Releases | Open Source Science

https://github.com/afsc-gap-products/akgfmaps - v4.0.8

akgfmaps 4.0.8 (July 9, 2025)

BUG FIX

Remove deprecated include.corners argument from getbaselayers() to align with the DESIGN_YEAR approach adopted in akgfmaps v4 (#163).

- R
Published by sean-rohan-NOAA 8 months ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.7

akgfmaps 4.0.7 (May 27, 2025)

BUG FIX

Refix stratum values for a few AI station grid cells (#158/#30).

FUNCTIONALITY CHANGES

getbaselayers() station.grid output includes STRATUM.
Add AREAID field to surveygrid in afscbottomtrawl_surveys.gpkg.

- R
Published by sean-rohan-NOAA 9 months ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.6

akgfmaps 4.0.6 (May 7, 2025)

Removed overlapping areas from GOA station grid and strata.

- R
Published by sean-rohan-NOAA 10 months ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.5

akgfmaps 4.0.5 (March 27, 2025)

BUG FIX

Fix missing snow crab stratum.

- R
Published by sean-rohan-NOAA 11 months ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.4

akgfmaps 4.0.4 (March 24, 2025)

BUG FIX

Fixed overlapping GOA 2025 survey stratum boundaries that occurred along the edges of NMFS areas and added the updated strata to the built-in data.

- R
Published by sean-rohan-NOAA 11 months ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.3

akgfmaps 4.0.3 (February 14, 2025)

BUG FIX

Fix bug caused by GDAL 3.10.1 not handling transformations for bbox class (issue #145).

FUNCTIONALITY CHANGES

Change latitude and longitude break intervals to use wider spacing.

- R
Published by sean-rohan-NOAA about 1 year ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.2

akgfmaps 4.0.2 (January 22, 2025)

BUG FIX

Fix bug in make2dgrid() that was causing errors for certain combinations of inputs.

FUNCTIONALITY CHANGES

generateregionzip() writes to geopackages instead of shape- files.

- R
Published by sean-rohan-NOAA about 1 year ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.1

akgfmaps 4.0.1 (January 7, 2025)

BUG FIX

Change STATION fields to use GRIDX-GRIDY-STRATUM naming convention.

- R
Published by sean-rohan-NOAA about 1 year ago

https://github.com/afsc-gap-products/akgfmaps - v4.0.0

akgfmaps 4.0.0 (January 3, 2025)

This major update replaces and updates shapefiles from multiple bottom trawl survey regions and adopts standard field naming conventions across regions. This update ensure consistency across survey spatial products but breaks backwards compatibility.

MAJOR CHANGES TO getbaselayers()

The function can retrieve layers for multiple regions at once, e.g.: getbaselayers(select.region = c("ebs", "ai"))
New design.year argument can retrieve layers for a specific survey design, such as the Gulf of Alaska survey design that was used from 1984-2023: getbaselayers(select.region = "goa", design.year = 1984)

If not specified, returns the most recent design.
The use.survey.bathymetry argument in getbaselayers() is now deprecated because they are unnecessary now that EBS bathymetry files have been updated.
A legacy version of the function, getbaselayers_v3(), and associated shapefiles are provided temporarily as a bridge to help with backwards compatibility.
Column names for sf objects returned by the function have changed to match GAP_PRODUCTS and RACEBASE.
- survey.area columns:
  - AREAID: AREAID used in GAP_PRODUCTS for the survey area.
  - SURVEYDEFINITIONID: Survey ID (6 = Chukchi, 47 = GOA, 52 = AI, 78 = EBS Slope, 98 = EBS shelf, 143 = NBS).
  - SURVEY_NAME: Name of the survey as a character vector (e.g., "Aleutian Islands Bottom Trawl Survey")
  - DESIGN_YEAR: Year the design was implemented.
  - AREA_M2: Area in m^2.
  - geometry: simple features WKT geometry
- survey.strata columns:
  - STRATUM: Survey stratum that corresponds with AREAID in GAPPRODUCTS or STRATUM in RACEBASE.
  - SURVEYDEFINITIONID: Same as above.
  - DESIGN_YEAR: Same as above.
  - AREA_M2: Same as above.
  - geometry: Same as above.
- survey.grid columns:
  - SURVEYDEFINITIONID: Same as above.
  - DESIGN_YEAR: Same as above.
  - GRIDID: Corresponds with AIGRIDID or GOA_GRIDID used by GAP.
  - STATION: Corresponds with STATIONID field in RACEBASE and STATION field in GAP_PRODUCTS.
  - AREA_M2: Same as above.
  - geometry: Same as above.

