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Merge pull request #199 from StoXProject/testing
Testing
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Diff for: ‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$
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^\.travis\.yml$
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^appveyor\.yml$
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^\.github
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^LICENSE$
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^doc$
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^docs$
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^pkgdown$
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^Meta$

Diff for: ‎.github/workflows/check-full.yaml

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config:
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# for windows and mac all builds are pushed to drat repo on merge to master (except pre-release builds), except 'next'
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- {os: macOS-latest, r: 'next', pkgext: '.tgz'} # will be tested without suggests
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# - {os: macOS-latest, r: 'next', pkgext: '.tgz'} # will be tested without suggests
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- {os: macOS-latest, r: '4.3', pkgext: '.tgz'} # will be tested without suggests
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- {os: macOS-latest, r: '4.4', pkgext: '.tgz'} # will be tested without suggests
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- {os: windows-latest, r: 'next', pkgext: '.zip'}
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# - {os: windows-latest, r: 'next', pkgext: '.zip'}
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- {os: windows-latest, r: '4.3', pkgext: '.zip'}
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- {os: windows-latest, r: '4.4', pkgext: '.zip'}
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# - {os: ubuntu-latest, r: 'next', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
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# 4.3 is pushed to drat repo on merge to master for ubunutu (except pre-release builds), update script if 4.3 is taken out
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# - {os: ubuntu-latest, r: 'next', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
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- {os: ubuntu-22.04, r: '4.3', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
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# 4.3 is pushed to drat repo on merge to master for ubunutu (except pre-release builds), update script if 4.3 is taken out
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- {os: ubuntu-22.04, r: '4.4', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
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env:
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "22.04"))')
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- name: Install MacOS system dependencies
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if: runner.os == 'macOS'
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run: |
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# gfortran may not exist in a period after a new R minor release:
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gfortranFile='/usr/local/bin/gfortran'
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if [ -f "$gfortranFile" ] ; then
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rm "$gfortranFile"
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fi
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rm '/usr/local/bin/2to3'
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rm '/usr/local/bin/2to3-3.11'
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rm '/usr/local/bin/idle3.11'
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rm '/usr/local/bin/idle3'
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rm '/usr/local/bin/pydoc3'
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rm '/usr/local/bin/python3'
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rm '/usr/local/bin/python3-config'
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rm '/usr/local/bin/pydoc3.11'
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rm '/usr/local/bin/python3.11'
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rm '/usr/local/bin/python3.11-config'
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rm -f '/usr/local/bin/gfortran'
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rm -f '/usr/local/bin/2to3'
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rm -f '/usr/local/bin/2to3-3.11'
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rm -f '/usr/local/bin/idle3'
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rm -f '/usr/local/bin/idle3.11'
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rm -f '/usr/local/bin/pydoc3'
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rm -f '/usr/local/bin/pydoc3.11'
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rm -f '/usr/local/bin/python3'
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rm -f '/usr/local/bin/python3.11'
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rm -f '/usr/local/bin/python3-config'
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rm -f '/usr/local/bin/python3.11-config'
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export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=false # This prevents Homebrew from re-installing R, which will lead to .Platform$pkgType = "source".
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brew install gdal udunits
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brew install gdal
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shell: bash
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- name: Prepare for dependencies on Linux
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if: runner.os == 'Linux'
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run: |
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sudo apt-get install libgdal-dev libproj-dev libgeos-dev libudunits2-dev
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sudo apt-get install -y libgdal-dev libproj-dev libgeos-dev libudunits2-dev
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shell: bash
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- name: Install dependencies on Linux

Diff for: ‎DESCRIPTION

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@@ -1,6 +1,6 @@
11
Package: RstoxFDA
2-
Version: 1.4.0
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Date: 2024-10-25
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Version: 1.6.0
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Date: 2025-03-18
44
Title: Fisheries Dependent Analysis with RstoX
55
Authors@R: c(
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person(given = "Edvin",
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RColorBrewer (>= 1.1-2),
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rnaturalearth (>= 1.0.1),
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rnaturalearthdata (>= 1.0.0),
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RstoxBase (>= 2.1.0),
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RstoxData (>= 2.1.0),
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RstoxBase (>= 2.1.1),
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RstoxData (>= 2.1.1),
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sf (>= 1.0.0),
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stats (>= 3.5.0),
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utils (>= 3.5.0)
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tinytest
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Additional_repositories:
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https://stoxproject.github.io/repo
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VignetteBuilder: knitr
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RoxygenNote: 7.3.2

