Fixed suggests dependent tests

.github/workflows/check-full.yaml

@@ -182,15 +182,15 @@ jobs:
         shell: Rscript {0}
 
       # turn off testing of suggestions for configurations where Reca is not provided in StoX package repositories
-      - name: Check without suggested dependencies
+      - 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: Check with suggested dependencies
+      - name: Check with suggest-dependencies
         if: runner.os != 'macOS' || (matrix.config.r!= 'next' && matrix.config.r!= '4.3')
         env:
           _R_CHECK_CRAN_INCOMING_: false

.github/workflows/test-coverage.yaml

@@ -2,6 +2,7 @@ on:
   push:
     branches:
       - master
+      - testing
   pull_request:
     branches:
       - testing

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))
+}

inst/tinytest/test-ConvergenceAnalysis.R

@@ -0,0 +1,45 @@
+# ECA tests are only run if Reca is installed.
+if (nchar(system.file(package="Reca"))>0){
+#context("Test StoxReportFunctions: ReportRecaParameterStatistics")
+StoxLandingFile <- system.file("testresources","StoxLandingData.rds", package="RstoxFDA")
+StoxLandingData <- readRDS(StoxLandingFile)
+StoxBioticFile <- system.file("testresources","StoxBioticData.rds", package="RstoxFDA")
+StoxBioticData <- readRDS(StoxBioticFile)
+StoxBioticData$Individual <- StoxBioticData$Individual[StoxBioticData$Individual$IndividualAge<4,]
+StoxBioticData$Haul$Gear <- StoxLandingData$Landing$Gear[c(1:20, 1:20, 1:5)]
+StoxBioticData$Station$Area <- StoxLandingData$Landing$Area[c(1:20, 1:20, 1:5)]
+prep <- RstoxFDA::PrepareRecaEstimate(StoxBioticData, StoxLandingData, FixedEffects = c(), RandomEffects = c("Gear", "Area"), CellEffect = c("All"), MinAge = 2, MaxAge = 3)
+
+fpath1 <- RstoxFDA:::makeTempDirReca("chain1")
+fpath2 <- RstoxFDA:::makeTempDirReca("chain2")
+fpath3 <- RstoxFDA:::makeTempDirReca("chain3")
+
+paramOut1 <- RstoxFDA::ParameterizeRecaModels(prep, 10, 50, 1, ResultDirectory = fpath1)
+paramOut2 <- RstoxFDA::ParameterizeRecaModels(prep, 10, 50, 1, ResultDirectory = fpath2)
+
+paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1)
+paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut2, paramSummary, AppendReport = TRUE)
+expect_true(RstoxFDA::is.ParameterizationSummaryData(paramSummary))
+
+RstoxFDA:::removeTempDirReca(fpath1)
+RstoxFDA:::removeTempDirReca(fpath2)
+RstoxFDA:::removeTempDirReca(fpath3)
+
+convergence <- RstoxFDA::ReportParameterConvergence(paramSummary)
+
+expect_true(RstoxFDA::is.ParameterConvergenceData(convergence))
+expect_true(nrow(convergence$ConvergenceReport) < 433)
+expect_true(nrow(convergence$ConvergenceReport) > 0)
+
+#construct three identical chains, should signal convergence
+paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1)
+paramOut1$GlobalParameters$GlobalParameters$resultdir="B"
+paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1, paramSummary, AppendReport = T)
+paramOut1$GlobalParameters$GlobalParameters$resultdir="C"
+paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1, paramSummary, AppendReport = T)
+
+#context("Check Gelman-Rubin for equal chains")
+convergence <- RstoxFDA::ReportParameterConvergence(paramSummary, Tolerance = 0)
+expect_equal(nrow(convergence$ConvergenceReport), 433)
+expect_true(all(abs(convergence$ConvergenceReport$GelmanRubinR-1)<.1))
+}

inst/tinytest/test-RecaFormatChecks.R

@@ -1,7 +1,7 @@
 # ECA tests are not run for platforms where Reca is not available from StoX repositories.
 # ECA tests are only run if Reca is installed.
 
