Merge pull request #109 from StoXProject/develop

Develop

.github/workflows/check-full.yaml

@@ -26,8 +26,8 @@ jobs:
         # for windows and mac all builds are pushed to drat repo on merge to master (except pre-release builds), except 'next'
 
         # 2023-08-23 fails, not getting Reca. Because it is not built yet for macos and next or 4.3.
-          #- {os: macOS-latest,   r: 'next', pkgext: '.tgz'}
-          #- {os: macOS-latest,   r: '4.3', pkgext: '.tgz'}
+          - {os: macOS-latest,   r: 'next', pkgext: '.tgz'} #tested without Reca
+          - {os: macOS-latest,   r: '4.3', pkgext: '.tgz'} #tested without Reca
           - {os: macOS-latest,   r: '4.2', pkgext: '.tgz'}
           - {os: macOS-latest,   r: '4.1',  pkgext: '.tgz'}
           - {os: macOS-latest,   r: '4.0',     pkgext: '.tgz'}
@@ -181,15 +181,26 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
+      # turn off testing of suggestions for configurations where Reca is not provided in StoX package repositories
+      - name: Check without suggest-dependencies
+        if: runner.os == 'macOS' && (matrix.config.r== 'next' || matrix.config.r== '4.3')
         env:
           _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_ : false
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
-      - name: Show testthat output
+      - name: Check with suggest-dependencies
+        if: runner.os != 'macOS' || (matrix.config.r!= 'next' && matrix.config.r!= '4.3')
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_ : true
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show unit test output
         if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload check results

.github/workflows/test-coverage.yaml

@@ -2,8 +2,10 @@ on:
   push:
     branches:
       - master
+      - testing
   pull_request:
     branches:
+      - testing
       - develop
 
 name: test-coverage

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: RstoxFDA
-Version: 1.3.0-9002
+Version: 1.3.0-9003
 Date: 2023-12-07
 Title: Fisheries Dependent Analysis with RstoX
 Authors@R: c(

R/CatchLotteryExample-datadoc.R

@@ -0,0 +1,23 @@
+#' Data from the Norwegian catch lottery sampling program.
+#'
+#' Example of data formatted as \code{\link[RstoxData]{StoxBioticData}}
+#' Hauls are primary sampling units, selected by Poission sampling with selection probabilities proportional to the catch size.
+#' The data contain North Sea herring samples from catch lottery sampling in 2022.
+#'
+#' @docType data
+#'
+#' @usage data(CatchLotteryExample)
+#'
+#' @format \code{\link[RstoxData]{StoxBioticData}}
+#'
+#' @keywords datasets
+#' @concept Analytical estimation
+#'
+#' @examples
+#'  RstoxFDA::plotArea(RstoxFDA::CatchLotteryExample$Station, 
+#'       areaDef=RstoxFDA::mainareaFdir2018, 
+#'       latCol = "Latitude", 
+#'       lonCol = "Longitude", 
+#'       areaLabels = TRUE)
+"CatchLotteryExample"
+

R/CatchLotterySamplingExample-datadoc.R

@@ -0,0 +1,24 @@
+#' Sampling parameters from the Norwegian catch lottery sampling program.
+#'
+#' Example of data formatted as \code{\link[RstoxFDA]{PSUSamplingParametersData}}
+#' Hauls are primary sampling units, selected by Poission sampling with selection probabilities proportional to the catch size.
+#' The data contain sampling parameters for North Sea herring samples from catch lottery sampling in 2022.
+#' 
+#' The corresponding samples are provided in \code{\link[RstoxFDA]{CatchLotteryExample}}
+#'
+#' @docType data
+#'
+#' @usage data(CatchLotterySamplingExample)
+#'
+#' @format \code{\link[RstoxData]{StoxBioticData}}
+#'
+#' @keywords datasets
+#' @concept Analytical estimation
+#'
+#' @examples
+#'  #all selected PSU that where actuall sampled are provided in CatchLotteryExample
+#'  sum(!is.na(CatchLotterySamplingExample$SelectionTable$SamplingUnitId))
+#'  sum(CatchLotterySamplingExample$SelectionTable$SamplingUnitId %in%
+#'        CatchLotteryExample$Haul$HaulKey)
+"CatchLotterySamplingExample"
+

R/RecaFormatChecks.R

@@ -185,7 +185,6 @@ checkWeightLength<-function(weightlength, landings){
 checkCovariateConsistency <- function(modelobj, landingscov){
   inlandings <- rownames(modelobj$info[modelobj$info[,"in.landings"]==1,])
   if (any(!(inlandings %in% names(landingscov)))){
-    browser()
     stop("some covariates labeled as in.landings are not found in corresponding covariate matrix in landings")
   }
 

R/RecaWrap.R

@@ -1108,3 +1108,9 @@ rEcaDataReport <- function(samples, landings, covariates){
   out <- data.table::as.data.table(out)
   return(out)
 }
+
+#' Runs Reca::eca.estimate. Provided so that tinytest unittest can be implemented in a way that is dependent on Reca being available
+#' @noRd
+eca.estimate <- function(AgeLength, WeightLength, Landings, GlobalParameters){
+  return(Reca::eca.estimate(AgeLength, WeightLength, Landings, GlobalParameters))
+}

R/StoxAnalyticalAnalysisFunctions.R

@@ -0,0 +1,3 @@
+#' @noRd
+PrepareHorvitzThompsonDomainEstimate <- function(){}
+