Diff for: ‎NAMESPACE

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export(AddAreaPositionStoxLanding)
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export(AddGearGroupStoxBiotic)
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export(AddGearGroupStoxLanding)
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export(AddLengthGroupStoxBiotic)
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export(AddPeriodStoxBiotic)
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export(AddPeriodStoxLanding)
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export(AddPsuStratificationVariables)
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export(AddStratumStoxBiotic)
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export(AddStratumStoxLanding)
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export(AggregateAnalyticalEstimate)
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export(AnalyticalPSUEstimate)
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export(AnalyticalPopulationEstimate)
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export(AnalyticalRatioEstimate)
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export(AssignPSUSamplingParameters)
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export(CollapseStrata)
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export(ComputeIndividualSamplingParameters)
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export(ComputePSUSamplingParameters)
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export(ConvertLengthBiotic)
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export(ConvertWeightBiotic)
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export(DefineAgeErrorMatrix)
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export(DefinePeriod)
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export(DefineStockSplittingParameters)
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export(DefineWeightConversionFactor)
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export(ExtendAnalyticalSamplingFrameCoverage)
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export(FilterAgeLengthOutliersStoxBiotic)
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export(FilterWeightLengthOutliersStoxBiotic)
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export(InterpolateAnalyticalDomainEstimates)
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export(LiftStrata)
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export(ListBioticDifference)
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export(LoadFdaStratumPolygon)
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export(ParameterizeRecaModels)
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export(PlotSamplingVariables)
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export(PrepareRecaEstimate)
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export(ReadLandingFDA)
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export(ReadPSUSamplingParameters)
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export(ReportAnalyticalCatchAtAge)
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export(ReportAnalyticalCatchAtLength)
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export(ReportAnalyticalLengthAtAge)
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export(ReportAnalyticalWeightAtAge)
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export(ReportFdaLandings)
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export(ReportFdaSOP)
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export(ReportFdaSampling)
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export(stoxFunctionAttributes)
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export(tabulateFisheries)
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export(writeSpDataFrameAsWKT)
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import(RstoxBase)
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import(methods)
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import(rnaturalearthdata)
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importFrom(data.table,.SD)
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importFrom(ggplot2,.data)

Diff for: ‎NEWS.md

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# RstoxFDA v1.6
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* Fixed issue with plotting with other column variables than 'Area' in PlotFisheriesOverviewSpatial (#147)
3+
* Fixed ordering of age groups in ReportAnalyticalCatchAtAge (#134)
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* Added documentation for ECA convergence analsysis (#153)
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* Added functions for analytical catch at age estimation (ComputePSUSamplingParameters, ComputeIndividualSamplingParameters, AssignPSUSamplingParameters, AnalyticalPSUEstimate, AnalyticalPopulationEstimate, AnalyticalRatioEstimate, ReportAnalyticalCatchAtAge, InterpolateAnalyticalDomainEstimates, ExtendAnalyticalSamplingFrameCoverage, ComputePSUSamplingParameters, AddPsuStratificationVariables, AddLengthGroupStoxBiotic, ReportAnalyticalCatchAtLength, ReportAnalyticalLengthAtAge, ReportAnalyticalWeightAtAge)
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* Converted area code resources from sp SpatialPolygons to sf data.frames, reflecting changes in RstoxBase v 2. Breaks compatibility with RstoxBase < 2.
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* Made definition of coordinates used for appendAreaCodes and DefineAreaPosition stricter (now always centroids)
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* Made appendAreaCodes and DefineAreaPosition look for intersects in mercator projection
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* Changed ReadLandingFDA to use ForceUnique as implemented in RstoxData v 2. Breaks compatibility with RstoxData < 2
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* Changed the signature of mergePolygons to work with sf data.frames rather than sp SpatialPolygons.
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* Changed the definition neighbours in DefineCarNeighbours from polygons touching to polygons within 1 metre distance in mercator projection.
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* Changed areaCodeConversionTable to work with provided area definitions in mercator projection
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# RstoxFDA v1.4
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* Converted area code resources from sp SpatialPolygons to sf data.frames, reflecting changes in RstoxBase v 2. Breaks compatibility with RstoxBase < 2.
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* Changed ReadLandingFDA to use ForceUnique as implemented in RstoxData v 2. Breaks compatibility with RstoxData < 2
@@ -17,6 +31,18 @@
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* Added guidance to vignettes about how to deal with several hauls assigned the same station when the field 'station' is not correctly filled in NMDbiotic.
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* Added workaround so that the non-linear option for lgamodel can be used with with all version of Reca.
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# RstoxFDA v1.3-9002
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* Fixed issue with PlotMeanWeightAtAge and PlotMeanLengthAtAge that would not plot mean values for configurations with no grouping variables
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* Fixed issue where the DefineCarNeighbours would format column headers differently depending on the chosen DefinitionMethods. The column header 'CarValue' is now consistently written in the singular form, which means that output from the DefinitionMethod 'StratumPolygon' has changed, and the json schema for CarNeighbours has changed.
37+
* Fixed the behavior of AddStratumStoxLanding so that it assigns area NA, rather than halting with error, when positions cannot be assigned to an area.
38+
* Fixed the behavior of ReportFdaSampling to count catches as unique hauls (column Haul on StoxBiotic$Haul), rather than stations. Improved documentation for the same function.
39+
* Added checking on the validity of IntervalWidths in report functions that report Reca-credible intervals
40+
* Clarified various warnings and error messages.
41+
* Made provision of area definition optional in PlotArea, so that the function can be used to examine the spatial distribution of data without providing a spatial coding system, or to just make maps without providing either data or area definitions.
42+
* Refactored to get rid of usages of ggplot::aes_string which is soft deprecated by ggplot.
43+
* Added guidance to vignettes about how to deal with several hauls assigned the same station when the field 'station' is not correctly filled in NMDbiotic.
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* Added workaround so that the non-linear option for lgamodel can be used with with all version of Reca.
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# RstoxFDA v1.2.0 (2023-01-24)
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* Bumped version number in order to get latest release in line with semantic versioning
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* Fixed json-schema for AgeErrorMatrix (#75)
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# RstoxFDA v1.1.0 (2022-11-26)
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* contrary to what version numbers indicate, this was released before v1.1.0-9001.
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* contrary to what version numbers indicate, this was released before v1.1.0-9001.