MAJOR CHANGES TO VECTOR GEOMETRY FILES

1) Bottom trawl survey layer field names have been standardized across regions. 2) Bottom trawl survey layers are provided in geopackages (.gpkg) instead of standalone shapefiles. - Groundfish/BTS: - /inst/extdata/afscbottomtrawlsurveys.gpkg - Crab strata: - /inst/extdata/allcrabfromakgfmapsgrid.gpkg 3) INPFC strata for bottom trawl surveys are in /inst/extdata/afscbottomtrawlsurveys.gpkg

- R
Published by sean-rohan-NOAA about 1 year ago

https://github.com/afsc-gap-products/akgfmaps - v3.6.2

akgfmaps 3.6.2 (January 2, 2024)

BUG FIX

Fixed gap in GOA stratum polygon around Samalga Pass to close issue #104.

- R
Published by sean-rohan-NOAA about 1 year ago

https://github.com/afsc-gap-products/akgfmaps - v3.6.1

akgfmaps 3.6.1 (December 20, 2024)

BUG FIX

Correct coordinates for longline survey station 20 by replacing inst/extdata/LLSurveyStations_Active2023.shp with inst/extdata/LonglineStationsActive.shp
Revert EBS shelf stratum shapefile to 2022 version.
Remove land area (STRATUM = 0) from GOA survey area polygon in inst/extdata/goa_area.shp
Remove land area (STRATUM = 0) from AI survey area polygon in inst/extdata/ai_area.shp

- R
Published by sean-rohan-NOAA about 1 year ago

https://github.com/afsc-gap-products/akgfmaps - v3.6.0

akgfmaps 3.6.0 (December 11, 2024)

FUNCTIONALITY CHANGES

rasterizeandmask() no longer supports 'raster' class from the raster package.
Functions that allow set.crs = "auto" now use Alaska Albers Equal Area (EPSG:3338) by default instead of region-specific PROJ4s strings. The change is intended to ensure forward compatibility by using 'standard' coordinate reference systems.

NEW FEATURES

Added new functions to access layers that were included in akmarineareas2 (github.com/MattCallahan-NOAA/akmarineareas2).
- getadfgareas(): Alaska Department of Fish and Game (ADFG) Statistical Areas
- getesrregions(): Alaska Ecosystem Status Report (ESR) regions
- getbsierpregions(): Bering Sea Integrated Ecosystem Research Program (BSIERP) regions

Layers are retrieved from a file Geodatabase (.gdb; inst/extdata/AlaskaMarineManagement_Areas.gdb) provided by Matt Callahan -- thanks, Matt!

Added getcrabstrata() function to retrieve crab stratum layers. Support for Bristol Bay RKC, Pribilof Islands RKC, Pribilof Islands BKC, St. Matthew's BKC, Norton Sound RKC, eastern Bering Sea snow crab, and eastern Bering Sea Tanner crab. Layers provided by Emily Ryznar -- thanks, Emily!
getbaselayers(high.resolution.coast = TRUE) returns high resolution (1:63,360 scale) 2017 Alaska Department of Natural Resources coastline shapefile (https://tinyurl.com/4hvr3psb). The high resolution version is recommended for spatial analyses that require masking. The default option (high.resolution.coast = FALSE) returns a lower resolution coastline that loads faster and is suitable for general mapping/visualization.

