetClosureAreas_20211021.R index 12d1338..51f97a6 100644 --- a/R/data_GillnetClosureAreas_20211021.R +++ b/R/data_GillnetClosureAreas_20211021.R @@ -1,50 +1,17 @@ #' Gillnet Closure Areas #' -#' An sf object containing the Closure areas for Gillnets -#' Specifically Closed Area 1 and Nantucket Lightship Closure Area +#' @description An \code{sf} object containing the closure areas for gillnets. +#' Specifically Closed Area 1 and Nantucket Lightship Closure Area. #' -#' @format A data frame/ sf object (2 x 25) +#' @format An \code{sf} object #' \describe{ #' \item{Geometry type}{POLYGON} #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -70.33333 ymin: 40.33333 xmax: -68.5 ymax: 41.5} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{2 x 25} +#' \item{Features}{2 x 26} #' \item{Metadata}{See source} -#' -#' -#' \item{GARFO_ID}{A unique identifier used to identify and track this feature; -#' a new GARFO_ID is generated for each version of a Regulated Area, including -#' proposed or final versions (i.e. whenever boundaries or attributes are -#' changed, edited or updated)} -#' \item{AREANAME}{Official name of the Proposed Area, usually the area name as it will be printed in the CFR.} -#' \item{COMMNAME}{Most commonly used name. May be identical to AREANAME, an abbreviation of AREANAME, or a different name altogether.} -#' \item{AREAGROUP}{Specifies if the Proposed Area is part of a group of related areas.} -#' \item{DESCRIBE}{A brief description of the purpose of the Proposed Area.} -#' \item{CFRTITLE}{CFR Title citation where the Proposed Area will be legally defined} -#' \item{CFRPT}{ACFR Part citation where the Proposed Area will be legally defined} -#' \item{CFRPTTXT}{CFR Part citation header text} -#' \item{CFRSUB}{CFR Subpart citation where the Proposed Area will be legally defined} -#' \item{CFRSUBTXT}{CFR Subpart citation header text} -#' \item{CFRSXN}{CFR Section citation where the Proposed Area will be legally defined} -#' \item{CFRSXNTXT}{CFR Section citation header text} -#' \item{CFRPARA}{CFR Paragraph citation where the Proposed Area will be legally defined} -#' \item{CFRPARATXT}{CFR Paragraph citation header text} -#' \item{FRCITE}{Federal Register citation of proposed rule containing the Proposed Area spatial definition.} -#' \item{FRDATE}{Federal Register citation date of proposed rule containing the Proposed Area spatial definition.} -#' \item{EFFECTDATE}{Date Regulated Area officially became law, or most recent modification. For Proposed Areas, this field will be blank because the area is not yet law.} -#' \item{SOURCE}{If Proposed Area will be defined in the CFR, this is the citation for the Amendment/Framework/etc. that will establish the area. If the Proposed Area will not be defined in the CFR, this is the alternative source citation that will establish the area.} -#' \item{RECURST}{Annually recurring date Proposed Area would become active} -#' \item{RECUREND}{Annually recurring date Proposed Area would become inactive} -#' \item{GISAUTHOR}{Name of the NOAA staff person who created the GIS feature} -#' \item{CREATED}{Creation date of the GIS feature} -#' \item{AREANOTES}{Miscellaneous notes regarding the Proposed Area or feature} -#' \item{X}{x coordinate of polygon center} -#' \item{Y}{y coordinate of polygon center} -#' } -#' -#'@section Contact: -#'andrew.beet at noaa.gov +#' } #' #' #' @docType data @@ -52,4 +19,12 @@ #' @usage data("GillnetClosureAreas_20211021") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/resource/map/gillnet-closure-areas} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(GillnetClosureAreas_20211021) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(GillnetClosureAreas_20211021)) +#' } NULL diff --git a/R/data_Great_South_Channel_Restricted_Trap_Pot_Area.R b/R/data_Great_South_Channel_Restricted_Trap_Pot_Area.R index e970461..8180ed8 100644 --- a/R/data_Great_South_Channel_Restricted_Trap_Pot_Area.R +++ b/R/data_Great_South_Channel_Restricted_Trap_Pot_Area.R @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -69.75 ymin: 41 xmax: -68.21667 ymax: 42.16667} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{1 x 25} +#' \item{Features}{1 x 26} #' \item{Metadata}{See source} #' } #' @@ -17,4 +17,12 @@ #' @usage data("Great_South_Channel_Restricted_Trap_Pot_Area") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/resource/map/great-south-channel-restricted-area} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(Great_South_Channel_Restricted_Trap_Pot_Area) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(Great_South_Channel_Restricted_Trap_Pot_Area)) +#' } NULL diff --git a/R/data_Herring_Management_Areas.R b/R/data_Herring_Management_Areas.R index 5ecb9cc..76297e1 100644 --- a/R/data_Herring_Management_Areas.R +++ b/R/data_Herring_Management_Areas.R @@ -1,6 +1,6 @@ #' @title Herring Management Areas #' -#' @description An \code{sf} object depicting the boundaries of the Herring Management Areas +#' @description An \code{sf} object depicting the boundaries of the Herring Management Areas. #' #' @format An \code{sf} object: #' \describe{ @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -78.57412 ymin: 33.81288 xmax: -65.69947 ymax: 45.1918} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{4 x 25} +#' \item{Features}{4 x 26} #' \item{Metadata}{See source} #' } #' @@ -18,4 +18,12 @@ #' @usage data("Herring_Management_Areas") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/resource/map/herring-management-areas} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(Herring_Management_Areas) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(Herring_Management_Areas)) +#' } NULL diff --git a/R/data_LMA1_Restricted_Area_FR.R b/R/data_LMA1_Restricted_Area_FR.R index 0a50f54..1d0b77f 100644 --- a/R/data_LMA1_Restricted_Area_FR.R +++ b/R/data_LMA1_Restricted_Area_FR.R @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -69.6128 ymin: 42.89198 xmax: -68.28787 ymax: 43.73333} #' \item{Geodetic CRS}{WGS 84} -#' \item{Features}{1 x 25} +#' \item{Features}{1 x 26} #' \item{Metadata}{See source} #' } #' @@ -17,4 +17,12 @@ #' @usage data("LMA1_Restricted_Area_FR") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/resource/map/lma-1-restricted-area} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(LMA1_Restricted_Area_FR) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(LMA1_Restricted_Area_FR)) +#' } NULL diff --git a/R/data_NAFO_Divsions_2021_line_enclosed.R b/R/data_NAFO_Divisions_2021_line_enclosed.R similarity index 70% rename from R/data_NAFO_Divsions_2021_line_enclosed.R rename to R/data_NAFO_Divisions_2021_line_enclosed.R index 1f70f4e..6a7fff3 100644 --- a/R/data_NAFO_Divsions_2021_line_enclosed.R +++ b/R/data_NAFO_Divisions_2021_line_enclosed.R @@ -1,6 +1,6 @@ #' @title NAFO Divisions (Bounded) #' -#' @description An \code{sf} object that depicts the boundaries of the NAFO regions +#' @description An \code{sf} object that depicts the boundaries of the NAFO regions. #' #' @format An \code{sf} object: #' \describe{ @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{38 x 5} +#' \item{Features}{38 x 6} #' \item{Metadata}{See source} #' } #' @@ -17,4 +17,12 @@ #' @usage data("NAFO_Divisions_2021_line_enclosed") #' @keywords datasets #' @source \url{https://www.nafo.int/Data/GIS} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(NAFO_Divisions_2021_line_enclosed) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(NAFO_Divisions_2021_line_enclosed)) +#' } NULL diff --git a/R/data_NAFO_Divsions_2021_line_not_enclosed.R b/R/data_NAFO_Divisions_2021_line_not_enclosed.R similarity index 69% rename from R/data_NAFO_Divsions_2021_line_not_enclosed.R rename to R/data_NAFO_Divisions_2021_line_not_enclosed.R index 1829e9f..597f243 100644 --- a/R/data_NAFO_Divsions_2021_line_not_enclosed.R +++ b/R/data_NAFO_Divisions_2021_line_not_enclosed.R @@ -1,6 +1,6 @@ #' @title NAFO Divisions (Not Bounded) #' -#' @description An \code{sf} object that depicts the boundaries of the NAFO regions +#' @description An \code{sf} object that depicts the boundaries of the NAFO regions. #' #' @format An \code{sf} object: #' \describe{ @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{42 x 7} +#' \item{Features}{42 x 8} #' \item{Metadata}{See source} #' } #' @@ -17,4 +17,12 @@ #' @usage data("NAFO_Divisions_2021_line_not_enclosed") #' @keywords datasets #' @source \url{https://www.nafo.int/Data/GIS} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(NAFO_Divisions_2021_line_not_enclosed) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(NAFO_Divisions_2021_line_not_enclosed)) +#' } NULL diff --git a/R/data_NAFO_Divsions_2021_poly_clipped.R b/R/data_NAFO_Divisions_2021_poly_clipped.R similarity index 70% rename from R/data_NAFO_Divsions_2021_poly_clipped.R rename to R/data_NAFO_Divisions_2021_poly_clipped.R index ec73ee9..b6126ac 100644 --- a/R/data_NAFO_Divsions_2021_poly_clipped.R +++ b/R/data_NAFO_Divisions_2021_poly_clipped.R @@ -1,6 +1,6 @@ #' @title NAFO Divisions (Polygon clipped to coastline) #' -#' @description An \code{sf} object that depicts the boundaries of the NAFO regions +#' @description An \code{sf} object that depicts the boundaries of the NAFO regions. #' #' @format An \code{sf} object: #' \describe{ @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{39 x 8} +#' \item{Features}{39 x 9} #' \item{Metadata}{See source} #' } #' @@ -17,4 +17,12 @@ #' @usage data("NAFO_Divisions_2021_poly_clipped") #' @keywords datasets #' @source \url{https://www.nafo.int/Data/GIS} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(NAFO_Divisions_2021_poly_clipped) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(NAFO_Divisions_2021_poly_clipped)) +#' } NULL diff --git a/R/data_NAFO_Divsions_2021_poly_not_clipped.R b/R/data_NAFO_Divisions_2021_poly_not_clipped.R similarity index 70% rename from R/data_NAFO_Divsions_2021_poly_not_clipped.R rename to R/data_NAFO_Divisions_2021_poly_not_clipped.R index 929ae43..f63c866 100644 --- a/R/data_NAFO_Divsions_2021_poly_not_clipped.R +++ b/R/data_NAFO_Divisions_2021_poly_not_clipped.R @@ -1,6 +1,6 @@ #' @title NAFO Divisions (Polygon not clipped to coastline) #' -#' @description An \code{sf} object that depicts the boundaries of the NAFO regions +#' @description An \code{sf} object that depicts the boundaries of the NAFO regions. #' #' @format An \code{sf} object: #' \describe{ @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{38 x 8} +#' \item{Features}{38 x 9} #' \item{Metadata}{See source} #' } #' @@ -17,4 +17,12 @@ #' @usage data("NAFO_Divisions_2021_poly_not_clipped") #' @keywords datasets #' @source \url{https://www.nafo.int/Data/GIS} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(NAFO_Divisions_2021_poly_not_clipped) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(NAFO_Divisions_2021_poly_not_clipped)) +#' } NULL diff --git a/R/data_Neus_atlantis.R b/R/data_Neus_atlantis.R index 68e6454..bb8d263 100644 --- a/R/data_Neus_atlantis.R +++ b/R/data_Neus_atlantis.R @@ -1,6 +1,6 @@ #' Northeast US (NEUS) atlantis model domain #' -#' An sf object containing the box level boundaries used in the Northeast Atlantis ecosystem end to end model +#' @description An \code{sf} object containing the box level boundaries used in the Northeast Atlantis ecosystem end to end model. #' #' @format An \code{sf} object: #' \describe{ @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -76.45919 ymin: 34.76128 xmax: -63.42171 ymax: 46.11478} #' \item{Geodetic CRS}{WGS 83} -#' \item{Features}{30 x 10} +#' \item{Features}{30 x 11} #' \item{Metadata}{See source} #' } #' @@ -18,4 +18,12 @@ #' @keywords datasets #' #' @source \url{https://github.com/NOAA-EDAB/neus-atlantis/wiki/Spatial-extent-of-model} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(Neus_atlantis) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(Neus_atlantis)) +#' } NULL diff --git a/R/data_Scallop_Rotational_Areas_20230411.R b/R/data_Scallop_Rotational_Areas_20230411.R new file mode 100644 index 0000000..b9f1a40 --- /dev/null +++ b/R/data_Scallop_Rotational_Areas_20230411.R @@ -0,0 +1,31 @@ +#' Scallop Restricted Area +#' +#' @description An \code{sf} object containing the Scallop Restricted Areas. +#' Specifically Area I, II, Nantucket Lightship North, Nantucket Lightship West, New York Bight, and Elephant Trunk. +#' +#' @format