Catch lottery stox4

.Rbuildignore

@@ -1,8 +1,8 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
-^appveyor\.yml$
 ^\.github
 ^LICENSE$
 ^doc$
+^docs$
+^pkgdown$
 ^Meta$

.github/workflows/check-full.yaml

@@ -27,17 +27,17 @@ jobs:
 
           - {os: macOS-latest,   r: 'next', pkgext: '.tgz'} # will be tested without suggests
           - {os: macOS-latest,   r: '4.3', pkgext: '.tgz'} # will be tested without suggests
-          - {os: macOS-latest,   r: '4.2', pkgext: '.tgz'} # will be tested without suggests
+          - {os: macOS-latest,   r: '4.4', pkgext: '.tgz'} # will be tested without suggests
 
           - {os: windows-latest, r: 'next', pkgext: '.zip'} 
           - {os: windows-latest, r: '4.3', pkgext: '.zip'}
-          - {os: windows-latest, r: '4.2', pkgext: '.zip'}
+          - {os: windows-latest, r: '4.4', pkgext: '.zip'}
 
 
           - {os: ubuntu-latest,  r: 'next', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
           - {os: ubuntu-22.04,   r: '4.3',  pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
-          # 4.2 is pushed to drat repo on merge to master for ubunutu (except pre-release builds), update script if 4.2 is taken out
-          - {os: ubuntu-22.04,   r: '4.2',  pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
+          # 4.4 is pushed to drat repo on merge to master for ubunutu (except pre-release builds), update script if 4.4 is taken out
+          - {os: ubuntu-22.04,   r: '4.4',  pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -98,7 +98,7 @@ jobs:
           while read -r cmd
           do
             eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "22.04"))')
 
       - name: Install MacOS system dependencies
         if: runner.os == 'macOS'
@@ -224,7 +224,7 @@ jobs:
           path: check
 
       - name: Build package source archive from branches develop, testing and master
-        if: runner.os == 'Linux' && matrix.config.r == '4.2' && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop')
+        if: runner.os == 'Linux' && matrix.config.r == '4.4' && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop')
         run: |
           pkgbuild::build(".", dest_path = ".", binary = FALSE)
           system(paste0("PKG_FREL=", Sys.getenv("PKG_FILE"), " >> ", Sys.getenv("GITHUB_ENV")))
@@ -243,7 +243,7 @@ jobs:
 
     ## 5a. Upload to the official (DRAT) repo, but only from the master branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config:
       - name: Upload to the official (DRAT) repo
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.2') ) && github.event_name == 'push' && github.ref_name == 'master'
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.4') ) && github.event_name == 'push' && github.ref_name == 'master'
         env:
           BUILD_NUMBER: ${{ github.sha  }}
           DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }}
@@ -253,7 +253,7 @@ jobs:
 
       ## 5b. Upload to the (DRAT) testingRepo, but only from the testing branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config:
       - name: Upload to the testing (DRAT) repo
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.2') ) && github.event_name == 'push' && github.ref_name == 'testing'
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.4') ) && github.event_name == 'push' && github.ref_name == 'testing'
         env:
           BUILD_NUMBER: ${{ github.sha  }}
           DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }}
@@ -263,7 +263,7 @@ jobs:
 
       ## 5c. Upload to the (DRAT) unstableRepo, but only from the develop branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config:
       - name: Upload to the unstable (DRAT) repo
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.2') ) && github.event_name == 'push' && github.ref_name == 'develop'
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.4') ) && github.event_name == 'push' && github.ref_name == 'develop'
         env:
           BUILD_NUMBER: ${{ github.sha  }}
           DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }}
@@ -277,7 +277,7 @@ jobs:
       ###############################
 