IMPROVEMENTS

Removed dplyr and raster removed from imports/dependencies.

BUG FIX

Rename inst/extadata/NMFS Reporting Areas.shp to inst/extadata/NMFSReportingAreas.shp to meet recommended portability standards for R packages.

- R
Published by sean-rohan-NOAA about 1 year ago

https://github.com/afsc-gap-products/akgfmaps - 3.5.4

akgfmaps 3.5.4 (September 23, 2024)

BUG FIX

Fix label formatting issue in makeidwmap() and makeidwstack().

- R
Published by sean-rohan-NOAA over 1 year ago

https://github.com/afsc-gap-products/akgfmaps - 3.5.3

akgfmaps 3.5.3 (May 22, 2024)

BUG FIX

NMFS Statistical Area 659 is now included in the output of getnmfsareas(). It had been erroneously not included in the output.

- R
Published by sean-rohan-NOAA almost 2 years ago

https://github.com/afsc-gap-products/akgfmaps - 3.5.2

akgfmaps 3.5.2 (May 20, 2024)

IMPROVEMENTS

Replace PROJ4 strings with EPSG IDs.

- R
Published by sean-rohan-NOAA almost 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.5.1

akgfmaps 3.5.1 (April 10, 2024)

IMPROVEMENTS

getbaselayers() now accepts an argument to split land polygons into east and west when set.crs is a geographic coordinate system. The default is to split using split.land.at.180 = TRUE. Set this to FALSE when shifting coordinates afterwards.

NEW FEATURES

Added makewkttable(), a function that calculates areas of simple features geometries in km^2, then converts simple features objects to data.frames where well-known text (WKT) strings represent geometries.

- R
Published by sean-rohan-NOAA almost 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.5.0

akgfmaps 3.5.0 (March 19, 2024)

FUNCTIONALITY CHANGES

The 2024 EBS shelf survey will not include corner stations around the Pribilof Islands and St. Matthew. Therefore, getbaselayers() now returns a survey.grid without corner stations for the EBS/SEBS. Users can still access a survey.grid with corner stations by setting include.corners = TRUE in getbaselayers, i.e.:

getbaselayers(include.corners = TRUE)

https://github.com/afsc-gap-products/akgfmaps - v3.4.2

akgfmaps 3.4.2 (January 16, 2024)

BUG FIX

Temporary fix to address functionality change in sf::stmakevalid(). See: https://github.com/r-spatial/sf/issues/2315

- R
Published by sean-rohan-NOAA about 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.4.1

akgfmaps 3.4.1 (December 19, 2023)

FUNCTIONALITY CHANGES

The select.region argument in get_base_layers() no longer accepts "inpfc.goa" or "inpfc.ai". Instead, the function returns an inpfc.stratum layer when select.region is "ai", "ai.east", "ai.west", "ai.central", "goa", "goa.east", or "goa.west".
Added fix.invalid.geom argument to to get_base_layers() that causes the function to run fix_geometry() on sf outputs to correct degenerate geometry and dateline wrapping issues that can arise when spatial operations are performed in certain projections.

- R
Published by sean-rohan-NOAA about 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.4.0

akgfmaps 3.4.0 (December 11, 2023)

FUNCTIONALITY CHANGES

Removed unused NMFSstatareas.shp from inst/extdata. The file had been included for testing purposes.
When Inf is the upper break for set.breaks in makeidwmap() or makeidwstack(), it will be ommitted from the upper break label. For example, if the upper break was '>500-Inf', the label will now read >500.

NEW FEATURES

Added a new generateregionzip() function that creates a zip file with regional shapefiles from the outputs of getbaselayers().

IMPROVEMENTS

Added plot outputs to evalplotbreaks() function to facilitate visual exploration of breaks for mapping.
Added NBS noodle bryozoan (NOODLES) and 2018 EBS yellowfin sole (YFS2018) example data sets for demos.