An \code{sf} object +#' \describe{ +#' \item{Geometry type}{POLYGON} +#' \item{Dimension}{XY} +#' \item{Bounding box}{xmin: -8274749 ymin: 4602998 xmax: -7333888 ymax: 5087139} +#' \item{Geodetic CRS}{WGS 84 / Pseudo-Mercator} +#' \item{Features}{6 x 26} +#' \item{Metadata}{See source} +#' } +#' +#' +#' +#' @docType data +#' @name Scallop_Rotational_Areas_20230411 +#' @usage data("Scallop_Rotational_Areas_20230411") +#' @keywords datasets +#' @source \url{https://www.fisheries.noaa.gov/resource/map/atlantic-sea-scallop-managed-waters-fishing-year-2023} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(Scallop_Rotational_Areas_20230411) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(Scallop_Rotational_Areas_20230411)) +#' } +NULL diff --git a/R/data_Shellfish_strata.R b/R/data_Shellfish_strata.R index dbfefdd..4d283e9 100644 --- a/R/data_Shellfish_strata.R +++ b/R/data_Shellfish_strata.R @@ -1,3 +1,5 @@ +#' `r lifecycle::badge("deprecated")` +#' #' Shellfish strata (Clam and Scallop surveys) #' #' An sf object containing the Clam and Scallop survey strata @@ -8,7 +10,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -75.95982 ymin: 35.50142 xmax: -65.89944 ymax: 42.16817} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{97 x 9} +#' \item{Features}{97 x 10} #' \item{Metadata}{See source} #' } #' @@ -18,4 +20,5 @@ #' @usage data("Shellfish_Strata") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/inport/item/33466} +#' @note Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/maps/noaa::atlantic-surfclam-and-ocean-quahog-survey/about} or \url{https://mdeb-nefsc-noaa.hub.arcgis.com/maps/noaa::sea-scallop-survey/about} instead. NULL diff --git a/R/data_Shrimp_strata.R b/R/data_Shrimp_strata.R index 54ec8de..49845bc 100644 --- a/R/data_Shrimp_strata.R +++ b/R/data_Shrimp_strata.R @@ -1,3 +1,5 @@ +#' `r lifecycle::badge("deprecated")` +#' #' Shrimp survey strata #' #' An sf object containing the Shrimp survey strata @@ -8,7 +10,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -70.68152 ymin: 41.08476 xmax: -67.99941 ymax: 44.08762} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{12 x 4} +#' \item{Features}{12 x 5} #' \item{Metadata}{See source} #' } #' @@ -18,4 +20,5 @@ #' @usage data("Shrimp_Strata") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/inport/item/33470} +#' @note Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/datasets/noaa::northern-shrimp-survey/about} instead. NULL diff --git a/R/data_Statistical_Areas_2010.R b/R/data_Statistical_Areas_2010.R index d6e4a3d..f96cb92 100644 --- a/R/data_Statistical_Areas_2010.R +++ b/R/data_Statistical_Areas_2010.R @@ -1,15 +1,15 @@ #' Greater Atlantic Region Statistical Areas #' -#' An sf object containing the Greater Atlantic Region Statistical Areas. -#' Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/ +#' @description An \code{sf} object containing the Greater Atlantic Region Statistical Areas. +#' Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/. #' -#' @format A data frame/ sf object (135 x 1) +#' @format An \code{sf} object: #' \describe{ #' \item{Geometry type}{MULTIPOLYGON} #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -81.53406 ymin: 24 xmax: -42 ymax: 52.25} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{135 x 1} +#' \item{Features}{135 x 4} #' \item{Metadata}{See source} #' } #' @@ -19,4 +19,12 @@ #' @keywords datasets #' #' @source \url{https://www.fisheries.noaa.gov/resource/map/greater-atlantic-region-statistical-areas} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(Statistical_Areas_2010) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(Statistical_Areas_2010)) +#' } NULL diff --git a/R/data_Statistical_Areas_2010_withNames.R b/R/data_Statistical_Areas_2010_withNames.R index af05cd7..eb4651a 100644 --- a/R/data_Statistical_Areas_2010_withNames.R +++ b/R/data_Statistical_Areas_2010_withNames.R @@ -1,17 +1,16 @@ #' Greater Atlantic Region Statistical Areas #' -#' An sf object containing the Greater Atlantic Region Statistical Areas. -#' With name labels -#' Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/ +#' @description An \code{sf} object containing the Greater Atlantic Region Statistical Areas with name labels. +#' Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/. #' -#' @format A data frame/ sf object (135 x 6) +#' @format A \code{sf} object: #' \describe{ #' \item{Geometry type}{MULTIPOLYGON} #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -81.53406 ymin: 24 xmax: -42 ymax: 52.25} #' \item{Geodetic CRS}{NAD83} #' \item{Metadata}{See source} -#' \item{Features}{135 x 1} +#' \item{Features}{135 x 7} #' } #' #' @docType data @@ -20,4 +19,12 @@ #' @keywords datasets #' #' @source \url{https://www.fisheries.noaa.gov/resource/map/greater-atlantic-region-statistical-areas} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(Statistical_Areas_2010_withNames) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(Statistical_Areas_2010_withNames)) +#' } NULL diff --git a/R/data_amapps_grid.R b/R/data_amapps_grid.R index 272fcd9..bd9b2a3 100644 --- a/R/data_amapps_grid.R +++ b/R/data_amapps_grid.R @@ -10,7 +10,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -820443.2 ymin: -1234728 xmax: 1579557 ymax: 2045272} #' \item{Projected CRS}{unnamed} -#' \item{Features}{78720 x 1} +#' \item{Features}{78720 x 2} #' \item{Source}{data-raw/gis/AMAPPS_10km_grid.tif} #' } #' diff --git a/R/data_epu_sf.R b/R/data_epu_sf.R index 88d715c..fc84525 100644 --- a/R/data_epu_sf.R +++ b/R/data_epu_sf.R @@ -1,15 +1,15 @@ #' Ecological Production Units #' -#' An sf object containing the Northeast US shelf Ecological Production Units (EPUs). +#' @description An \code{sf} object containing spatial data for the Northeast US shelf Ecological Production Units (EPUs). #' Ecological Production Units (EPUs) delineate regions unique in physiographic, oceanographic and biotic aspects on the Northeast U.S. Continental Shelf, representing an area of approximately 264,000 km within the 200 m isobath. There are four EPUs on the Shelf, including the Mid-Atlantic Bight (MAB), Georges Bank (GB), Gulf of Maine (GOM), and Scotian Shelf (SS). The Scotian Shelf lies outside the management domain of US Fishery Management Councils and is generally not considered in State of the Ecosystem Reports. #' -#' @format A data frame/ \code{sf} object +#' @format An \code{sf} object #' \describe{ #' \item{Geometry type}{MULTIPOLYGON} #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -77 ymin: 35.8327 xmax: -65.66667 ymax: 44.66667} #' \item{Geodetic CRS}{ +proj=longlat +lat_0=40 +lon_0=-77+x_0=0 +y_0=0 +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0} -#' \item{Features}{4 x 3} +#' \item{Features}{4 x 4} #' \item{Metadata}{See source} #' } #' @@ -17,6 +17,14 @@ #' @docType data #' @name epu_sf #' @usage data("epu_sf") -#' @keywords datasets +#' @keywords {datasets} #' @source \url{https://noaa-edab.github.io/tech-doc/epu.html} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(epu_sf) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(epu_sf)) +#' } NULL diff --git a/R/data_final_mass_inshore_stat.R b/R/data_final_mass_inshore_stat.R index ba3c07d..444202d 100644 --- a/R/data_final_mass_inshore_stat.R +++ b/R/data_final_mass_inshore_stat.R @@ -8,7 +8,7 @@ #' \item{Dimension}{XY} #' \item{Bounding box}{xmin: -71.12554 ymin: 41.18887 xmax: -69.86013 ymax: 42.87647} #' \item{Geodetic CRS}{NAD83} -#' \item{Features}{14 x 4} +#' \item{Features}{14 x 5} #' \item{Metadata}{See source} #' } #' @@ -18,4 +18,12 @@ #' @usage data("final_mass_inshore_stat") #' @keywords datasets #' @source \url{https://www.fisheries.noaa.gov/inport/item/33467} +#' @examples +#' \dontrun{ +#' # Load the dataset +#' data(final_mass_inshore_stat) +#' +#' # Plot the geometry +#' plot(sf::st_geometry(final_mass_inshore_stat)) +#' } NULL diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 0000000..7be60d4 --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,19 @@ +## Issue deprecation warning +.onAttach <- function(libname, pkgname) { + packageStartupMessage( + paste( + "Note: The following datasets are deprecated and will be removed in a future version:", + " • BTS_Strata", + " • EcoMon_Strata", + " • Shellfish_Strata", + " • Shrimp_Strata", + "Please use https://mdeb-nefsc-noaa.hub.arcgis.com/datasets instead:", + " +/noaa::bottom-trawl-survey/about", + " +/noaa::ecosystem-monitoring-survey/about", + " +/noaa::atlantic-surfclam-and-ocean-quahog-survey/about", + " +/noaa::sea-scallop-survey/about", + " +/noaa::northern-shrimp-survey/about", + sep = "\n" + ) + ) +} diff --git a/README.md b/README.md index 14bff16..3fad141 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,15 @@ -# NEFSCspatial +# NEFSCspatial package logo -[![gitleaks](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/secretScan.yml/badge.svg)](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/secretScan.yml) [![gh-pages](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/pkgdown.yml) +[![gitleaks](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/secretScan.yml/badge.svg)](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/secretScan.yml) +[![gh-pages](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/pkgdown.yml) +[![R-CMD-check](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NEFSC/NEFSC-Spatial/actions/workflows/R-CMD-check.yaml) A repository of spatial data (vectors) in simple features [`sf`](https://r-spatial.github.io/sf/) format. ### Installation ``` -remotes::install_github("NEFSC/NEFSC-Spatial") +pak::pak("NEFSC/NEFSC-Spatial") ``` ### Legal disclaimer diff --git a/data-raw/create_leaflet_maps.R b/data-raw/create_leaflet_maps.R deleted file mode 100644 index dff1137..0000000 --- a/data-raw/create_leaflet_maps.R +++ /dev/null @@ -1,87 +0,0 @@ -# needed libraries -library(NEFSCspatial) - -# delete leaflet maps -file.remove(list.files(here::here('pkgdown/leaflet_maps'), full.names = TRUE)) - -# delete leaflet *.Rmds -leaflet_rmd <- here::here('vignettes/articles') |> - list.files(full.names = TRUE) -keep_rmd <- grep(pattern = "ContributeSpatialData|teamMembers", x = leaflet_rmd) -leaflet_rmd <- leaflet_rmd[-keep_rmd] -file.remove(leaflet_rmd) - -# list of exported data objects -exp_data <- ls("package:NEFSCspatial") - -# ignore certain data sets, leaflet fails to render for some reason (maybe too big) -exp_data <- exp_data[-which(exp_data %in% c("amapps_grid"))] - -# loop through data and make leaflet maps -for (i in exp_data) { - - # load data - data(list = i) - - # get data - sf_data <- get(i) - - # make valid, if needed - if (any(sf::st_is_valid(sf_data) != TRUE)) { - sf_data <- sf_data |> - sf::st_make_valid() - } - - # change crs, if needed - if (sf::st_crs(sf_data) != sf::st_crs(4326)) { - sf_data <- sf_data |> - sf::st_transform(4326) - } - - # bounding box - bbox <- sf_data |> - sf::st_bbox() |> - as.vector() - - # leaflet map - leaflet_map <- leaflet::leaflet(width = '100%') |> - leaflet::addTiles(urlTemplate = "http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png") |> - leaflet::fitBounds(lng1 = bbox[1], lat1 = bbox[2], lng2 = bbox[3], lat2 = bbox[4]) |> - leaflet::addPolygons(data = sf_data, popup = i) - - # save the map - saveRDS(leaflet_map, here::here(paste0("pkgdown/leaflet_maps/", i, "_leaflet.rds"))) - - # write *.Rmd file - sink(file = here::here(paste0("vignettes/articles/", i, "_leaflet.Rmd"))) - - # header - cat("--- \n") - cat(paste0("title: '", i, "' \n")) - cat("output: html_document \n") - cat("--- \n\n") - - # load map - cat("```{r, echo = FALSE, warning = FALSE} \n") - cat("library(leaflet) \n") - cat(paste0("m <- readRDS(here::here('pkgdown/leaflet_maps/", i, "_leaflet.rds')) \n")) - cat("``` \n\n") - - # map - cat("```{r, echo = FALSE} \n") - cat("m \n") - cat("```") - - sink() - -} - -# modify _pkgdown.yml -yaml_file <- yaml::read_yaml(here::here('pkgdown/_pkgdown.yml')) - -# add menu items -mod_menu = lapply(X = exp_data, FUN = function(X) { list(text = X, href = paste0('articles/', X, '_leaflet.html')) }) -yaml_file$navbar$components$map$menu <- mod_menu - -# output -yaml::write_yaml(x = yaml_file, file = here::here('pkgdown/_pkgdown.yml')) diff --git a/data-raw/create_sf_data_from_shp.R b/data-raw/create_sf_data_from_shp.R index b944dad..05c7c0b 100644 --- a/data-raw/create_sf_data_from_shp.R +++ b/data-raw/create_sf_data_from_shp.R @@ -11,42 +11,42 @@ #' library(magrittr) -create_sf_data_from_shp <- function(filePath,overwrite=F,addCentroids=T,shapefilenm=NULL) { - +create_sf_data_from_shp <- function( + filePath, + overwrite = F, + addCentroids = T, + shapefilenm = NULL +) { # turn off spherical geometry sf::sf_use_s2(F) # get filename #overwrite filename with custom name - if(!is.null(shapefilenm)) { + if (!is.null(shapefilenm)) { fileName <- shapefilenm } else { - fileName <- gsub(".shp$","",filePath) - fileName <- tail(unlist(strsplit(fileName,"/")),1) + fileName <- gsub(".shp$", "", filePath) + fileName <- tail(unlist(strsplit(fileName, "/")), 1) } fn <- fileName # read in shapefile - layer <- sf::st_read(dsn=filePath) + layer <- sf::st_read(dsn = filePath) # add XY locations for center of each polygon - if(addCentroids) { - centroids <- sf::st_coordinates(sf::st_centroid(layer)) - layer <- cbind(layer,centroids) + if (addCentroids) { + centroids <- sf::st_coordinates(sf::st_centroid(layer)) + layer <- cbind(layer, centroids) } # assigns name to layer object - assign(fileName,layer) - - + assign(fileName, layer) - print(here::here("data",paste0(fn,".rdata"))) + print(here::here("data", paste0(fn, ".rdata"))) # exports - if(overwrite) { - save(list=fileName,file=here::here("data",paste0(fn,".rda"))) - + if (overwrite) { + save(list = fileName, file = here::here("data", paste0(fn, ".rda"))) } #do.call(myfun, list(as.name(fileName), overwrite = TRUE)) return(layer) - } diff --git a/data-raw/find_mdeb_data.R b/data-raw/find_mdeb_data.R new file mode 100644 index 0000000..4e3292e --- /dev/null +++ b/data-raw/find_mdeb_data.R @@ -0,0 +1,57 @@ +#' Find available data hosted on the MDEB (Marine Development and Ecology Branch) GIS Data Hub +#' hosted on NOAA's Geoplatform +#' +#' @description +#' This function retrieves the data available on the +#' \href{https://mdeb-nefsc-noaa.hub.arcgis.com/}{MDEB GIS Data Hub}. +#' +#' @return A tibble with the following columns: +#' \item{title}{Name of the NOAA Geoplatform feature service} +#' \item{name}{Name of the hosted feature layer in the feature service} +#' \item{id}{Feature layer ID, a unique identifier assigned to layers within a feature service} +#' \item{url}{URL of the NOAA Geoplatform feature layer} +#' +#' @examples +#' # Retrieve a list of available data +#' mdeb_data <- find_mdeb_data() +#' mdeb_data +#' +#' @export + +find_mdeb_data <- function() { + # url of the MDEB GIS Data Hub search API + mdeb_hub = "https://mdeb-nefsc-noaa.hub.arcgis.com/api/search/v1/collections/all/items" + # scrape json to get all feature services + catalog_items <- mdeb_hub |> + jsonlite::fromJSON() + # count the number of available services + num_items <- catalog_items$numberMatched + # pull all feature service items (API default = 10) + catalog_items_v2 <- paste0(mdeb_hub, "?limit=", num_items) |> + jsonlite::fromJSON() + # extract metadata properties + available_datasets <- catalog_items_v2$features$properties |> + dplyr::filter(grepl("FeatureServer", url)) |> + dplyr::select(title, url) + # format metadata for each feature service as json + available_dataset_layers <- available_datasets |> + dplyr::mutate(layerurl = paste0(url, "?f=pjson")) + # create a new data frame to store the results + dataset_metadata <- NULL + # find if there are multiple feature layers per service + for (idataset in 1:nrow(available_dataset_layers)) { + dataset_url <- available_dataset_layers[idataset, ] + dataset_json_url <- dataset_url$layerurl + # request the json format for the metadata + wp <- dataset_json_url |> + jsonlite::fromJSON() + # create tibble for output + av = wp$layers |> + dplyr::mutate(dataset_url) |> + dplyr::mutate(url = paste0(url, '/', id)) |> + dplyr::select(title, name, id, url) |> + dplyr::as_tibble() + dataset_metadata <- dplyr::bind_rows(dataset_metadata, av) + } + return(dataset_metadata) +} diff --git a/data-raw/generate_roxygen_mdeb.R b/data-raw/generate_roxygen_mdeb.R new file mode 100644 index 0000000..a68e179 --- /dev/null +++ b/data-raw/generate_roxygen_mdeb.R @@ -0,0 +1,66 @@ +# function to generate a consistent Roxygen file for data documentation +generate_roxygen_mdeb <- function(dataset_name, title, description) { + + # check that dataset_name has an *.rda ext + stopifnot(endsWith(dataset_name, '.rda')) + + # load data + load(here::here('data', dataset_name)) + + # re-assign + mdeb_obj <- dataset_name |> + tools::file_path_sans_ext() |> + get() + + # extract metadata + geometry_type <- sf::st_geometry_type(mdeb_obj) |> + unique() |> + as.character() + dimension <- sf::st_dimension(mdeb_obj) |> + unique() + dimension_type <- ifelse(dimension == 2, 'XY', NA_character_) + bbox <- sf::st_bbox(mdeb_obj) + projection <- sf::st_crs(mdeb_obj, parameters = TRUE)$Name + num_features <- nrow(mdeb_obj) + num_columns <- ncol(mdeb_obj) + + # build the file path + file_path <- file.path("R", paste0("data-", tools::file_path_sans_ext(dataset_name), ".R")) + + # substitute values into the template + roxygen_content <- glue::glue(" +#' { title } +#' +#' @description { description } +#' +#' @format An \\code{{sf}} object: +#' \\describe{{ +#' \\item{{Geometry type}}{{{ geometry_type }}} +#' \\item{{Dimension}}{{{ dimension_type }}} +#' \\item{{Bounding box}}{{xmin: { round(bbox['xmin'], 1) } ymin: { round(bbox['ymin'], 1) } xmax: { round(bbox['xmax'], 1) } ymax: { round(bbox['ymax'], 1) }}} +#' \\item{{Projected CRS}}{{{ projection }}} +#' \\item{{Features}}{{{ num_features } x { num_columns }} +#' \\item{{Metadata}}{{See source}} +#' }} +#' +#' @docType data +#' @name { tools::file_path_sans_ext(dataset_name) } +#' @usage data('{ tools::file_path_sans_ext(dataset_name) }') +#' @keywords {{datasets}} +#' @source {{https://mdeb-nefsc-noaa.hub.arcgis.com/}} +#' @examples +#' \\dontrun{{ +#' # Load the dataset +#' data({ tools::file_path_sans_ext(dataset_name) }) +#' +#' # Plot the geometry +#' plot(sf::st_geometry({ tools::file_path_sans_ext(dataset_name) })) +#' }} +NULL +") + + # write content to file + writeLines(roxygen_content, con = file_path) + message(glue::glue("Generated Roxygen file for '{ tools::file_path_sans_ext(dataset_name) }' at: { file_path }")) + +} diff --git a/data-raw/get_mdeb_data.R b/data-raw/get_mdeb_data.R new file mode 100644 index 0000000..0ba3173 --- /dev/null +++ b/data-raw/get_mdeb_data.R @@ -0,0 +1,59 @@ +#' Get data from the MDEB (Marine Development and Ecology Branch) GIS Data Hub +#' hosted on NOAA's Geoplatform +#' +#' @description +#' This function retrieves data from the \href{https://mdeb-nefsc-noaa.hub.arcgis.com/}{MDEB GIS Data Hub}. +#' +#' @param dataset_name Name of the dataset to retrieve. +#' @param dataset_id ID of the dataset layer to retrieve. +#' +#' @section Available data: +#' The list of available data and corresponding REST URLs +#' can be found by running `find_mdeb_data()`. +#' +#' @return An sf data.frame-like object +#' +#' @examples +#' # Pull EcoMon Survey strata from MDEB GIS Data Hub +#' ecomon_strata <- get_mdeb_data(dataset_name = "Ecosystem Monitoring Survey", dataset_id = 1) +#' # Plot the data +#' plot(ecomon_strata) +#' +#' @export + +get_mdeb_data <- function(dataset_name = NULL, dataset_id = NULL) { + # check if dataset_name, dataset_id is NULL + if (is.null(dataset_name) || is.null(dataset_id)) { + message( + "Neither dataset_name or id can be NULL. + To find the list of available datasets, please use run + find_mdeb_data()." + ) + return() + } + + allData <- find_mdeb_data() + set <- allData |> + dplyr::filter(title == dataset_name, id == dataset_id) + + if (nrow(set) == 0) { + stop( + "Data set not found. To find the list of available datasets, please use run + find_mdeb_data()" + ) + } + + rest_url <- paste0(set$url, "/query") + + dataset <- httr2::request(rest_url) |> + httr2::req_url_query(where = "1=1", outFields = "*", f = "geoJSON") |> + httr2::req_perform() + if (dataset$status_code == 200) { + dataset_sf = dataset |> + httr2::resp_body_string() |> + sf::read_sf() + return(dataset_sf) + } else { + message("URL returned status code: ", dataset$status_code) + } +} diff --git a/data-raw/get_mdeb_for_package.R b/data-raw/get_mdeb_for_package.R new file mode 100644 index 0000000..df8c84b --- /dev/null +++ b/data-raw/get_mdeb_for_package.R @@ -0,0 +1,65 @@ +#' Pull all content from MDEB data hub and create sf objects +#' +#' Pulls the data and converts to sf, then saves as part of the package +#' +#' +#' + +source(here::here("data-raw/find_mdeb_data.R")) +source(here::here("data-raw/get_mdeb_data.R")) +source(here::here("data-raw/generate_roxygen_mdeb.R")) + +get_mdeb_for_package <- function(overwrite = FALSE) { + # find all the data set on the MDEB HUB + datasets <- find_mdeb_data() + + # loop through each and save as rda file. + # also create documentation for each dataset + for (ids in 1:nrow(datasets)) { + dataset <- datasets[ids, ] + message("Processing: ", dataset$title) + data <- get_mdeb_data(dataset$title, dataset$id) + if (!is.null(data)) { + # Save the data as an R object in the package + dataset_name <- tolower(gsub("SMIT_", "", dataset$name)) + fn <- dataset_name + assign(dataset_name, data) + if (overwrite) { + save( + list = dataset_name, + file = here::here("data", paste0(fn, ".rda")) + ) + } + # Grab description from metadata (if available) + fs_layer <- paste0(dataset$url, '?f=pjson') |> + httr2::request() |> + httr2::req_perform() |> + httr2::resp_body_json() + dataset_description <- fs_layer$description + # Work around for now, until the descriptions are populated for each layer in the Hub + if (dataset_description != '') { + modified_dataset_description <- paste0( + 'An \\code{sf} object containing spatial data for the ', + dataset$title, + '. ', + dataset_description + ) + } else { + modified_dataset_description <- paste0( + 'An \\code{sf} object containing spatial data for the ', + dataset$title, + '.' + ) + } + # Generate Roxygen data doc + generate_roxygen_mdeb( + dataset_name = paste0(dataset_name, '.rda'), + title = dataset$title, + description = modified_dataset_description + ) + # save(data, file = here::here("data",)) + } else { + message("No data found for: ", dataset$name) + } + } +} diff --git a/data-raw/standardize_data_dims.R b/data-raw/standardize_data_dims.R new file mode 100644 index 0000000..b3c084d --- /dev/null +++ b/data-raw/standardize_data_dims.R @@ -0,0 +1,43 @@ +## check and update dimension of data to be consistent + +## list of datasets +all_data <- data(package = 'NEFSCspatial') + +## extract names +data_names <- all_data$results[, 'Item'] +data_names <- data_names[!data_names %in% c('ecomon_stations')] + +## loop through each dataset +for (i in data_names) { + + # load data + load(here::here('data', paste0(i, '.rda'))) + + # re-assign + data_obj <- i |> + get() + + # dimensions + num_features <- nrow(data_obj) + num_columns <- ncol(data_obj) + data_dim <- glue::glue("#' \\item{{Features}}{{{ num_features } x { num_columns }}") + + # build the file path + file_path <- file.path("R", paste0("data_", i, ".R")) + if (!file.exists(file_path)) file_path <- file.path("R", paste0("data-", i, ".R")) + + # read in data documentation + data_doc <- readLines(con = file_path) + + # find Features + replace_id = grep(pattern = 'Features', x = data_doc) + stopifnot(length(replace_id) == 1) + + # replace + data_doc[replace_id] <- data_dim + + # write + writeLines(data_doc, con = file_path) + message(glue::glue("Updated Roxygen file for '{ i }' at: { file_path }")) + +} diff --git a/data/Herring_Management_Areas.rda b/data/Herring_Management_Areas.rda index 2560b6b..9118bd1 100644 Binary files a/data/Herring_Management_Areas.rda and b/data/Herring_Management_Areas.rda differ 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b/data/sc_strata.rda new file mode 100644 index 0000000..942f6be Binary files /dev/null and b/data/sc_strata.rda differ diff --git a/data/scallop_strata.rda b/data/scallop_strata.rda new file mode 100644 index 0000000..f9ecc44 Binary files /dev/null and b/data/scallop_strata.rda differ diff --git a/data/scallop_strata_historic.rda b/data/scallop_strata_historic.rda new file mode 100644 index 0000000..2080880 Binary files /dev/null and b/data/scallop_strata_historic.rda differ diff --git a/data/seal_stations.rda b/data/seal_stations.rda new file mode 