       - name: Create release on GitHub and upload files for testing branch
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.2') ) && github.event_name == 'push' && github.ref_name == 'testing'
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.4') ) && github.event_name == 'push' && github.ref_name == 'testing'
         uses: ncipollo/release-action@v1
         with:
           allowUpdates: true
@@ -288,7 +288,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Create release on GitHub and upload files for master branch
-        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.2') ) && github.event_name == 'push' && github.ref_name == 'master'
+        if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.4') ) && github.event_name == 'push' && github.ref_name == 'master'
         uses: ncipollo/release-action@v1
         with:
           allowUpdates: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RstoxFDA
-Version: 1.5.0-9002
-Date: 2024-11-11
+Version: 1.5.0-9003
+Date: 2025-01-24
 Title: Fisheries Dependent Analysis with RstoX
 Authors@R: c(
   person(given = "Edvin", 
@@ -10,7 +10,7 @@ Authors@R: c(
   person(given = "Arne Johannes", 
     family = "Holmin", 
     role = "aut"))
-Depends: R (>= 4.2)
+Depends: R (>= 4.3)
 Description: Fisheries dependent analysis, including running the Estimated Catch at Age
   model through the Reca package developed by the Norwegian Computing Center.
 URL: https://github.com/StoXProject/RstoxFDA
@@ -26,8 +26,8 @@ Imports:
     RColorBrewer (>= 1.1-2),
     rnaturalearth (>= 1.0.1),
     rnaturalearthdata (>= 1.0.0),
-    RstoxBase (>= 2.0.1-9005),
-    RstoxData (>= 2.0.1-9007),
+    RstoxBase (>= 2.1.2-9002),
+    RstoxData (>= 2.1.2-9001),
     sf (>= 1.0.0),
     stats (>= 3.5.0),
     utils (>= 3.5.0)
@@ -38,4 +38,5 @@ Suggests:
     tinytest
 Additional_repositories: 
     https://stoxproject.github.io/repo
+VignetteBuilder: knitr
 RoxygenNote: 7.3.2

NAMESPACE

@@ -3,29 +3,33 @@
 export(AddAreaPositionStoxLanding)
 export(AddGearGroupStoxBiotic)
 export(AddGearGroupStoxLanding)
+export(AddLengthGroupStoxBiotic)
 export(AddPeriodStoxBiotic)
 export(AddPeriodStoxLanding)
+export(AddPsuStratificationVariables)
 export(AddStratumStoxBiotic)
 export(AddStratumStoxLanding)
+export(AggregateAnalyticalEstimate)
 export(AnalyticalPSUEstimate)
 export(AnalyticalPopulationEstimate)
 export(AnalyticalRatioEstimate)
 export(AssignPSUSamplingParameters)
 export(CollapseStrata)
+export(ComputeIndividualSamplingParameters)
+export(ComputePSUSamplingParameters)
 export(ConvertLengthBiotic)
 export(ConvertWeightBiotic)
 export(DefineAgeErrorMatrix)
 export(DefineAreaPosition)
 export(DefineCarNeighbours)
-export(DefineIndividualSamplingParameters)
 export(DefineLengthConversionParameters)
-export(DefinePSUSamplingParameters)
 export(DefinePeriod)
-export(DefineSamplingHierarchy)
 export(DefineStockSplittingParameters)
 export(DefineWeightConversionFactor)
+export(ExtendAnalyticalSamplingFrameCoverage)
 export(FilterAgeLengthOutliersStoxBiotic)
 export(FilterWeightLengthOutliersStoxBiotic)
+export(InterpolateAnalyticalDomainEstimates)
 export(LiftStrata)
 export(ListBioticDifference)
 export(LoadFdaStratumPolygon)
@@ -41,7 +45,11 @@ export(PlotSamplingOverviewCell)
 export(PlotSamplingVariables)
 export(PrepareRecaEstimate)
 export(ReadLandingFDA)
+export(ReadPSUSamplingParameters)
 export(ReportAnalyticalCatchAtAge)
+export(ReportAnalyticalCatchAtLength)
+export(ReportAnalyticalLengthAtAge)
+export(ReportAnalyticalWeightAtAge)
 export(ReportFdaLandings)
 export(ReportFdaSOP)
 export(ReportFdaSampling)
@@ -116,5 +124,8 @@ export(sourceLogbookColumns)
 export(stoxFunctionAttributes)
 export(tabulateFisheries)
 export(writeSpDataFrameAsWKT)
+import(RstoxBase)
+import(methods)
+import(rnaturalearthdata)
 importFrom(data.table,.SD)
 importFrom(ggplot2,.data)