-if (length(system.file(package="Reca"))>0){
+if (nchar(system.file(package="Reca"))>0){
 
 StoxLandingFile <- system.file("testresources","StoxLandingData.rds", package="RstoxFDA")
 StoxLandingData <- readRDS(StoxLandingFile)

inst/tinytest/test-RecaWrap.R

@@ -1,7 +1,6 @@
-# ECA tests are not run for platforms where Reca is not available from StoX repositories.
 # ECA tests are only run if Reca is installed.
 
-if (length(system.file(package="Reca"))>0){
+if (nchar(system.file(package="Reca"))>0){
 
 fishdata <- data.table::as.data.table(readRDS(system.file(package = "RstoxFDA", "testresources", "fishdata.rda")))
 landings <- data.table::as.data.table(readRDS(system.file(package = "RstoxFDA", "testresources", "landings.rda")))

inst/tinytest/test-StoxAnalysisFunctions.R

@@ -1,7 +1,7 @@
 # Tests StoX analysis functions that interfaces Reca.
 # ECA tests are only run if Reca is installed.
 
-if (length(system.file(package="Reca"))>0){
+if (nchar(system.file(package="Reca"))>0){
   #context("Test ParameterizeRecaModels cache")
   StoxBioticFile <- system.file("testresources","StoxBioticData.rds", package="RstoxFDA")
   StoxBioticData <- readRDS(StoxBioticFile)

inst/tinytest/test-StoxDataTypes.R

@@ -11,5 +11,8 @@ expect_true(RstoxFDA:::is.POSIXct(as.POSIXct(Sys.Date())))
 expect_true(RstoxFDA:::is.RecaPrediction(RstoxFDA::recaPrediction))
 
 #context("Test is.RecaResult")
+# ECA tests are only run if Reca is installed.
+if (nchar(system.file(package="Reca"))>0){
 suppressWarnings(ex<-RstoxFDA::RunRecaEstimate(RstoxFDA::recaDataExample, 100,100))
 expect_true(RstoxFDA:::is.RecaResult(ex))
+}

inst/tinytest/test-StoxReportFunctions.R

@@ -10,50 +10,6 @@ expect_true(!any(is.na(decomp$MeanWeightByAge$SD)))
 expect_true(!any(is.na(decomp$MeanWeightByAge$Low)))
 expect_true(!any(is.na(decomp$MeanWeightByAge$High)))
 
-#context("Test StoxReportFunctions: ReportRecaParameterStatistics")
-StoxLandingFile <- system.file("testresources","StoxLandingData.rds", package="RstoxFDA")
-StoxLandingData <- readRDS(StoxLandingFile)
-StoxBioticFile <- system.file("testresources","StoxBioticData.rds", package="RstoxFDA")
-StoxBioticData <- readRDS(StoxBioticFile)
-StoxBioticData$Individual <- StoxBioticData$Individual[StoxBioticData$Individual$IndividualAge<4,]
-StoxBioticData$Haul$Gear <- StoxLandingData$Landing$Gear[c(1:20, 1:20, 1:5)]
-StoxBioticData$Station$Area <- StoxLandingData$Landing$Area[c(1:20, 1:20, 1:5)]
-prep <- RstoxFDA::PrepareRecaEstimate(StoxBioticData, StoxLandingData, FixedEffects = c(), RandomEffects = c("Gear", "Area"), CellEffect = c("All"), MinAge = 2, MaxAge = 3)
-
-fpath1 <- RstoxFDA:::makeTempDirReca("chain1")
-fpath2 <- RstoxFDA:::makeTempDirReca("chain2")
-fpath3 <- RstoxFDA:::makeTempDirReca("chain3")
-
-paramOut1 <- RstoxFDA::ParameterizeRecaModels(prep, 10, 50, 1, ResultDirectory = fpath1)
-paramOut2 <- RstoxFDA::ParameterizeRecaModels(prep, 10, 50, 1, ResultDirectory = fpath2)
-
-paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1)
-paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut2, paramSummary, AppendReport = TRUE)
-expect_true(RstoxFDA::is.ParameterizationSummaryData(paramSummary))
-
-RstoxFDA:::removeTempDirReca(fpath1)
-RstoxFDA:::removeTempDirReca(fpath2)
-RstoxFDA:::removeTempDirReca(fpath3)
-
-convergence <- RstoxFDA::ReportParameterConvergence(paramSummary)
-
-expect_true(RstoxFDA::is.ParameterConvergenceData(convergence))
-expect_true(nrow(convergence$ConvergenceReport) < 433)
-expect_true(nrow(convergence$ConvergenceReport) > 0)
-
-#construct three identical chains, should signal convergence
-paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1)
-paramOut1$GlobalParameters$GlobalParameters$resultdir="B"
-paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1, paramSummary, AppendReport = T)
-paramOut1$GlobalParameters$GlobalParameters$resultdir="C"
-paramSummary <- RstoxFDA::ReportRecaParameterStatistics(paramOut1, paramSummary, AppendReport = T)
-
-#context("Check Gelman-Rubin for equal chains")
-convergence <- RstoxFDA::ReportParameterConvergence(paramSummary, Tolerance = 0)
-expect_equal(nrow(convergence$ConvergenceReport), 433)
-expect_true(all(abs(convergence$ConvergenceReport$GelmanRubinR-1)<.1))
-
-
 #context("Test StoxReportFunctions: ReportRecaCatchStatistics")
 predictiondatafile <- system.file("testresources","stocksplitpred.rds", package="RstoxFDA")
 catchAtAgeFlat <- readRDS(system.file("testresources", "recaPredictionFlat.rds", package="RstoxFDA"))

