NEWS

akgfmaps 4.0.1 (January 7, 2025)
----------------------------------------------------------------

BUG FIX

- Change STATION fields to use GRID_X-GRID_Y-STRATUM naming
  convention.


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 get_base_layers()

  - The function can retrieve layers for multiple regions at
    once, e.g.:
        get_base_layers(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:
        get_base_layers(select.region = "goa", design.year = 1984)

    If not specified, returns the most recent design.
  - The use.survey.bathymetry argument in get_base_layers() is now
    deprecated because they are unnecessary now that EBS bathymetry
    files have been updated.
  - A legacy version of the function, get_base_layers_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:
      - AREA_ID: AREA_ID used in GAP_PRODUCTS for the survey
        area.
      - SURVEY_DEFINITION_ID: 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 AREA_ID
      in GAP_PRODUCTS or STRATUM in RACEBASE.
      - SURVEY_DEFINITION_ID: Same as above.
      - DESIGN_YEAR: Same as above.
      - AREA_M2: Same as above.
      - geometry: Same as above.
    - survey.grid columns:
      - SURVEY_DEFINITION_ID: Same as above.
      - DESIGN_YEAR: Same as above.
      - GRID_ID: Corresponds with AI_GRIDID 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/afsc_bottom_trawl_surveys.gpkg
      - Crab strata:
        - /inst/extdata/all_crab_from_akgfmaps_grid.gpkg
  3) INPFC strata for bottom trawl surveys are in
      /inst/extdata/afsc_bottom_trawl_surveys.gpkg


akgfmaps 3.6.2 (January 2, 2024)
----------------------------------------------------------------

BUG FIX

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


akgfmaps 3.6.1 (December 20, 2024)
----------------------------------------------------------------

BUG FIX

- Correct coordinates for longline survey station 20 by replacing
  inst/extdata/LL_Survey_Stations_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


akgfmaps 3.6.0 (December 12, 2024)
----------------------------------------------------------------

FUNCTIONALITY CHANGES

- rasterize_and_mask() 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).

  - get_adfg_areas(): Alaska Department of Fish and Game (ADFG)
    Statistical Areas
  - get_esr_regions(): Alaska Ecosystem Status Report (ESR)
    regions
  - get_bsierp_regions(): Bering Sea Integrated Ecosystem
    Research Program (BSIERP) regions

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

- Added get_crab_strata() 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!
- get_base_layers(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/NMFS_Reporting_Areas.shp to meet recommended
  portability standards for R packages.


akgfmaps 3.5.4 (September 23, 2024)
----------------------------------------------------------------

BUG FIX

- Fix label formatting issue in make_idw_map() and
  make_idw_stack().


akgfmaps 3.5.3 (May 22, 2024)
----------------------------------------------------------------

BUG FIX

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


akgfmaps 3.5.2 (May 20, 2024)
----------------------------------------------------------------

IMPROVEMENTS

- Replace PROJ4 strings with EPSG IDs.


akgfmaps 3.5.1 (April 10, 2024)
----------------------------------------------------------------

IMPROVEMENTS

- get_base_layers() 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 make_wkt_table(), 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.


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,
  get_base_layers() 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
  get_base_layers, i.e.:

    get_base_layers(include.corners = TRUE)

  See also:

  DeFilippo, L., Kotwicki, S., Barnett, L., Richar, J., Litzow,
    M.A., Stockhausen, W.T., Palof, K., 2023. Evaluating the
    impacts of reduced sampling density in a systematic
    fisheries- independent survey design. Front. Mar. Sci. 10,
    1–16. https://doi.org/10.3389/fmars.2023.1219283


akgfmaps 3.4.2 (January 16, 2024)
----------------------------------------------------------------

BUG FIX

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


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.

akgfmaps 3.4.0 (December 11, 2023)
----------------------------------------------------------------

FUNCTIONALITY CHANGES

- Removed unused NMFS_stat_areas.shp from inst/extdata. The file
  had been included for testing purposes.
- When Inf is the upper break for set.breaks in make_idw_map()
  or make_idw_stack(), 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 generate_region_zip() function that creates a
  zip file with regional shapefiles from the outputs of
  get_base_layers().

IMPROVEMENTS

- Added plot outputs to eval_plot_breaks() 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 (bs_grid.shp, bs_grid_w_corners.shp)
  with new files that correct a degenerate vertex for cell L-15.
- Added temporary fix (st_make_valid()) to fix ring intersections
  for REP_AREA 630 and 650 polygons.
- Fixed non-functional set.crs argument in get_inpfc_strata().


akgfmaps 3.3.1 (November 27, 2023)
----------------------------------------------------------------

BUG FIX

- Convert x to a data.frame in make_idw_map() and make_idw_stack()
  to prevent indexing errors when argument to x is a tibble.


akgfmaps 3.3.0 (October 19, 2023)
----------------------------------------------------------------

NEW FEATURE

- Added an include_grid_cell argument to make_2d_grid() that
  makes the function return columns with the center coordinates
  (lon_plot, lat_plot) 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.