100644 index 0000000..502f304 Binary files /dev/null and b/data/seal_stations.rda differ diff --git a/data/turtle_strata.rda b/data/turtle_strata.rda new file mode 100644 index 0000000..ec217a5 Binary files /dev/null and b/data/turtle_strata.rda differ diff --git a/man/BTS_Strata.Rd b/man/BTS_Strata.Rd index 72b8bb2..20f27b7 100644 --- a/man/BTS_Strata.Rd +++ b/man/BTS_Strata.Rd @@ -3,7 +3,7 @@ \docType{data} \name{BTS_Strata} \alias{BTS_Strata} -\title{NEFSC Bottom Trawl Survey Strata} +\title{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}} \format{ An \code{sf} object: \describe{ @@ -11,7 +11,7 @@ An \code{sf} object: \item{dimension}{XY} \item{Bounding box}{xmin: -79.18422 ymin: 32.50221 xmax: -65.16869 ymax: 44.83202} \item{Geodetic CRS}{NAD 83} -\item{Features}{185 x 9} +\item{Features}{185 x 10} \item{Metadata}{See source} } } @@ -24,7 +24,13 @@ An \code{sf} object: data("BTS_Strata") } \description{ +NEFSC Bottom Trawl Survey Strata +} +\details{ An \code{sf} object containing the boundaries of the NEFSC bottom trawl survey strata. This set of strata is considered historical. (Pre 2000). } +\note{ +Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/datasets/noaa::bottom-trawl-survey/about} instead. +} \keyword{datasets} diff --git a/man/EcoMon_Strata.Rd b/man/EcoMon_Strata.Rd index 654f83f..f31b80d 100644 --- a/man/EcoMon_Strata.Rd +++ b/man/EcoMon_Strata.Rd @@ -3,7 +3,7 @@ \docType{data} \name{EcoMon_Strata} \alias{EcoMon_Strata} -\title{Ecosystem Monitoring Cruise (EcoMon) strata} +\title{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}} \format{ A data frame/ \code{sf} object \describe{ @@ -11,7 +11,7 @@ A data frame/ \code{sf} object \item{Dimension}{XY} \item{Bounding box}{xmin: -75.96791 ymin: 35.14219 xmax: -65.16869 ymax: 44.48558} \item{Geodetic CRS}{NAD83} -\item{Features}{47 x 3} +\item{Features}{47 x 4} \item{Metadata}{See source} } } @@ -22,6 +22,12 @@ A data frame/ \code{sf} object data("EcoMon_Strata") } \description{ +Ecosystem Monitoring Cruise (EcoMon) strata +} +\details{ An sf object containing the EcoMon strata } +\note{ +Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/datasets/noaa::ecosystem-monitoring-survey/about} instead. +} \keyword{datasets} diff --git a/man/GillnetClosureAreas_20211021.Rd b/man/GillnetClosureAreas_20211021.Rd index ca61c81..8228b4e 100644 --- a/man/GillnetClosureAreas_20211021.Rd +++ b/man/GillnetClosureAreas_20211021.Rd @@ -5,43 +5,14 @@ \alias{GillnetClosureAreas_20211021} \title{Gillnet Closure Areas} \format{ -A data frame/ sf object (2 x 25) +An \code{sf} object \describe{ \item{Geometry type}{POLYGON} \item{Dimension}{XY} \item{Bounding box}{xmin: -70.33333 ymin: 40.33333 xmax: -68.5 ymax: 41.5} \item{Geodetic CRS}{NAD83} -\item{Features}{2 x 25} +\item{Features}{2 x 26} \item{Metadata}{See source} - -\item{GARFO_ID}{A unique identifier used to identify and track this feature; -a new GARFO_ID is generated for each version of a Regulated Area, including -proposed or final versions (i.e. whenever boundaries or attributes are -changed, edited or updated)} -\item{AREANAME}{Official name of the Proposed Area, usually the area name as it will be printed in the CFR.} -\item{COMMNAME}{Most commonly used name. May be identical to AREANAME, an abbreviation of AREANAME, or a different name altogether.} -\item{AREAGROUP}{Specifies if the Proposed Area is part of a group of related areas.} -\item{DESCRIBE}{A brief description of the purpose of the Proposed Area.} -\item{CFRTITLE}{CFR Title citation where the Proposed Area will be legally defined} -\item{CFRPT}{ACFR Part citation where the Proposed Area will be legally defined} -\item{CFRPTTXT}{CFR Part citation header text} -\item{CFRSUB}{CFR Subpart citation where the Proposed Area will be legally defined} -\item{CFRSUBTXT}{CFR Subpart citation header text} -\item{CFRSXN}{CFR Section citation where the Proposed Area will be legally defined} -\item{CFRSXNTXT}{CFR Section citation header text} -\item{CFRPARA}{CFR Paragraph citation where the Proposed Area will be legally defined} -\item{CFRPARATXT}{CFR Paragraph citation header text} -\item{FRCITE}{Federal Register citation of proposed rule containing the Proposed Area spatial definition.} -\item{FRDATE}{Federal Register citation date of proposed rule containing the Proposed Area spatial definition.} -\item{EFFECTDATE}{Date Regulated Area officially became law, or most recent modification. For Proposed Areas, this field will be blank because the area is not yet law.} -\item{SOURCE}{If Proposed Area will be defined in the CFR, this is the citation for the Amendment/Framework/etc. that will establish the area. If the Proposed Area will not be defined in the CFR, this is the alternative source citation that will establish the area.} -\item{RECURST}{Annually recurring date Proposed Area would become active} -\item{RECUREND}{Annually recurring date Proposed Area would become inactive} -\item{GISAUTHOR}{Name of the NOAA staff person who created the GIS feature} -\item{CREATED}{Creation date of the GIS feature} -\item{AREANOTES}{Miscellaneous notes regarding the Proposed Area or feature} -\item{X}{x coordinate of polygon center} -\item{Y}{y coordinate of polygon center} } } \source{ @@ -51,12 +22,16 @@ changed, edited or updated)} data("GillnetClosureAreas_20211021") } \description{ -An sf object containing the Closure areas for Gillnets -Specifically Closed Area 1 and Nantucket Lightship Closure Area +An \code{sf} object containing the closure areas for gillnets. +Specifically Closed Area 1 and Nantucket Lightship Closure Area. } -\section{Contact}{ +\examples{ +\dontrun{ +# Load the dataset +data(GillnetClosureAreas_20211021) -andrew.beet at noaa.gov +# Plot the geometry +plot(sf::st_geometry(GillnetClosureAreas_20211021)) +} } - \keyword{datasets} diff --git a/man/Great_South_Channel_Restricted_Trap_Pot_Area.Rd b/man/Great_South_Channel_Restricted_Trap_Pot_Area.Rd index 9aafe33..bc2e29a 100644 --- a/man/Great_South_Channel_Restricted_Trap_Pot_Area.Rd +++ b/man/Great_South_Channel_Restricted_Trap_Pot_Area.Rd @@ -12,7 +12,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -69.75 ymin: 41 xmax: -68.21667 ymax: 42.16667} \item{Geodetic CRS}{NAD83} -\item{Features}{1 x 25} +\item{Features}{1 x 26} \item{Metadata}{See source} } } @@ -25,4 +25,13 @@ data("Great_South_Channel_Restricted_Trap_Pot_Area") \description{ An \code{sf} object that depicts the boundaries of the Great South Channel Restricted Area in effect from April 1 to June 30 annually for the NOAA Fisheries Service’s Greater Atlantic Regional Fisheries Office (GARFO). } +\examples{ +\dontrun{ +# Load the dataset +data(Great_South_Channel_Restricted_Trap_Pot_Area) + +# Plot the geometry +plot(sf::st_geometry(Great_South_Channel_Restricted_Trap_Pot_Area)) +} +} \keyword{datasets} diff --git a/man/Herring_Management_Areas.Rd b/man/Herring_Management_Areas.Rd index d8dbf9e..75fc664 100644 --- a/man/Herring_Management_Areas.Rd +++ b/man/Herring_Management_Areas.Rd @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -78.57412 ymin: 33.81288 xmax: -65.69947 ymax: 45.1918} \item{Geodetic CRS}{NAD83} -\item{Features}{4 x 25} +\item{Features}{4 x 26} \item{Metadata}{See source} } } @@ -22,6 +22,15 @@ An \code{sf} object: data("Herring_Management_Areas") } \description{ -An \code{sf} object depicting the boundaries of the Herring Management Areas +An \code{sf} object depicting the boundaries of the Herring Management Areas. +} +\examples{ +\dontrun{ +# Load the dataset +data(Herring_Management_Areas) + +# Plot the geometry +plot(sf::st_geometry(Herring_Management_Areas)) +} } \keyword{datasets} diff --git a/man/LMA1_Restricted_Area_FR.Rd b/man/LMA1_Restricted_Area_FR.Rd index 98a4dbd..a86bb08 100644 --- a/man/LMA1_Restricted_Area_FR.Rd +++ b/man/LMA1_Restricted_Area_FR.Rd @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -69.6128 ymin: 42.89198 xmax: -68.28787 ymax: 43.73333} \item{Geodetic CRS}{WGS 84} -\item{Features}{1 x 25} +\item{Features}{1 x 26} \item{Metadata}{See source} } } @@ -24,4 +24,13 @@ data("LMA1_Restricted_Area_FR") \description{ An \code{sf} object that depicts the boundaries of the Lobster Management Area One Restricted Area in effect annually from October 1 to January 30 for the NOAA Fisheries Service’s Greater Atlantic Regional Fisheries Office (GARFO). } +\examples{ +\dontrun{ +# Load the dataset +data(LMA1_Restricted_Area_FR) + +# Plot the geometry +plot(sf::st_geometry(LMA1_Restricted_Area_FR)) +} +} \keyword{datasets} diff --git a/man/NAFO_Divisions_2021_line_enclosed.Rd b/man/NAFO_Divisions_2021_line_enclosed.Rd index 3313313..53cf968 100644 --- a/man/NAFO_Divisions_2021_line_enclosed.Rd +++ b/man/NAFO_Divisions_2021_line_enclosed.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_NAFO_Divsions_2021_line_enclosed.R +% Please edit documentation in R/data_NAFO_Divisions_2021_line_enclosed.R \docType{data} \name{NAFO_Divisions_2021_line_enclosed} \alias{NAFO_Divisions_2021_line_enclosed} @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} \item{Geodetic CRS}{NAD83} -\item{Features}{38 x 5} +\item{Features}{38 x 6} \item{Metadata}{See source} } } @@ -22,6 +22,15 @@ An \code{sf} object: data("NAFO_Divisions_2021_line_enclosed") } \description{ -An \code{sf} object that depicts the boundaries of the NAFO regions +An \code{sf} object that depicts the boundaries of the NAFO regions. +} +\examples{ +\dontrun{ +# Load the dataset +data(NAFO_Divisions_2021_line_enclosed) + +# Plot the geometry +plot(sf::st_geometry(NAFO_Divisions_2021_line_enclosed)) +} } \keyword{datasets} diff --git a/man/NAFO_Divisions_2021_line_not_enclosed.Rd b/man/NAFO_Divisions_2021_line_not_enclosed.Rd index 3c62d69..1b76625 100644 --- a/man/NAFO_Divisions_2021_line_not_enclosed.Rd +++ b/man/NAFO_Divisions_2021_line_not_enclosed.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_NAFO_Divsions_2021_line_not_enclosed.R +% Please edit documentation in R/data_NAFO_Divisions_2021_line_not_enclosed.R \docType{data} \name{NAFO_Divisions_2021_line_not_enclosed} \alias{NAFO_Divisions_2021_line_not_enclosed} @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} \item{Geodetic CRS}{NAD83} -\item{Features}{42 x 7} +\item{Features}{42 x 8} \item{Metadata}{See source} } } @@ -22,6 +22,15 @@ An \code{sf} object: data("NAFO_Divisions_2021_line_not_enclosed") } \description{ -An \code{sf} object that depicts the boundaries of the NAFO regions +An \code{sf} object that depicts the boundaries of the NAFO regions. +} +\examples{ +\dontrun{ +# Load the dataset +data(NAFO_Divisions_2021_line_not_enclosed) + +# Plot the geometry +plot(sf::st_geometry(NAFO_Divisions_2021_line_not_enclosed)) +} } \keyword{datasets} diff --git a/man/NAFO_Divisions_2021_poly_clipped.Rd b/man/NAFO_Divisions_2021_poly_clipped.Rd index 422ef52..494f9ef 100644 --- a/man/NAFO_Divisions_2021_poly_clipped.Rd +++ b/man/NAFO_Divisions_2021_poly_clipped.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_NAFO_Divsions_2021_poly_clipped.R +% Please edit documentation in R/data_NAFO_Divisions_2021_poly_clipped.R \docType{data} \name{NAFO_Divisions_2021_poly_clipped} \alias{NAFO_Divisions_2021_poly_clipped} @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} \item{Geodetic CRS}{NAD83} -\item{Features}{39 x 8} +\item{Features}{39 x 9} \item{Metadata}{See source} } } @@ -22,6 +22,15 @@ An \code{sf} object: data("NAFO_Divisions_2021_poly_clipped") } \description{ -An \code{sf} object that depicts the boundaries of the NAFO regions +An \code{sf} object that depicts the boundaries of the NAFO regions. +} +\examples{ +\dontrun{ +# Load the dataset +data(NAFO_Divisions_2021_poly_clipped) + +# Plot the geometry +plot(sf::st_geometry(NAFO_Divisions_2021_poly_clipped)) +} } \keyword{datasets} diff --git a/man/NAFO_Divisions_2021_poly_not_clipped.Rd b/man/NAFO_Divisions_2021_poly_not_clipped.Rd index 39daeeb..55cf44b 100644 --- a/man/NAFO_Divisions_2021_poly_not_clipped.Rd +++ b/man/NAFO_Divisions_2021_poly_not_clipped.