Doc cleanup

DESCRIPTION

@@ -2,8 +2,8 @@ Package: NEFSCspatial
 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("Kimberly", "Bastille", email = "kimberly.bastille@noaa.gov", role = "aut"),
-             person("Joshua", "Hatch", email = "joshua.hatch@noaa.gov", role = "aut"))
+             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 or raster objects for the Northeast Fisheries Science Center
@@ -29,7 +29,7 @@ Suggests:
     hexSticker,
     ggimage,
     dplyr,
-    leaflet,
+    ggplot2,
     jsonlite,
     httr2, 
     gt

R/data-mass_inshore_strata.R

@@ -17,7 +17,7 @@
 #' @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)  }
+#' [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

R/data_GillnetClosureAreas_20211021.R

@@ -1,55 +1,30 @@
 #' 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 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
 #' @name GillnetClosureAreas_20211021
 #' @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

R/data_Great_South_Channel_Restricted_Trap_Pot_Area.R

@@ -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

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{
@@ -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

R/data_LMA1_Restricted_Area_FR.R

@@ -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

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{
@@ -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

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{
@@ -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

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{
@@ -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

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{
@@ -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

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{
@@ -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

R/data_Scallop_Rotational_Areas_20230411.R

@@ -1,25 +1,31 @@
 #' Scallop Restricted Area
 #'
-#' An sf object containing the Scallop Restricted Areas
-#' Specifically Area I, II, Nantucket Lightship North, Nantucket Lightship West, New York Bight, Elephant Trunk
+#' @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 A data frame / sf object (6 x 25)
+#' @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}
-#'   }
+#'  }
 #'
-#'@section Contact:
-#'andrew.beet at noaa.gov
 #'
 #'
 #' @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

R/data_Statistical_Areas_2010.R

@@ -1,9 +1,9 @@
 #' 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}
@@ -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

R/data_Statistical_Areas_2010_withNames.R

@@ -1,10 +1,9 @@
 #' 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}
@@ -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

R/data_epu_sf.R

@@ -1,9 +1,9 @@
 #' 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}
@@ -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

R/data_final_mass_inshore_stat.R

@@ -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

README.md

@@ -1,4 +1,4 @@
-# NEFSCspatial  <img src="man/figures/logo.png" align="right" height="200" />
+# NEFSCspatial  <img src="man/figures/logo.png" align="right" height="200" alt = "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)
@@ -9,7 +9,7 @@ A repository of spatial data (vectors) in simple features [`sf`](https://r-spati
 ### Installation
 
 ``` 
-remotes::install_github("NEFSC/NEFSC-Spatial")
+pak::pak("NEFSC/NEFSC-Spatial")
 ```
 
 ### Legal disclaimer