BUG FIX

Replaced Bering Sea survey grids (bsgrid.shp, bsgridwcorners.shp) with new files that correct a degenerate vertex for cell L-15.
Added temporary fix (stmakevalid()) to fix ring intersections for REP_AREA 630 and 650 polygons.
Fixed non-functional set.crs argument in getinpfcstrata().

- R
Published by sean-rohan-NOAA about 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.3.1

akgfmaps 3.3.1 (November 27, 2023)

BUG FIX

Convert x to a data.frame in makeidwmap() and makeidwstack() to prevent indexing errors when argument to x is a tibble.

- R
Published by sean-rohan-NOAA about 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.3.0

akgfmaps 3.3.0 (October 19, 2023)

NEW FEATURE

Added an includegridcell argument to make2dgrid() that makes the function return columns with the center coordinates (lonplot, latplot) of each grid cell prior to intersecting with the user-provided sf object (passed to obj argument). Centroids for intersected grid polygons are still returned by the function for use in spatial analyses and index production (e.g. VAST, sdmTMB) because they are the center of grid cells after intersecting with stratum shapefiles. The centroid prior to intersection is more useful for plotting gridded data with- out prior transformation.

USAGE - Return coordinates for plotting gridded data using make2dgrid() - Diagram in NEWS

- R
Published by sean-rohan-NOAA over 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.2.0

akgfmaps 3.2.0 (October 6, 2023)

BUG FIX

Replaced Aleutian Islands survey grid shapefile (inst/extdata/ai_grid.shp) with a new version that corrects mislabeled stratum IDs. New shapefile provided by Ned Laman (NOAA/AFSC).
Replaced Aleutian Islands survey area shapefile (inst/extdata/ai_area.shp) with a version that excludes Bowers Ridge.

FUNCTIONALITY CHANGES

Modified getbaselayers() to filters out Aleutian Islands survey.grid cells with STRATUM >= 800 (Bowers Ridge). This change was made because Bowers Ridge stations are not part of the standard survey grid, are not included in stratum area calculations, are not used for index production and have not been sampled by a RACE Aleutian Islands bottom trawl survey since 1986. Bowers Ridge grid cells are still included in the Aleutian Islands survey grid shapefile (/inst/extdata/ai_grid.shp).
getbaselayers() now filters out Aleutian Islands and Gulf of Alaska survey.grid cells with STRATUM=0 (land). STRATUM 0 cells are still included in the survey grid shapefiles for the Aleutian Islands (/inst/extdata/aigrid.shp) and Gulf of Alaska (/inst/extdata/goagrid.shp).

NEW FEATURES

Added key.title.units argument to makeidwmap() that allows users to use their own unit label instead of the default 'CPUE (kg/ha)'. Example usage:
- makeidwmap(key.title.units = 'CPUE (#/ha)')
Added internal .check_region() function to check that user- specified region choices are valid and avoid cryptic error messages.

- R
Published by sean-rohan-NOAA over 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.1.0

NEW FEATURES

Added a getinpfcstrata() function that uses survey stratum shapefiles to create an INPFC stratum sf POLYGON for the goa or ai. The function can be called directly or through the getbaselayers() function. Code examples:
- getbaselayers(select.region = "inpfc.goa")
- getbaselayers(select.region = "inpfc.ai")
- getinpfcstrata(select.region = "goa")
- getinpfcstrata(select.region = "ai")
Added a NMFS statistical area shapefile that can be accessed using a new getnmfsareas() function. The NMFS areas are also accessible using the getbaselayers function. Code examples:
- getbaselayers(select.region = "nmfs")
- getnmfsareas()

- R
Published by sean-rohan-NOAA over 2 years ago

https://github.com/afsc-gap-products/akgfmaps - v3.0.0

akgfmaps 3.0.0 (May 19, 2023)

NEW FEATURES

Added a makeidwstack() function that creates multilayer SpatRaster objects where interpolations are conducted by grouping variables (such as YEAR). Intended to reduce unnecessary run-times and post-hoc manipulation when generating maps for multiple years.