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data_NAFO_Divsions_2021_poly_not_clipped.R +% Please edit documentation in R/data_NAFO_Divisions_2021_poly_not_clipped.R \docType{data} \name{NAFO_Divisions_2021_poly_not_clipped} \alias{NAFO_Divisions_2021_poly_not_clipped} @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -80 ymin: 35 xmax: -42 ymax: 78.16667} \item{Geodetic CRS}{NAD83} -\item{Features}{38 x 8} +\item{Features}{38 x 9} \item{Metadata}{See source} } } @@ -22,6 +22,15 @@ An \code{sf} object: data("NAFO_Divisions_2021_poly_not_clipped") } \description{ -An \code{sf} object that depicts the boundaries of the NAFO regions +An \code{sf} object that depicts the boundaries of the NAFO regions. +} +\examples{ +\dontrun{ +# Load the dataset +data(NAFO_Divisions_2021_poly_not_clipped) + +# Plot the geometry +plot(sf::st_geometry(NAFO_Divisions_2021_poly_not_clipped)) +} } \keyword{datasets} diff --git a/man/NEFSCspatial-package.Rd b/man/NEFSCspatial-package.Rd new file mode 100644 index 0000000..5b6e742 --- /dev/null +++ b/man/NEFSCspatial-package.Rd @@ -0,0 +1,32 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/NEFSCspatial-package.R +\docType{package} +\name{NEFSCspatial-package} +\alias{NEFSCspatial} +\alias{NEFSCspatial-package} +\title{NEFSCspatial: Spatial data package for regions in the northeast atlantic} +\description{ +\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} + +Provides spatial data as sf or raster objects for the Northeast Fisheries Science Center +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/NEFSC/NEFSC-Spatial/} + \item \url{https://nefsc.github.io/NEFSC-Spatial/} + \item Report bugs at \url{https://github.com/NEFSC/NEFSC-Spatial/issues} +} + +} +\author{ +\strong{Maintainer}: Andy Beet \email{andrew.beet@noaa.gov} (\href{https://orcid.org/0000-0001-8270-7090}{ORCID}) + +Authors: +\itemize{ + \item Joshua Hatch \email{joshua.hatch@noaa.gov} + \item Kimberly Bastille \email{kimberly.bastille@noaa.gov} +} + +} +\keyword{internal} diff --git a/man/Neus_atlantis.Rd b/man/Neus_atlantis.Rd index 7d0067e..9436e1c 100644 --- a/man/Neus_atlantis.Rd +++ b/man/Neus_atlantis.Rd @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -76.45919 ymin: 34.76128 xmax: -63.42171 ymax: 46.11478} \item{Geodetic CRS}{WGS 83} -\item{Features}{30 x 10} +\item{Features}{30 x 11} \item{Metadata}{See source} } } @@ -22,6 +22,15 @@ An \code{sf} object: data("Neus_atlantis") } \description{ -An sf object containing the box level boundaries used in the Northeast Atlantis ecosystem end to end model +An \code{sf} object containing the box level boundaries used in the Northeast Atlantis ecosystem end to end model. +} +\examples{ +\dontrun{ +# Load the dataset +data(Neus_atlantis) + +# Plot the geometry +plot(sf::st_geometry(Neus_atlantis)) +} } \keyword{datasets} diff --git a/man/Scallop_Rotational_Areas_20230411.Rd b/man/Scallop_Rotational_Areas_20230411.Rd new file mode 100644 index 0000000..978d24b --- /dev/null +++ b/man/Scallop_Rotational_Areas_20230411.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data_Scallop_Rotational_Areas_20230411.R +\docType{data} +\name{Scallop_Rotational_Areas_20230411} +\alias{Scallop_Rotational_Areas_20230411} +\title{Scallop Restricted Area} +\format{ +An \code{sf} object +\describe{ +\item{Geometry type}{POLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -8274749 ymin: 4602998 xmax: -7333888 ymax: 5087139} +\item{Geodetic CRS}{WGS 84 / Pseudo-Mercator} +\item{Features}{6 x 26} +\item{Metadata}{See source} +} +} +\source{ +\url{https://www.fisheries.noaa.gov/resource/map/atlantic-sea-scallop-managed-waters-fishing-year-2023} +} +\usage{ +data("Scallop_Rotational_Areas_20230411") +} +\description{ +An \code{sf} object containing the Scallop Restricted Areas. +Specifically Area I, II, Nantucket Lightship North, Nantucket Lightship West, New York Bight, and Elephant Trunk. +} +\examples{ +\dontrun{ +# Load the dataset +data(Scallop_Rotational_Areas_20230411) + +# Plot the geometry +plot(sf::st_geometry(Scallop_Rotational_Areas_20230411)) +} +} +\keyword{datasets} diff --git a/man/Shellfish_Strata.Rd b/man/Shellfish_Strata.Rd index 86f0c2a..dd10681 100644 --- a/man/Shellfish_Strata.Rd +++ b/man/Shellfish_Strata.Rd @@ -3,7 +3,7 @@ \docType{data} \name{Shellfish_Strata} \alias{Shellfish_Strata} -\title{Shellfish strata (Clam and Scallop surveys)} +\title{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}} \format{ A data frame/ \code{sf} object \describe{ @@ -11,7 +11,7 @@ A data frame/ \code{sf} object \item{Dimension}{XY} \item{Bounding box}{xmin: -75.95982 ymin: 35.50142 xmax: -65.89944 ymax: 42.16817} \item{Geodetic CRS}{NAD83} -\item{Features}{97 x 9} +\item{Features}{97 x 10} \item{Metadata}{See source} } } @@ -22,6 +22,12 @@ A data frame/ \code{sf} object data("Shellfish_Strata") } \description{ +Shellfish strata (Clam and Scallop surveys) +} +\details{ An sf object containing the Clam and Scallop survey strata } +\note{ +Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/maps/noaa::atlantic-surfclam-and-ocean-quahog-survey/about} or \url{https://mdeb-nefsc-noaa.hub.arcgis.com/maps/noaa::sea-scallop-survey/about} instead. +} \keyword{datasets} diff --git a/man/Shrimp_Strata.Rd b/man/Shrimp_Strata.Rd index 4edcbc2..f771a95 100644 --- a/man/Shrimp_Strata.Rd +++ b/man/Shrimp_Strata.Rd @@ -3,7 +3,7 @@ \docType{data} \name{Shrimp_Strata} \alias{Shrimp_Strata} -\title{Shrimp survey strata} +\title{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}} \format{ A data frame/ \code{sf} object \describe{ @@ -11,7 +11,7 @@ A data frame/ \code{sf} object \item{Dimension}{XY} \item{Bounding box}{xmin: -70.68152 ymin: 41.08476 xmax: -67.99941 ymax: 44.08762} \item{Geodetic CRS}{NAD83} -\item{Features}{12 x 4} +\item{Features}{12 x 5} \item{Metadata}{See source} } } @@ -22,6 +22,12 @@ A data frame/ \code{sf} object data("Shrimp_Strata") } \description{ +Shrimp survey strata +} +\details{ An sf object containing the Shrimp survey strata } +\note{ +Use \url{https://mdeb-nefsc-noaa.hub.arcgis.com/datasets/noaa::northern-shrimp-survey/about} instead. +} \keyword{datasets} diff --git a/man/Statistical_Areas_2010.Rd b/man/Statistical_Areas_2010.Rd index a1914b8..7c8968e 100644 --- a/man/Statistical_Areas_2010.Rd +++ b/man/Statistical_Areas_2010.Rd @@ -5,13 +5,13 @@ \alias{Statistical_Areas_2010} \title{Greater Atlantic Region Statistical Areas} \format{ -A data frame/ sf object (135 x 1) +An \code{sf} object: \describe{ \item{Geometry type}{MULTIPOLYGON} \item{Dimension}{XY} \item{Bounding box}{xmin: -81.53406 ymin: 24 xmax: -42 ymax: 52.25} \item{Geodetic CRS}{NAD83} -\item{Features}{135 x 1} +\item{Features}{135 x 4} \item{Metadata}{See source} } } @@ -22,7 +22,16 @@ A data frame/ sf object (135 x 1) data("Statistical_Areas_2010") } \description{ -An sf object containing the Greater Atlantic Region Statistical Areas. -Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/ +An \code{sf} object containing the Greater Atlantic Region Statistical Areas. +Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/. +} +\examples{ +\dontrun{ +# Load the dataset +data(Statistical_Areas_2010) + +# Plot the geometry +plot(sf::st_geometry(Statistical_Areas_2010)) +} } \keyword{datasets} diff --git a/man/Statistical_Areas_2010_withNames.Rd b/man/Statistical_Areas_2010_withNames.Rd index 76be5c8..c42f835 100644 --- a/man/Statistical_Areas_2010_withNames.Rd +++ b/man/Statistical_Areas_2010_withNames.Rd @@ -5,14 +5,14 @@ \alias{Statistical_Areas_2010_withNames} \title{Greater Atlantic Region Statistical Areas} \format{ -A data frame/ sf object (135 x 6) +A \code{sf} object: \describe{ \item{Geometry type}{MULTIPOLYGON} \item{Dimension}{XY} \item{Bounding box}{xmin: -81.53406 ymin: 24 xmax: -42 ymax: 52.25} \item{Geodetic CRS}{NAD83} \item{Metadata}{See source} -\item{Features}{135 x 1} +\item{Features}{135 x 7} } } \source{ @@ -22,8 +22,16 @@ A data frame/ sf object (135 x 6) data("Statistical_Areas_2010_withNames") } \description{ -An sf object containing the Greater Atlantic Region Statistical Areas. -With name labels -Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/ +An \code{sf} object containing the Greater Atlantic Region Statistical Areas with name labels. +Pulled from ftp://ftp.nefsc.noaa.gov/pub/gis/. +} +\examples{ +\dontrun{ +# Load the dataset +data(Statistical_Areas_2010_withNames) + +# Plot the geometry +plot(sf::st_geometry(Statistical_Areas_2010_withNames)) +} } \keyword{datasets} diff --git a/man/amapps_grid.Rd b/man/amapps_grid.Rd index acd3b00..b9e5281 100644 --- a/man/amapps_grid.Rd +++ b/man/amapps_grid.Rd @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -820443.2 ymin: -1234728 xmax: 1579557 ymax: 2045272} \item{Projected CRS}{unnamed} -\item{Features}{78720 x 1} +\item{Features}{78720 x 2} \item{Source}{data-raw/gis/AMAPPS_10km_grid.tif} } } diff --git a/man/coastspan_strata.Rd b/man/coastspan_strata.Rd new file mode 100644 index 0000000..2c2e1f6 --- /dev/null +++ b/man/coastspan_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-coastspan_strata.R +\docType{data} +\name{coastspan_strata} +\alias{coastspan_strata} +\title{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} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('coastspan_strata') +} +\description{ +An \code{sf} object containing spatial data for the Cooperative Atlantic States Shark Pupping and Nursery Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(coastspan_strata) + +# Plot the geometry +plot(sf::st_geometry(coastspan_strata)) +} +} +\keyword{{datasets}} diff --git a/man/csbll_stations.Rd b/man/csbll_stations.Rd new file mode 100644 index 0000000..d7de154 --- /dev/null +++ b/man/csbll_stations.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-csbll_stations.R +\docType{data} +\name{csbll_stations} +\alias{csbll_stations} +\title{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} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('csbll_stations') +} +\description{ +An \code{sf} object containing spatial data for the Coastal Shark Bottom Longline Survey. Sampling stations for the Coastal Shark Bottom Longline Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(csbll_stations) + +# Plot the geometry +plot(sf::st_geometry(csbll_stations)) +} +} +\keyword{{datasets}} diff --git a/man/csbll_strata.Rd b/man/csbll_strata.Rd new file mode 100644 index 0000000..fa2f690 --- /dev/null +++ b/man/csbll_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-csbll_strata.R +\docType{data} +\name{csbll_strata} +\alias{csbll_strata} +\title{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} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('csbll_strata') +} +\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. +} +\examples{ +\dontrun{ +# Load the dataset +data(csbll_strata) + +# Plot the geometry +plot(sf::st_geometry(csbll_strata)) +} +} +\keyword{{datasets}} diff --git a/man/edna_stations.Rd b/man/edna_stations.Rd new file mode 100644 index 0000000..1f51b93 --- /dev/null +++ b/man/edna_stations.