  EXAMPLE

  Grid cell centroids before intersection (regularly-spaced):

                +-----------+-----------+
                |           |           |
                |           |           |
                |     x     |     x     |
                |           |           |
                |           |           |
                +-----------+-----------+

  Grid cell centroids after intersection (irregularly-spaced;
  useful for analyses that require accurate distances):

                +-----------+-----------+
                |          /|           |
                |    x    / |           |
                |        /  |     x     |
                |       / x |           |
                |      /    |           |
                +-----------+-----------+

  Grid cell centroids for plotting after intersection (still
  regularly-spaced):

                +-----------+-----------+
                |          /|           |
                |         / |           |
                |     X  /  |     x     |
                |       /   |           |
                |      /    |           |
                +-----------+-----------+

  USAGE

  See https://github.com/afsc-gap-products/akgfmaps/blob/main/assets/make_plot_grid.md


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 get_base_layers() 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).

- get_base_layers() 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/ai_grid.shp) and Gulf of
  Alaska (/inst/extdata/goa_grid.shp).


NEW FEATURES

- Added key.title.units argument to make_idw_map() that allows
  users to use their own unit label instead of the default
  'CPUE (kg/ha)'. Example usage:
    - make_idw_map(key.title.units = 'CPUE (#/ha)')

- Added internal .check_region() function to check that user-
  specified region choices are valid and avoid cryptic error
  messages.


akgfmaps 3.1.1 (September 27, 2023)
----------------------------------------------------------------

BUG FIX

Corrected INPFC_STRATUM name returned by get_inpfc_strata()
from 'Southeast' to 'Southeastern'


akgfmaps 3.1.0 (August 31, 2023)
----------------------------------------------------------------

NEW FEATURES

- Added a get_inpfc_strata() 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
  get_base_layers() function. Code examples:
    - get_base_layers(select.region = "inpfc.goa")
    - get_base_layers(select.region = "inpfc.ai")
    - get_inpfc_strata(select.region = "goa")
    - get_inpfc_strata(select.region = "ai")

- Added a NMFS statistical area shapefile that can be accessed
  using a new get_nmfs_areas() function. The NMFS areas are also
  accessible using the get_base_layers function. Code examples:
    - get_base_layers(select.region = "nmfs")
    - get_nmfs_areas()

akgfmaps 3.0.0 (May 19, 2023)
----------------------------------------------------------------

NEW FEATURES

- Added a make_idw_stack() 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,
  interp_2d_grid() and interp_3d_grid() are temporarily
  removed pending redevelopment.

- Restructured imports and dependencies to account for changes
  since the release of R 4.0.



akgfmaps 2.3.0 (December 5, 2022)
----------------------------------------------------------------

NEW FEATURES

- 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.


akgfmaps 2.2.0 (October 27, 2022)
----------------------------------------------------------------

NEW FEATURES

  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")


akgfmaps 2.1.0 (October 19, 2022)
----------------------------------------------------------------

NEW FEATURES

- Added EBS slope survey area and stratum shapefiles. Stratum
  shapefiles use stratum codes that match racebase.stratum.

- EBS slope layers can be accessed using:
  get_base_layers(select.region = "ebs.slope")


akgfmaps 2.0.0 (August 25, 2022)
----------------------------------------------------------------

FUNCTIONALITY CHANGES

- Shapefiles moved from /data/ to /inst/extdata/ to follow best
  practices for R packages.

- Change AI and GOA subarea plot boundary method in get_base_layers()
  to improve boundary delineation.

- Replaced Aleutian Islands survey grid shapefile with a file
  that includes more grid cell data (ai_grid.shp)

akgfmaps 1.9.0 (May 24, 2022)
----------------------------------------------------------------

BUG FIXES

- Fix error in survey grid handling by get_base_layers. Previous-
  ly, get_base_layers() 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 get_base_layers function
  so the function returns a survey.grid object no matter what.

IMPROVEMENTS

- make_idw_map() 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
  make_idw_map() is now based on the survey.area bounding box,
  replacing hard-coded presets.


akgfmaps 1.8.0 (March 16, 2022)
----------------------------------------------------------------


- Added a make_2d_grid() 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. interp_2d_grid,
  interp_3d_grid, normal_transformation, backtransform_normal.


akgfmaps 1.7.4 (November 4, 2021)
----------------------------------------------------------------

BUG FIX

- Fix EBS shelf station Y-01 selection.


akgfmaps 1.7.3 (October 29, 2021)
----------------------------------------------------------------

BUG FIX

- Fix bug where Y-23 was missing from the NBS survey grid.


akgfmaps 1.7.2 (September 29, 2021)
----------------------------------------------------------------

BUG FIX

- Fix EBS shelf stratum retrieval in akgfmaps::get_base_layers()
- Update NBS bounding box for interpolation.


akgfmaps 1.7.0 (September 26, 2021)
----------------------------------------------------------------

BUG FIX

- Fixed incorrect stratum naming for EBS shelf stratum 31.

IMPROVEMENTS

- Removed shapefiles that were only used for the SEBS; updated
  get_base_layers() to account for the change.