FUNCTIONALITY CHANGES

Removed raster and sp as dependencies and replaced raster functions with terra functions ahead of the 2023 retirement of rgdal and sp. Functions that previously generated RasterLayer and RasterBrick objects (raster package) now produce SpatRaster objects (terra package). Updated vignettes and demos to reflect changes.
To expedite transition away from sp and raster, interp2dgrid() and interp3dgrid() are temporarily removed pending redevelopment.
Restructured imports and dependencies to account for changes since the release of R 4.0.

- R
Published by sean-rohan-NOAA almost 3 years ago

https://github.com/afsc-gap-products/akgfmaps - v2.3.0

Updates: - New option to return extrapolation.grid as an sf or stars object using the extrapolation.grid.type argument in make_idw_map(), where make_idw_map(extrapolation.grid.type = 'stars') returns the extrapolation.grid as a stars object (default), make_idw_map(extrapolation.grid.type = 'sf') returns an sf object containing POLYGON/MULTIPOLYGON geometries that are masked to the survey area extent, and make_idw_map(extrapolation.grid.type = 'sf.simple') returns an sf object containing POLYGON/MULTIPOLYGON geometries that are maxed to the survey area extent and with lines simplified using ms_simplify from the rmapshaper package. - Added reproject_gebco() function to reproject GEBCO bathymetry (netCDF file) to a new raster and calculate slope and aspect rasters from the new bathymetry raster.

- R
Published by sean-rohan-NOAA about 3 years ago

https://github.com/afsc-gap-products/akgfmaps - v2.2.1 - Add EBS slope strata

Add plotting options for EBS Slope subareas 1-6 ("bssa1", "bssa2", etc.).

For example, EBS slope subarea 1 layers and default plot extents can be retrieved using:

get_base_layers(select.region = "bssa1")

- R
Published by sean-rohan-NOAA over 3 years ago

https://github.com/afsc-gap-products/akgfmaps - v2.1.0

Added EBS slope survey area and stratum shapefiles. Stratum shapefiles use stratum codes that match racebase.stratum.
EBS slope layers can be accessed using getbaselayers(select.region = "ebs.slope")

- R
Published by sean-rohan-NOAA over 3 years ago

https://github.com/afsc-gap-products/akgfmaps - v2.0.0

Updates:

Shapefiles moved from /data/ to /inst/extdata/ to follow best practices for R packages.
Change AI and GOA subarea plot boundary method in getbaselayers() to improve boundary delineation.
Replaced Aleutian Islands survey grid shapefile with a file that includes more grid cell data (ai_grid.shp)

- R
Published by sean-rohan-NOAA over 3 years ago

https://github.com/afsc-gap-products/akgfmaps - v1.9.0

Updates: - Fix error in survey grid handling by getbaselayers. Previously, getbaselayers had an argument return.survey.grid that had a default = FALSE. The function was only supposed to return a survey grid when return.survey.grid = TRUE, but it was returning the grid in the default CRS for the shapefile when return.survey.grid = FALSE. The return.survey.grid argument has been removed from the getbaselayers function so the function returns a survey.grid object no matter what. - makeidwmap extrapolation grid now uses the survey.area bounding box to set the extent for the extrapolation grid, replacing hard-coded presets. - The default plot boundary (plot.boundary) returned by makeidwmap is now based on the survey.area bounding box, replacing hard-coded presets.

- R
Published by sean-rohan-NOAA over 3 years ago

https://github.com/afsc-gap-products/akgfmaps - v1.8.0

Changes: - Added a make2dgrid() function to replicate a workflow for producing interpolation grids in ArcMap using fishnet. - Made functions that were designed for a specific project internal functions and moved to utils.R (e.g. interp2dgrid, interp3dgrid, normaltransformation, backtransformnormal.

- R
Published by sean-rohan-NOAA almost 4 years ago