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-edna_stations.R +\docType{data} +\name{edna_stations} +\alias{edna_stations} +\title{eDNA Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POINT} +\item{Dimension}{NA} +\item{Bounding box}{xmin: -75.5 ymin: 36 xmax: -65.4 ymax: 44.5} +\item{Projected CRS}{WGS 84} +\item{Features}{35 x 13} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('edna_stations') +} +\description{ +An \code{sf} object containing spatial data for the eDNA Survey. Sampling stations for the eDNA Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(edna_stations) + +# Plot the geometry +plot(sf::st_geometry(edna_stations)) +} +} +\keyword{{datasets}} diff --git a/man/edna_strata.Rd b/man/edna_strata.Rd new file mode 100644 index 0000000..22cd809 --- /dev/null +++ b/man/edna_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-edna_strata.R +\docType{data} +\name{edna_strata} +\alias{edna_strata} +\title{eDNA Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{MULTIPOLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -76 ymin: 35.1 xmax: -65.2 ymax: 44.5} +\item{Projected CRS}{WGS 84} +\item{Features}{48 x 11} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('edna_strata') +} +\description{ +An \code{sf} object containing spatial data for the eDNA Survey. Scientific survey strata for the eDNA Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(edna_strata) + +# Plot the geometry +plot(sf::st_geometry(edna_strata)) +} +} +\keyword{{datasets}} diff --git a/man/epu_sf.Rd b/man/epu_sf.Rd index 9b4323c..a21f88f 100644 --- a/man/epu_sf.Rd +++ b/man/epu_sf.Rd @@ -5,13 +5,13 @@ \alias{epu_sf} \title{Ecological Production Units} \format{ -A data frame/ \code{sf} object +An \code{sf} object \describe{ \item{Geometry type}{MULTIPOLYGON} \item{Dimension}{XY} \item{Bounding box}{xmin: -77 ymin: 35.8327 xmax: -65.66667 ymax: 44.66667} \item{Geodetic CRS}{ +proj=longlat +lat_0=40 +lon_0=-77+x_0=0 +y_0=0 +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0} -\item{Features}{4 x 3} +\item{Features}{4 x 4} \item{Metadata}{See source} } } @@ -22,7 +22,16 @@ A data frame/ \code{sf} object data("epu_sf") } \description{ -An sf object containing the Northeast US shelf Ecological Production Units (EPUs). +An \code{sf} object containing spatial data for the Northeast US shelf Ecological Production Units (EPUs). Ecological Production Units (EPUs) delineate regions unique in physiographic, oceanographic and biotic aspects on the Northeast U.S. Continental Shelf, representing an area of approximately 264,000 km within the 200 m isobath. There are four EPUs on the Shelf, including the Mid-Atlantic Bight (MAB), Georges Bank (GB), Gulf of Maine (GOM), and Scotian Shelf (SS). The Scotian Shelf lies outside the management domain of US Fishery Management Councils and is generally not considered in State of the Ecosystem Reports. } -\keyword{datasets} +\examples{ +\dontrun{ +# Load the dataset +data(epu_sf) + +# Plot the geometry +plot(sf::st_geometry(epu_sf)) +} +} +\keyword{{datasets}} diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg new file mode 100644 index 0000000..b61c57c --- /dev/null +++ b/man/figures/lifecycle-deprecated.svg @@ -0,0 +1,21 @@ + + lifecycle: deprecated + + + + + + + + + + + + + + + lifecycle + + deprecated + + diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg new file mode 100644 index 0000000..5d88fc2 --- /dev/null +++ b/man/figures/lifecycle-experimental.svg @@ -0,0 +1,21 @@ + + lifecycle: experimental + + + + + + + + + + + + + + + lifecycle + + experimental + + diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg new file mode 100644 index 0000000..9bf21e7 --- /dev/null +++ b/man/figures/lifecycle-stable.svg @@ -0,0 +1,29 @@ + + lifecycle: stable + + + + + + + + + + + + + + + + lifecycle + + + + stable + + + diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg new file mode 100644 index 0000000..db8d757 --- /dev/null +++ b/man/figures/lifecycle-superseded.svg @@ -0,0 +1,21 @@ + + lifecycle: superseded + + + + + + + + + + + + + + + lifecycle + + superseded + + diff --git a/man/final_mass_inshore_stat.Rd b/man/final_mass_inshore_stat.Rd index 45f8cfa..677db61 100644 --- a/man/final_mass_inshore_stat.Rd +++ b/man/final_mass_inshore_stat.Rd @@ -11,7 +11,7 @@ An \code{sf} object: \item{Dimension}{XY} \item{Bounding box}{xmin: -71.12554 ymin: 41.18887 xmax: -69.86013 ymax: 42.87647} \item{Geodetic CRS}{NAD83} -\item{Features}{14 x 4} +\item{Features}{14 x 5} \item{Metadata}{See source} } } @@ -24,4 +24,13 @@ data("final_mass_inshore_stat") \description{ An \code{sf} object containing the boundaries of the Massachusetts Inshore statistical areas. } +\examples{ +\dontrun{ +# Load the dataset +data(final_mass_inshore_stat) + +# Plot the geometry +plot(sf::st_geometry(final_mass_inshore_stat)) +} +} \keyword{datasets} diff --git a/man/gombll_strata.Rd b/man/gombll_strata.Rd new file mode 100644 index 0000000..623790a --- /dev/null +++ b/man/gombll_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-gombll_strata.R +\docType{data} +\name{gombll_strata} +\alias{gombll_strata} +\title{Gulf of Maine Bottom Longline Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -70.7 ymin: 42 xmax: -67.4 ymax: 43.4} +\item{Projected CRS}{WGS 84} +\item{Features}{6 x 9} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('gombll_strata') +} +\description{ +An \code{sf} object containing spatial data for the Gulf of Maine Bottom Longline Survey. Scientific survey strata for the Gulf of Maine Bottom Longline Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(gombll_strata) + +# Plot the geometry +plot(sf::st_geometry(gombll_strata)) +} +} +\keyword{{datasets}} diff --git a/man/gombll_substrata.Rd b/man/gombll_substrata.Rd new file mode 100644 index 0000000..f9ff490 --- /dev/null +++ b/man/gombll_substrata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-gombll_substrata.R +\docType{data} +\name{gombll_substrata} +\alias{gombll_substrata} +\title{Gulf of Maine Bottom Longline Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{MULTIPOLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -70.7 ymin: 42 xmax: -67.4 ymax: 43.4} +\item{Projected CRS}{WGS 84} +\item{Features}{12 x 14} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('gombll_substrata') +} +\description{ +An \code{sf} object containing spatial data for the Gulf of Maine Bottom Longline Survey. Scientific survey substrata for the Gulf of Maine Bottom Longline Survey. The survey substrata give further details on bottom-type (smooth or rough bottom) encountered in the survey area. +} +\examples{ +\dontrun{ +# Load the dataset +data(gombll_substrata) + +# Plot the geometry +plot(sf::st_geometry(gombll_substrata)) +} +} +\keyword{{datasets}} diff --git a/man/hl_strata.Rd b/man/hl_strata.Rd new file mode 100644 index 0000000..523f01c --- /dev/null +++ b/man/hl_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-hl_strata.R +\docType{data} +\name{hl_strata} +\alias{hl_strata} +\title{Hook and Line Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -75.9 ymin: 35.3 xmax: -68.6 ymax: 41.8} +\item{Projected CRS}{WGS 84} +\item{Features}{1 x 6} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('hl_strata') +} +\description{ +An \code{sf} object containing spatial data for the Hook and Line Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(hl_strata) + +# Plot the geometry +plot(sf::st_geometry(hl_strata)) +} +} +\keyword{{datasets}} diff --git a/man/mass_inshore_strata.Rd b/man/mass_inshore_strata.Rd new file mode 100644 index 0000000..9e663b7 --- /dev/null +++ b/man/mass_inshore_strata.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-mass_inshore_strata.R +\docType{data} +\name{mass_inshore_strata} +\alias{mass_inshore_strata} +\title{Massachusetts Inshore State Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{MULTIPOLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: 231326.1 ymin: 772098.2 xmax: 336448.2 ymax: 958709} +\item{Projected CRS}{NAD83 / Massachusetts Mainland} +\item{Features}{42 x 8} +\item{Metadata}{See source} +} +} +\source{ +{https://www.mass.gov/info-details/review-trawl-survey-updates. Division of Marine Fisheries - New Bedford Office. For more info contact the +\href{https://www.mass.gov/info-details/dmf-staff-directory#fisheries-biology-recreational-fishing-survey-and-assessment}{Resource Assessment Project Leader}. } +} +\usage{ +data('mass_inshore_strata') +} +\description{ +An \code{sf} object containing spatial data for the Massachusetts Inshore State Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(mass_inshore_strata) + +# Plot the geometry +plot(sf::st_geometry(mass_inshore_strata)) +} +} +\keyword{{datasets}} diff --git a/man/mmst_strata.Rd b/man/mmst_strata.Rd new file mode 100644 index 0000000..bba2d7e --- /dev/null +++ b/man/mmst_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-mmst_strata.R +\docType{data} +\name{mmst_strata} +\alias{mmst_strata} +\title{Marine Mammal and Sea Turtle Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -82.1 ymin: 24.2 xmax: -61.8 ymax: 45.2} +\item{Projected CRS}{WGS 84} +\item{Features}{7 x 6} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('mmst_strata') +} +\description{ +An \code{sf} object containing spatial data for the Marine Mammal and Sea Turtle Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(mmst_strata) + +# Plot the geometry +plot(sf::st_geometry(mmst_strata)) +} +} +\keyword{{datasets}} diff --git a/man/narw_lines.Rd b/man/narw_lines.Rd new file mode 100644 index 0000000..111b6b5 --- /dev/null +++ b/man/narw_lines.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-narw_lines.R +\docType{data} +\name{narw_lines} +\alias{narw_lines} +\title{North Atlantic Right Whale Aerial Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{MULTILINESTRING} +\item{Dimension}{NA} +\item{Bounding box}{xmin: -76 ymin: 36.7 xmax: -66.9 ymax: 44.8} +\item{Projected CRS}{WGS 84} +\item{Features}{80 x 6} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('narw_lines') +} +\description{ +An \code{sf} object containing spatial data for the North Atlantic Right Whale Aerial Survey. Aerial survey lines for the North Atlantic Right Whale Aerial Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(narw_lines) + +# Plot the geometry +plot(sf::st_geometry(narw_lines)) +} +} +\keyword{{datasets}} diff --git a/man/narw_strata.Rd b/man/narw_strata.Rd new file mode 100644 index 0000000..2df5027 --- /dev/null +++ b/man/narw_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-narw_strata.R +\docType{data} +\name{narw_strata} +\alias{narw_strata} +\title{North Atlantic Right Whale Aerial Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{MULTIPOLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -76 ymin: 36.7 xmax: -66.9 ymax: 44.8} +\item{Projected CRS}{WGS 84} +\item{Features}{1 x 5} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('narw_strata') +} +\description{ +An \code{sf} object containing spatial data for the North Atlantic Right Whale Aerial Survey. Scientific survey strata for the North Atlantic Right Whale Aerial Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(narw_strata) + +# Plot the geometry +plot(sf::st_geometry(narw_strata)) +} +} +\keyword{{datasets}} diff --git a/man/oq_strata.Rd b/man/oq_strata.Rd new file mode 100644 index 0000000..00573c1 --- /dev/null +++ b/man/oq_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-oq_strata.R +\docType{data} +\name{oq_strata} +\alias{oq_strata} +\title{Atlantic Surfclam and Ocean Quahog Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{MULTIPOLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -74.9 ymin: 36.5 xmax: -66.5 ymax: 42.1} +\item{Projected CRS}{WGS 84} +\item{Features}{12 x 20} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('oq_strata') +} +\description{ +An \code{sf} object containing spatial data for the Atlantic Surfclam and Ocean Quahog Survey. Scientific survey strata for Ocean Quahog Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(oq_strata) + +# Plot the geometry +plot(sf::st_geometry(oq_strata)) +} +} +\keyword{{datasets}} diff --git a/man/pam_deployments.Rd b/man/pam_deployments.Rd new file mode 100644 index 0000000..ccb5919 --- /dev/null +++ b/man/pam_deployments.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-pam_deployments.R +\docType{data} +\name{pam_deployments} +\alias{pam_deployments} +\title{Passive Acoustic Monitoring Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POINT} +\item{Dimension}{NA} +\item{Bounding box}{xmin: -75.7 ymin: 36.5 xmax: -66.9 ymax: 44.8} +\item{Projected CRS}{WGS 84} +\item{Features}{82 x 23} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('pam_deployments') +} +\description{ +An \code{sf} object containing spatial data for the Passive Acoustic Monitoring Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(pam_deployments) + +# Plot the geometry +plot(sf::st_geometry(pam_deployments)) +} +} +\keyword{{datasets}} diff --git a/man/sc_strata.Rd b/man/sc_strata.Rd new file mode 100644 index 0000000..61a27f7 --- /dev/null +++ b/man/sc_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-sc_strata.R +\docType{data} +\name{sc_strata} +\alias{sc_strata} +\title{Atlantic Surfclam and Ocean Quahog Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{MULTIPOLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -76 ymin: 36.5 xmax: -66.9 ymax: 42.1} +\item{Projected CRS}{WGS 84} +\item{Features}{12 x 7} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('sc_strata') +} +\description{ +An \code{sf} object containing spatial data for the Atlantic Surfclam and Ocean Quahog Survey. Scientific survey strata for the Atlantic Surfclam Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(sc_strata) + +# Plot the geometry +plot(sf::st_geometry(sc_strata)) +} +} +\keyword{{datasets}} diff --git a/man/scallop_strata.Rd b/man/scallop_strata.Rd new file mode 100644 index 0000000..24f0b2d --- /dev/null +++ b/man/scallop_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-scallop_strata.R +\docType{data} +\name{scallop_strata} +\alias{scallop_strata} +\title{Sea Scallop Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -74.9 ymin: 36.6 xmax: -66.3 ymax: 42.2} +\item{Projected CRS}{WGS 84} +\item{Features}{23 x 8} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('scallop_strata') +} +\description{ +An \code{sf} object containing spatial data for the Sea Scallop Survey. The current (as of 2025) NEFSC Scallop Strata (SAMS). Starting in 2025, a spatially balanced form of stratified random sampling called \if{html}{\out{}}Generalized Random Tessellation Stratified (GRTS) was implemented, along with a switch to using Scallop Area Management Simulator (SAMS)\if{html}{\out{}} areas as survey strata. While still a form of stratified random sampling, this method prevents random stations from being placed very close together. Use of the SAMS areas as strata ensures that sampling is more useful to management.\if{html}{\out{