NEWS.md

@@ -1,3 +1,25 @@
+# 1.5.0-9003
+* Added function to annotate length groups: AddLengthGroupStoxBiotic (#163), and report total catch by age group: ReportAnalyticalCatchAtLength (#150)
+* Added function to report mean of weight and length by age: ReportAnalyticalLengthAtAge, and ReportAnalyticalWeightAtAge (#150).
+* Added function for annotating stratification variables to sampling parameters: AddPsuStratificationVariables (#163)
+* Added function for aggregating estimates over strata: AggregateAnalyticalEstimate (#164)
+* Added option for computing sampling parameters for Proportion Poisson Sampling from data records (option DefinitionMethod='ProportionalPoissonSampling' to ComputePSUSamplingParameters) (#165)
+* Added functions for sampling frame expansion: ExtendAnalyticalSamplingFrameCoverage, and domain interpolation: InterpolateAnalyticalDomainEstimates (#154)
+* AnalyticalRatioEstimate is simplified, and no longer provides the (unreleased) method option. Support for the method "TotalDomainWeight" has been dropped.
+* Changed naming conventions for domains in AnalyticalPopulationEstimateData.
+* Removed the table SampleSummary from the data type AnalyticalPopulationEstimateData.
+* Changed how Stratification variables and Domain variables are matched to landings with AnalyticalRatioEstimate (# 125)
+* Replaced DefinePSUSamplingParameters (processdata) with ComputePSUSamplingParameters (no processdata) and ReadPSUSamplingParameters (no processdata). This change breaks some pre-release projects (v. v1.3-9006). (#127)
+* Replaced DefineIndividualSamplingParameters (processdata) with ComputeIndividualSamplingParameters (no processdata). This change breaks some pre-release projects (v. v1.3-9006).
+* Added documentation for ECA convergence analsysis (#153)
+* Fixed issue with reporting IndividualAge as SamplingVariable in ReportFdaSampling (#146)
+* Fixed issue with running RunRecaModels with temporal resolution 'month' (#144)
+* Fixed issue with plotting with other column variables than 'Area' in PlotFisheriesOverviewSpatial (#147)
+* Fixed naming of age groups in reports from analytical estimates (#145)
+* Fixed documentation for handling NA age groups (#151)
+* Fixed issue with using integer columns in landings as stratification column in ratio estimates (#133)
+* Fixed error message when analytical catch at age reports are attempted without 'IndividualAge' in the domain definition (#126).
+
 # 1.5.0-9002
 * Fixed ordering of age groups in ReportAnalyticalCatchAtAge (#134)
 * Improved Error messages in AnalyticalRatioEstimate (#131)
@@ -26,7 +48,7 @@
 * Changed analytical variance estimator of means to a less conservative one.
 
 # RstoxFDA v1.3-9005
-* Added functions for analytical catch at age estimation (DefinePSUSamplingParameters, DefineIndividualSamplingParameters, AssignPSUSamplingParameters, AnalyticalPSUEstimate, AnalyticalPopulationEstimate, AnalyticalRatioEstimate, ReportAnalyticalCatchAtAge)
+* Added functions for analytical catch at age estimation (DefinePSUSamplingParameters, ComputeIndividualSamplingParameters, AssignPSUSamplingParameters, AnalyticalPSUEstimate, AnalyticalPopulationEstimate, AnalyticalRatioEstimate, ReportAnalyticalCatchAtAge)
 * Converted area code resources from sp SpatialPolygons to sf data.frames, reflecting changes in RstoxBase v 2. Breaks compatibility with RstoxBase < 2.
 * Changed ReadLandingFDA to use ForceUnique as implemented in RstoxData v 2. Breaks compatibility with RstoxData < 2
 * Made definition of coordinates used for appendAreaCodes and DefineAreaPosition stricter (now always centroids)
@@ -60,4 +82,4 @@
 * Fixed json-schema for AgeErrorMatrix (#75)
 
 # RstoxFDA v1.1.0 (2022-11-26)
-* contrary to what version numbers indicate, this was released before v1.1.0-9001.
+* contrary to what version numbers indicate, this was released before v1.1.0-9001.

R/GSAsubAreas-datadoc.R

@@ -21,6 +21,7 @@
 #' 
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #' 
 #'
 #' @examples

R/ICESareas-datadoc.R

@@ -28,6 +28,7 @@
 #' 
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #' 
 #' @seealso \code{\link[RstoxFDA]{ICESsubArea}}, \code{\link[RstoxFDA]{ICESdivision}}, \code{\link[RstoxFDA]{ICESsubDivision}}, and \code{\link[RstoxFDA]{ICESunit}}
 #' for polygon files separating the different levels of ICES areas.

R/ICESdivision-datadoc.R

@@ -16,6 +16,7 @@
 #'
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #'
 #' @examples
 #'  # plot ICES areas

R/ICESrectangles-datadoc.R

@@ -30,6 +30,7 @@
 #'
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #'
 #' @examples
 #'  # plot statistical rectangles in 27.3.a

R/ICESsubArea-datadoc.R

@@ -15,6 +15,7 @@
 #'
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #'
 #' @examples
 #'  # plot ICES areas

R/ICESsubDivision-datadoc.R

@@ -16,6 +16,7 @@
 #'
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #'
 #' @examples
 #'  # plot ICES areas

R/ICESunit-datadoc.R

@@ -16,6 +16,7 @@
 #'
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #'
 #' @examples
 #'  # plot ICES areas

R/NAFOareas-datadoc.R

@@ -20,6 +20,7 @@
 #'
 #' @concept area code polygons
 #' @keywords datasets
+#' @import RstoxBase
 #'
 #' @examples
 #'  # combine NAFO and mainarea and plot