Diff for: ‎R/GSAsubAreas-datadoc.R

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#'
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#' @concept area code polygons
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#' @keywords datasets
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#' @import RstoxBase
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#'
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#'
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#' @examples

Diff for: ‎R/ICESareas-datadoc.R

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#'
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#' @concept area code polygons
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#' @keywords datasets
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#' @import RstoxBase
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#'
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#' @seealso \code{\link[RstoxFDA]{ICESsubArea}}, \code{\link[RstoxFDA]{ICESdivision}}, \code{\link[RstoxFDA]{ICESsubDivision}}, and \code{\link[RstoxFDA]{ICESunit}}
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#' for polygon files separating the different levels of ICES areas.

Diff for: ‎R/ICESdivision-datadoc.R

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#'
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#' @concept area code polygons
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#' @examples
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#' # plot ICES areas

Diff for: ‎R/ICESrectangles-datadoc.R

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#'
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#' @concept area code polygons
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#' @keywords datasets
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#' @import RstoxBase
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#'
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#' @examples
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#' # plot statistical rectangles in 27.3.a

Diff for: ‎R/ICESsubArea-datadoc.R

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#'
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#' @concept area code polygons
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#'
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#' # plot ICES areas

Diff for: ‎R/ICESsubDivision-datadoc.R

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#'
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#' # plot ICES areas

Diff for: ‎R/ICESunit-datadoc.R

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#'
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#' @concept area code polygons
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#' # plot ICES areas

Diff for: ‎R/NAFOareas-datadoc.R

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#'
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#' @concept area code polygons
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#' @keywords datasets
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#' @import RstoxBase
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#'
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#' @examples
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#' # combine NAFO and mainarea and plot

Diff for: ‎R/StoxAnalysisFunctions.R

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@@ -263,6 +263,7 @@ warnMissingLandings <- function(StoxBiotic, StoxLanding, effects){
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#' and \code{\link[RstoxData]{AddToStoxBiotic}} for adding otolith-type to samples for stock-splitting analysis.
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#' @concept StoX-Reca functions
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#' @concept StoX-functions
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#' @import RstoxBase
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#' @export
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#' @md
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PrepareRecaEstimate <- function(StoxBioticData, StoxLandingData, FixedEffects=character(), RandomEffects=character(), UseCarEffect=FALSE, CarEffect=character(), CarNeighbours, UseAgingError=FALSE, AgeErrorMatrix, UseStockSplitting=FALSE, UseStockSplittingError=FALSE, StockSplittingParameters, CellEffect=c("Off", "All"), MinAge=integer(), MaxAge=integer(), MaxLength=numeric(), LengthResolution=numeric(), HatchDay=integer()){
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701702
quarter <- data.table::quarter(StoxLandingData$Landing$CatchDate)
702703
}
703704
else if (TemporalResolution == "Month"){
704-
month <- month(StoxLandingData$Landing$CatchDate)
705+
month <- data.table::month(StoxLandingData$Landing$CatchDate)
705706
}
706707
else if (TemporalResolution == "Day"){
707708
date <- StoxLandingData$Landing$CatchDate

Diff for: ‎R/StoxAnalyticalAnalysisFunctions.R

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