inst/tinytest/test-ecaOuputputConversion.R

@@ -1,7 +1,7 @@
 
 # ECA tests are only run if Reca is installed.
 
-if (length(system.file(package="Reca"))>0){
+if (nchar(system.file(package="Reca"))>0){
 
 #context("test-StoxAnalysisFunctions: tests RecaResult conversion")
 ecaResult <- readRDS(system.file("testresources","ecaResult.rds", package="RstoxFDA"))
@@ -72,7 +72,8 @@ prep <- RstoxFDA:::PrepareRecaEstimate(StoxBioticData, StoxLandingData, FixedEff
 fpath <- RstoxFDA:::makeTempDirReca()
 RecaData <- RstoxFDA::convertRecaData(prep, nSamples = 10, burnin = 50, thin=1, resultdir = fpath, delta.age = .001, fitfile = "fit", seed = 42, lgamodel = "log-linear")
 sanitizeRecaInput(RecaData$AgeLength, RecaData$WeightLength, RecaData$Landings, RecaData$GlobalParameters, stage="parameterize")
-est<-Reca::eca.estimate(RecaData$AgeLength, RecaData$WeightLength, RecaData$Landings, RecaData$GlobalParameters)
+
+est<-RstoxFDA:::eca.estimate(RecaData$AgeLength, RecaData$WeightLength, RecaData$Landings, RecaData$GlobalParameters)
 RstoxFDA:::removeTempDirReca(fpath)
 }
 

inst/tinytest/test-lengthGroupCollapse.R

@@ -1,3 +1,7 @@
+# ECA tests are only run if Reca is installed.
+
+if (nchar(system.file(package="Reca"))>0){
+
 StoxLandingFile <- system.file("testresources","StoxLandingData.rds", package="RstoxFDA")
 StoxLandingData <- readRDS(StoxLandingFile)
 
@@ -41,3 +45,5 @@ reportCAALwoLength <- RstoxFDA::ReportRecaCatchAtLengthAndAge(results)
 expect_equal(nrow(reportCAALwLength$NbyLength), 2158)
 expect_equal(nrow(reportCAALwoLength$NbyLength), 26)
 expect_equal(sum(reportCAALwoLength$NbyLength$CatchAtLength), sum(reportCAALwLength$NbyLength$CatchAtLength))
+
+}

tests/testAgainstStoxPrep.R

@@ -7,7 +7,7 @@ library(data.table)
 
 # ECA tests are only run if Reca is installed.
 
-if (length(system.file(package="Reca"))>0){
+if (nchar(system.file(package="Reca"))>0){
 
 
 stoxRobj <- readRDS(system.file(package = "RstoxFDA", "testresources", "oldstoxprepreca"))
@@ -43,4 +43,4 @@ tabStox <- RstoxFDA::makeResultTableRECA(stoxRecaResults$prediction)
 
 #RstoxFDA::plotCatchAtAge(prepRecaResults$prediction, title="RecaPrep results")
 #RstoxFDA::plotCatchAtAge(stoxRecaResults$prediction, title="StoxPrep results")
-}
+}