- Updated SEBS survey area in ebs_survey_boundary.shp to omit
  boundaries in order to be consistent with old OFIS boundaries.

- Updated survey area calculations in sbs_survey_boundary.shp

- Updated tests to account for changes in survey area calculated
  from pixels after St. Matthew, St. George, St. Paul, Hall
  Island were removed from the survey area.


akgfmaps 1.6.4-1.6.5 (September 24, 2021)
----------------------------------------------------------------

DOCUMENTATION

- Minor tweaks to functions and documentation to provide NBS
  support.


akgfmaps 1.6.3 (September 16, 2021)
----------------------------------------------------------------

BUG FIX

- Fixed NBS land retrieval in get_base_layers()

NEW FEATURES

- Added automatic NBS layer generation to generate_region_guide()


akgfmaps 1.6.2 (September 15, 2021)
----------------------------------------------------------------

- Add NBS CRS and default plotting options to get_base_layers()


akgfmaps 1.6.1 (May 17, 2021)
----------------------------------------------------------------

NEW FEATURES

- Added survey grids for the EBS/NBS shelf, Gulf of Alaska, and
  Aleutian Islands, which can be accessed using
  get_base_layers(return.survey.grid = TRUE).


akgfmaps 1.6.0 (May 13, 2021)
----------------------------------------------------------------

NEW FEATURES

- Added standard shapefiles for plotting for the Aleutian Islands
  and Gulf of Alaska, including subareas (Western, Central, Eastern
  Aleutian Islands; Western and Eastern Gulf of Alaska).

- Set up automatic layer retrieval using the get_base_layers(),
  including defining new automatic default projections for newly
  supported regions.

- New regions for get_base_layers(select.region = [region])
    - "ai": Aleutian Islands
    - "ai.west": Western Aleutian Islands
    - "ai.central": Central Aleutian Islands
    - "ai.east": Eastern Aleutian Islands
    - "goa": Gulf of Alaska
    - "goa.west": Western Gulf of Alaska
    - "goa.east": Eastern Gulf of Alaska


FUNCTIONALITY CHANGES

- Changed default use.survey.bathymetry argument in
  get_base_layers() from FALSE to TRUE
  (i.e., default get_base_layers(use.survey.bathymetry = TRUE)).


akgfmaps 1.5.1 (February 9, 2021)
----------------------------------------------------------------

BUG FIX

- Fixed bug with manual breaks.


akgfmaps 1.5.0 (February 8, 2021)
----------------------------------------------------------------

NEW FEATURES

- Added make_2d_grid() and make_3d_grid() functions for making
  extrpolation grids (2d and 3d)

BUG FIXES

- Fixed labeling bugs for small CPUE

- Updated and repaired vignettes from redesign


akgfmaps 1.4.0 (January 4, 2021)
----------------------------------------------------------------

NEW FEATURES

- Added functions for normal score transformation and back-transformation.


akgfmaps 1.3.0 (October 27, 2020)
----------------------------------------------------------------

BUG FIXES

- Fixed remaining error in make_idw_map vignette after switch
  back to stars following raster/stars PROJ6 update.

- In make_idw_map, changed default option for return.continuous.grid
  to TRUE.


akgfmaps 1.2.0 (July 29, 2020)
----------------------------------------------------------------

NEW FEATURES

- Added option to use EBS stratum bathymetry instead of regional
  bathymetry in make_idw_plot.

FUNCTIONALITY CHANGES

- Undid various workarounds that had been set up to deal with
  inconsistent compatibility with PROJ6 among dependencies.
  All dependencies are now PROJ6 compliant.


akgfmaps 1.1.0 (July 15, 2020)
----------------------------------------------------------------

NEW FEATURES

- Updated make_idw_map() to facilitate use of 'survey' bathymetry
  for inverse distance weighted interpolation maps.

- Added generate_layer_guide() to allow users to produce a pdf
  catalog of layers that are included in the package by default.


akgfmaps 1.0.0 (July 13, 2020)
----------------------------------------------------------------

NEW FEATURES

- Added support for SEBS and NEBS strata (with calculated areas)

- Added support for Chukchi Sea

- Initial support for contiguous Chukchi Sea-Bering Sea mapping.

FUNCTIONALITY CHANGES

- Updated shapefiles to have consistent file naming conventions.


akgfmaps 1.0.0 (June 5, 2020)
----------------------------------------------------------------

BUG FIXES/FUNCTIONALITY CHANGES

- Numerous changes to functions to ensure compliance with
  PROJ6/GDAL3.


akgfmaps 0.4.0 (May 25, 2020)
----------------------------------------------------------------

NEW FEATURES

- Added get_base_layers() function to retrieve and project shape-
  files for EBS and NBS survey regions.


akgfmaps 0.3.0 (March 4, 2020)
----------------------------------------------------------------

- Update documentation to help troubleshoot installation errors.


akgfmaps 0.2.0 (February 25, 2020)
----------------------------------------------------------------

- Basic IDW functions for tech memos and presentations.