}} +} +\examples{ +\dontrun{ +# Load the dataset +data(scallop_strata) + +# Plot the geometry +plot(sf::st_geometry(scallop_strata)) +} +} +\keyword{{datasets}} diff --git a/man/scallop_strata_historic.Rd b/man/scallop_strata_historic.Rd new file mode 100644 index 0000000..404be23 --- /dev/null +++ b/man/scallop_strata_historic.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-scallop_strata_historic.R +\docType{data} +\name{scallop_strata_historic} +\alias{scallop_strata_historic} +\title{Sea Scallop Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -76 ymin: 35.5 xmax: -65.9 ymax: 42.2} +\item{Projected CRS}{WGS 84} +\item{Features}{97 x 13} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('scallop_strata_historic') +} +\description{ +An \code{sf} object containing spatial data for the Sea Scallop Survey. The historic (pre-2025) NEFSC Shellfish Strata. The standardized scallop dredge survey has been conducted since 1975 (annually since 1977) and employs a stratified random sampling design. The original NEFSC Shellfish Strata were based primarily on depth and secondarily by latitude, and locations of sampling stations were randomly selected within each stratum prior to each annual cruise. +} +\examples{ +\dontrun{ +# Load the dataset +data(scallop_strata_historic) + +# Plot the geometry +plot(sf::st_geometry(scallop_strata_historic)) +} +} +\keyword{{datasets}} diff --git a/man/seal_stations.Rd b/man/seal_stations.Rd new file mode 100644 index 0000000..b517d68 --- /dev/null +++ b/man/seal_stations.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-seal_stations.R +\docType{data} +\name{seal_stations} +\alias{seal_stations} +\title{Seal Aerial Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POINT} +\item{Dimension}{NA} +\item{Bounding box}{xmin: -70.9 ymin: 41.3 xmax: -67 ymax: 44.9} +\item{Projected CRS}{WGS 84} +\item{Features}{1026 x 14} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('seal_stations') +} +\description{ +An \code{sf} object containing spatial data for the Seal Aerial Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(seal_stations) + +# Plot the geometry +plot(sf::st_geometry(seal_stations)) +} +} +\keyword{{datasets}} diff --git a/man/turtle_strata.Rd b/man/turtle_strata.Rd new file mode 100644 index 0000000..19e57e4 --- /dev/null +++ b/man/turtle_strata.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data-turtle_strata.R +\docType{data} +\name{turtle_strata} +\alias{turtle_strata} +\title{Turtle Ecology Survey} +\format{ +An \code{sf} object: +\describe{ +\item{Geometry type}{POLYGON} +\item{Dimension}{XY} +\item{Bounding box}{xmin: -82.1 ymin: 24.2 xmax: -61.8 ymax: 45.2} +\item{Projected CRS}{WGS 84} +\item{Features}{1 x 5} +\item{Metadata}{See source} +} +} +\source{ +{https://mdeb-nefsc-noaa.hub.arcgis.com/} +} +\usage{ +data('turtle_strata') +} +\description{ +An \code{sf} object containing spatial data for the Turtle Ecology Survey. +} +\examples{ +\dontrun{ +# Load the dataset +data(turtle_strata) + +# Plot the geometry +plot(sf::st_geometry(turtle_strata)) +} +} +\keyword{{datasets}} diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index 7bbcfc1..0a008df 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -1,4 +1,11 @@ url: https://nefsc.github.io/NEFSC-Spatial/ + +template: + bootstrap: 3 + +deploy: + install_metadata: true + navbar: structure: left: @@ -7,7 +14,6 @@ navbar: - reference - issue - articles - - map right: - search - github @@ -15,6 +21,7 @@ navbar: home: icon: fas fa-home fa-lg href: index.html + aria-label: Home getting started: text: Getting Started icon: fas fa-solid fa-play @@ -31,48 +38,10 @@ navbar: text: Articles icon: fas fa-file-contract fa-lg menu: - - text: Contributing to Package - href: articles/ContributeSpatialData.html + - text: MDEB datasets + href: articles/mdeb_datasets.html - text: Team Members href: articles/teamMembers.html - map: - text: Maps - icon: fas fa-map fa-lg - menu: - - text: BTS_Strata - href: articles/BTS_Strata_leaflet.html - - text: EcoMon_Strata - href: articles/EcoMon_Strata_leaflet.html - - text: epu_sf - href: articles/epu_sf_leaflet.html - - text: final_mass_inshore_stat - href: articles/final_mass_inshore_stat_leaflet.html - - text: GillnetClosureAreas_20211021 - href: articles/GillnetClosureAreas_20211021_leaflet.html - - text: Great_South_Channel_Restricted_Trap_Pot_Area - href: articles/Great_South_Channel_Restricted_Trap_Pot_Area_leaflet.html - - text: Herring_Management_Areas - href: articles/Herring_Management_Areas_leaflet.html - - text: LMA1_Restricted_Area_FR - href: articles/LMA1_Restricted_Area_FR_leaflet.html - - text: NAFO_Divisions_2021_line_enclosed - href: articles/NAFO_Divisions_2021_line_enclosed_leaflet.html - - text: NAFO_Divisions_2021_line_not_enclosed - href: articles/NAFO_Divisions_2021_line_not_enclosed_leaflet.html - - text: NAFO_Divisions_2021_poly_not_clipped - href: articles/NAFO_Divisions_2021_poly_not_clipped_leaflet.html - - text: NAFO_Divisions_2021_poly_clipped - href: articles/NAFO_Divisions_2021_poly_clipped_leaflet.html - - text: Neus_atlantis - href: articles/Neus_atlantis_leaflet.html - - text: Shellfish_Strata - href: articles/Shellfish_Strata_leaflet.html - - text: Statistical_Areas_2010 - href: articles/Statistical_Areas_2010_leaflet.html - - text: Statistical_Areas_2010_withNames - href: articles/Statistical_Areas_2010_withNames_leaflet.html - - text: Shrimp_Strata - href: articles/Shrimp_Strata_leaflet.html reference: - title: Fishing Areas / Management Areas desc: Areas in which fishing is reported @@ -85,24 +54,32 @@ reference: - title: Closed Areas desc: Areas in which fishing is restricted - contents: - - GillnetClosureAreas_20211021 - - LMA1_Restricted_Area_FR - - Great_South_Channel_Restricted_Trap_Pot_Area + - "GillnetClosureAreas_20211021" + - "LMA1_Restricted_Area_FR" + - "Great_South_Channel_Restricted_Trap_Pot_Area" + - "Scallop_Rotational_Areas_20230411" - title: Protected Species - contents: amapps_grid - title: Survey Strata desc: Areas in which survey sampling is reported - contents: - - BTS_Strata - - EcoMon_Strata - - Shellfish_Strata - - Shrimp_Strata + - "BTS_Strata" + - "EcoMon_Strata" + - "Shellfish_Strata" + - "Shrimp_Strata" + - contains("strata") + - ends_with("stations") + - ends_with("deployments") + - ends_with("lines") - title: Models desc: Areas defining model boundaries -- contents: Neus_atlantis +- contents: + - "Neus_atlantis" + + authors: Andy Beet: - href: https://github.com/andybeet + href: https://andybeet.com Kimberly Bastille: href: https://github.com/kimberly-bastille Joshua Hatch: diff --git a/pkgdown/favicon/apple-touch-icon.png b/pkgdown/favicon/apple-touch-icon.png index 255947b..a989060 100644 Binary files a/pkgdown/favicon/apple-touch-icon.png and 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mode 100644 index a11904d..0000000 Binary files a/pkgdown/leaflet_maps/epu_sf_leaflet.rds and /dev/null differ diff --git a/pkgdown/leaflet_maps/final_mass_inshore_stat_leaflet.rds b/pkgdown/leaflet_maps/final_mass_inshore_stat_leaflet.rds deleted file mode 100644 index a19f990..0000000 Binary files a/pkgdown/leaflet_maps/final_mass_inshore_stat_leaflet.rds and /dev/null differ diff --git a/vignettes/.gitignore b/vignettes/.gitignore index 097b241..fc13111 100644 --- a/vignettes/.gitignore +++ b/vignettes/.gitignore @@ -1,2 +1,3 @@ *.html *.R +articles/test_leaflet.Rmd diff --git a/vignettes/NEFSCspatial.Rmd b/vignettes/NEFSCspatial.Rmd index c603152..29c30d9 100644 --- a/vignettes/NEFSCspatial.Rmd +++ b/vignettes/NEFSCspatial.Rmd @@ -19,14 +19,24 @@ library(sf) library(NEFSCspatial) ``` -The spatial data bundled in this package are in `sf` format. For the data in `sf` format, you can view the fields simply by typing the name of the data set +The spatial data bundled in this package are in `sf` format. For the data in `sf` format, you can view the fields simply by typing the name of the data set. For example, lets look at the [`mass_inshore_strata`](../reference/mass_inshore_strata.html) data set ```{r data_sf} -NEFSCspatial::Shellfish_Strata +NEFSCspatial::mass_inshore_strata +``` + +## The footprint + +```{r plot_geom, fig.alt="Footprint"} +plot(sf::st_geometry(NEFSCspatial::mass_inshore_strata)) +``` + +## Footprint by fields + +To visualize the fields in data simply use the plot function + +```{r plot_sf, fig.alt = "Plot of NEFSCspatial massacusetts inshore survey strata"} +plot(NEFSCspatial::mass_inshore_strata) ``` -To visualize the data simply use the plot function -```{r plot_sf} -plot(NEFSCspatial::Shellfish_Strata) -``` \ No newline at end of file diff --git a/vignettes/articles/BTS_Strata_leaflet.Rmd b/vignettes/articles/BTS_Strata_leaflet.Rmd deleted file mode 100644 index 3ca3d36..0000000 --- a/vignettes/articles/BTS_Strata_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'BTS_Strata' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/BTS_Strata_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/ContributeSpatialData.Rmd b/vignettes/articles/ContributeSpatialData.Rmd deleted file mode 100644 index 255f570..0000000 --- a/vignettes/articles/ContributeSpatialData.Rmd +++ /dev/null @@ -1,58 +0,0 @@ ---- -title: "Contributing Spatial Data" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{Contributing Spatial Data} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} ---- - -```{r, include = FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>" -) -``` - -## Adding spatial data to the package. - -The initial step is to create an [issue](https://github.com/NEFSC/NEFSC-Spatial/issues/new/choose). Select the option "New Data Submission Request". Follow the guidelines in the template. - -All pull requests will be reviewed by a [team member](teamMembers.html) - -### For collaborators - -To process issues flagged as "New Data Submission Request" and add them to the `NEFSCspatial` package you will need to clone the repository, create a branch, then a pull request. - - * Clone the [repo](https://github.com/NEFSC/NEFSC-Spatial) - * Set up a new, version controlled, git project in Rstudio - * Create a new branch (in Rstudio) with the name "data_request_xx" where xx is the issue number - * Use one of the supplied functions in the [`data-raw`](https://github.com/NEFSC/NEFSC-Spatial/tree/main/data-raw) folder to convert the shapefile (.shp) file into the required format. If the spatial data is not a shapefile then you will need to include processing scripts. - * Create documentation for this data set and save it in the `R` folder. Documentation should consist of a single file with the extension `.R` with a file name `data_shapefilename.R`, where `shapefilename` is the name of the `rda` object. - * Include an entry in the `pkgdown/_pkgdown.yml` file under the heading `Spatial data` - * Commit your files - * Create a pull request documenting what you have included - * Link the issue to the pull request under the `Development` section of the pull request - * Assign 2 reviewers to your pull request. These must be [team members](teamMembers.html) - -### For non collaborators - -If you do not have access to contribute to the repository you can either wait for a team memeber to contact you regarding your data request or you can create a pull request. If you choose to create a pull request you will need to `fork` the repository, create a branch, then a pull request. - - * [Fork](https://github.com/NEFSC/NEFSC-Spatial/fork) the repository to your account - * Clone the forked repo - * Set up a new, version controlled, git project in Rstudio - * Create a new branch (in Rstudio) with the name "data_request_xx" where xx is the issue number - * Use one of the supplied [functions](#supplied-functions) in the [`data-raw`](https://github.com/NEFSC/NEFSC-Spatial/tree/main/data-raw) folder to convert your shapefile (.shp) file into the required format. If the spatial data is not a shapefile then you will need to include processing scripts. - * Create documentation for this data set and save it in the `R` folder. Documentation should consist of a single file with the extension `.R` with a file name `data_shapefilename.R`, where `shapefilename` is the name of the `rda` object. - * Include an entry in the `pkgdown/_pkgdown.yml` file under the heading `Spatial data` - * Commit your files - * Create a pull request documenting what you have included - * Link the issue to the pull request under the `Development` section of the pull request - * Assign 2 reviewers to your pull request. These must be [team members](teamMembers.html) - -## Supplied functions - -* create_sf_data_from_shp - To convert a shapefile you have stored locally on your machine to sf -* create_sf_data_from_url - Downloads a zip file from a website (containing shapefile(s)) and converts to sf -* create_sf_data_from_ftp - Downloads shapefile(s) from a public ftp site and converts to sf diff --git a/vignettes/articles/EcoMon_Strata_leaflet.Rmd b/vignettes/articles/EcoMon_Strata_leaflet.Rmd deleted file mode 100644 index a230c4a..0000000 --- a/vignettes/articles/EcoMon_Strata_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'EcoMon_Strata' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/EcoMon_Strata_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/GillnetClosureAreas_20211021_leaflet.Rmd b/vignettes/articles/GillnetClosureAreas_20211021_leaflet.Rmd deleted file mode 100644 index 7af370b..0000000 --- a/vignettes/articles/GillnetClosureAreas_20211021_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'GillnetClosureAreas_20211021' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/GillnetClosureAreas_20211021_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/Great_South_Channel_Restricted_Trap_Pot_Area_leaflet.Rmd b/vignettes/articles/Great_South_Channel_Restricted_Trap_Pot_Area_leaflet.Rmd deleted file mode 100644 index f1f41eb..0000000 --- a/vignettes/articles/Great_South_Channel_Restricted_Trap_Pot_Area_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'Great_South_Channel_Restricted_Trap_Pot_Area' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/Great_South_Channel_Restricted_Trap_Pot_Area_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/Herring_Management_Areas_leaflet.Rmd b/vignettes/articles/Herring_Management_Areas_leaflet.Rmd deleted file mode 100644 index b31a2d6..0000000 --- a/vignettes/articles/Herring_Management_Areas_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'Herring_Management_Areas' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/Herring_Management_Areas_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/LMA1_Restricted_Area_FR_leaflet.Rmd b/vignettes/articles/LMA1_Restricted_Area_FR_leaflet.Rmd deleted file mode 100644 index ba8e76d..0000000 --- a/vignettes/articles/LMA1_Restricted_Area_FR_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'LMA1_Restricted_Area_FR' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/LMA1_Restricted_Area_FR_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/NAFO_Divisions_2021_line_enclosed_leaflet.Rmd b/vignettes/articles/NAFO_Divisions_2021_line_enclosed_leaflet.Rmd deleted file mode 100644 index edb45f4..0000000 --- a/vignettes/articles/NAFO_Divisions_2021_line_enclosed_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'NAFO_Divisions_2021_line_enclosed' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/NAFO_Divisions_2021_line_enclosed_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/NAFO_Divisions_2021_line_not_enclosed_leaflet.Rmd b/vignettes/articles/NAFO_Divisions_2021_line_not_enclosed_leaflet.Rmd deleted file mode 100644 index e2cf17f..0000000 --- a/vignettes/articles/NAFO_Divisions_2021_line_not_enclosed_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'NAFO_Divisions_2021_line_not_enclosed' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/NAFO_Divisions_2021_line_not_enclosed_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/NAFO_Divisions_2021_poly_clipped_leaflet.Rmd b/vignettes/articles/NAFO_Divisions_2021_poly_clipped_leaflet.Rmd deleted file mode 100644 index c8ccfaa..0000000 --- a/vignettes/articles/NAFO_Divisions_2021_poly_clipped_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'NAFO_Divisions_2021_poly_clipped' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/NAFO_Divisions_2021_poly_clipped_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` diff --git a/vignettes/articles/NAFO_Divisions_2021_poly_not_clipped_leaflet.Rmd b/vignettes/articles/NAFO_Divisions_2021_poly_not_clipped_leaflet.Rmd deleted file mode 100644 index 29a42c8..0000000 --- a/vignettes/articles/NAFO_Divisions_2021_poly_not_clipped_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'NAFO_Divisions_2021_poly_not_clipped' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/NAFO_Divisions_2021_poly_not_clipped_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/Neus_atlantis_leaflet.Rmd b/vignettes/articles/Neus_atlantis_leaflet.Rmd deleted file mode 100644 index e78436d..0000000 --- a/vignettes/articles/Neus_atlantis_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'Neus_atlantis' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/Neus_atlantis_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/Shellfish_Strata_leaflet.Rmd b/vignettes/articles/Shellfish_Strata_leaflet.Rmd deleted file mode 100644 index e38071e..0000000 --- a/vignettes/articles/Shellfish_Strata_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'Shellfish_Strata' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/Shellfish_Strata_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/Shrimp_Strata_leaflet.Rmd b/vignettes/articles/Shrimp_Strata_leaflet.Rmd deleted file mode 100644 index f03e63d..0000000 --- a/vignettes/articles/Shrimp_Strata_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'Shrimp_Strata' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/Shrimp_Strata_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/Statistical_Areas_2010_leaflet.Rmd b/vignettes/articles/Statistical_Areas_2010_leaflet.Rmd deleted file mode 100644 index 06df418..0000000 --- a/vignettes/articles/Statistical_Areas_2010_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'Statistical_Areas_2010' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/Statistical_Areas_2010_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` diff --git a/vignettes/articles/Statistical_Areas_2010_withNames_leaflet.Rmd b/vignettes/articles/Statistical_Areas_2010_withNames_leaflet.Rmd deleted file mode 100644 index 1639c26..0000000 --- a/vignettes/articles/Statistical_Areas_2010_withNames_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'Statistical_Areas_2010_withNames' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/Statistical_Areas_2010_withNames_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` diff --git a/vignettes/articles/epu_sf_leaflet.Rmd b/vignettes/articles/epu_sf_leaflet.Rmd deleted file mode 100644 index e1c84bd..0000000 --- a/vignettes/articles/epu_sf_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'epu_sf' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/epu_sf_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/final_mass_inshore_stat_leaflet.Rmd b/vignettes/articles/final_mass_inshore_stat_leaflet.Rmd deleted file mode 100644 index 24d5548..0000000 --- a/vignettes/articles/final_mass_inshore_stat_leaflet.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: 'final_mass_inshore_stat' -output: html_document ---- - -```{r, echo = FALSE, warning = FALSE} -library(leaflet) -m <- readRDS(here::here('pkgdown/leaflet_maps/final_mass_inshore_stat_leaflet.rds')) -``` - -```{r, echo = FALSE} -m -``` \ No newline at end of file diff --git a/vignettes/articles/teamMembers.Rmd b/vignettes/articles/teamMembers.Rmd deleted file mode 100644 index d98dcac..0000000 --- a/vignettes/articles/teamMembers.Rmd +++ /dev/null @@ -1,16 +0,0 @@ ---- -title: "Team Members" -output: html_document ---- - -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` - -# Team members (in alphabetical order) - -|Avatar|Username|Division|Branch| -|---|---|---|---| -| | [kimberly-bastille](https://github.com/kimberly-bastille) | READ | SSB | -| | [andybeet](https://github.com/andybeet) | READ | EDAB | -| | [jmhatch](https://github.com/jmhatch) | PEMAD | OWEB | diff --git a/vignettes/mdeb_datasets.Rmd b/vignettes/mdeb_datasets.Rmd new file mode 100644 index 0000000..1c3eada --- /dev/null +++ b/vignettes/mdeb_datasets.Rmd @@ -0,0 +1,78 @@ +--- +title: "MDEB datasets" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{MDEB datasets} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +```{r setup, echo = FALSE} +library(NEFSCspatial) +``` + +The Northeast Fisheries Science Center Marine Development [GIS Data Hub](https://mdeb-nefsc-noaa.hub.arcgis.com/) created by the Marine Development and Ecology Branch (MDEB) host many spatial datasets. The `NEFSCspatial` package provides access to these datasets and serves them up as `sf` objects. + +A current list of all data sets included in the package: + +```{r finddatasets, eval = TRUE, echo = FALSE} +# url of the MDEB GIS Data Hub search API +mdeb_hub = "https://mdeb-nefsc-noaa.hub.arcgis.com/api/search/v1/collections/all/items" +# scrape json to get all feature services +catalog_items <- mdeb_hub |> + jsonlite::fromJSON() +# count the number of available services +num_items <- catalog_items$numberMatched +# pull all feature service items (API default = 10) +catalog_items_v2 <- paste0(mdeb_hub, "?limit=", num_items) |> + jsonlite::fromJSON() +# extract metadata properties +available_datasets <- catalog_items_v2$features$properties |> + dplyr::filter(grepl("FeatureServer", url)) |> + dplyr::select(title, url) +# format metadata for each feature service as json +available_dataset_layers <- available_datasets |> + dplyr::mutate(layerurl = paste0(url, "?f=pjson")) +# create a new data frame to store the results +dataset_metadata <- NULL +# find if there are multiple feature layers per service +for (idataset in 1:nrow(available_dataset_layers)) { + dataset_url <- available_dataset_layers[idataset, ] + dataset_json_url <- dataset_url$layerurl + # request the json format for the metadata + wp <- dataset_json_url |> + jsonlite::fromJSON() + # create tibble for output + av = wp$layers |> + dplyr::mutate(dataset_url) |> + dplyr::mutate(url = paste0(url, '/', id)) |> + dplyr::select(title, name, id, url) |> + dplyr::as_tibble() + dataset_metadata <- dplyr::bind_rows(dataset_metadata, av) +} + + +dataset_metadata |> + dplyr::select(-url) |> + dplyr::mutate(dataset_name = tolower(gsub("SMIT_", "", dataset_metadata$name))) |> + dplyr::select(title, dataset_name) |> + gt::gt() + +``` + + +We can then plot any attribute, for example the "SUBSTRATA" attribute of the `gombll_substrata` dataset: + +```{r plotecomon, eval = TRUE, echo = TRUE, fig.alt="Gulf of Maine Bottom Longline Survey substrata plot"} +gombll_substrata |> + ggplot2::ggplot() + + ggplot2::geom_sf(ggplot2::aes(fill = SUBSTRATA)) + +``` diff --git a/vignettes/teamMembers.Rmd b/vignettes/teamMembers.Rmd new file mode 100644 index 0000000..bcb305e --- /dev/null +++ b/vignettes/teamMembers.Rmd @@ -0,0 +1,20 @@ +--- +title: "Team Members" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Team Members} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +# Team members (in alphabetical order) + +|Avatar|Username|Division|Branch| +|---|---|---|---| +| Kimberly Bastille | [kimberly-bastille](https://github.com/kimberly-bastille) | READ | SSB | +| Andy Beet| [andybeet](https://github.com/andybeet) | READ | EDAB | +| Joshua Hatch | [jmhatch](https://github.com/jmhatch) | PEMAD | OWEB |