Merge pull request #364 from StoXProject/develop

Develop
StoXProject · Sep 18, 2024 · f359f8c · f359f8c
2 parents 880987c + e7f91ce
commit f359f8c
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diff --git a/.github/workflows/check-full.yaml b/.github/workflows/check-full.yaml
@@ -32,15 +32,15 @@ jobs:
           # - {os: macOS-latest,   r: '3.6',     pkgext: '.tgz'} # Not used in RstoxFramework
           - {os: windows-latest, r: 'release', pkgext: '.zip'}
           - {os: windows-latest, r: '4.3',     pkgext: '.zip'}
-          - {os: windows-latest, r: '4.2',     pkgext: '.zip'} # Temporarily disabling this due to new sf release not ready for R 4.2
+          # - {os: windows-latest, r: '4.2',     pkgext: '.zip'} # Removed due to sf failing to build
           # - {os: windows-latest, r: '4.1',     pkgext: '.zip'} # Disabled due to stringi failure
           #- {os: windows-latest, r: '4.0',     pkgext: '.zip',    rspm: "https://cloud.r-project.org"} # Too slow
           #- {os: windows-latest, r: '3.6',     pkgext: '.zip',    rspm: "https://cloud.r-project.org"} # Too slow
           - {os: ubuntu-latest,  r: 'release', 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"}
           - {os: ubuntu-22.04,   r: '4.2',     pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
-          - {os: ubuntu-20.04,   r: '4.1',     pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
-          - {os: ubuntu-20.04,   r: '4.0',     pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
+          # - {os: ubuntu-20.04,   r: '4.1',     pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} # Removed due to sf failing to build
+          # - {os: ubuntu-20.04,   r: '4.0',     pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} # Removed due to sf failing to build
           #- {os: ubuntu-20.04,   r: '3.6',     pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
 
     env:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RstoxBase
-Version: 2.0.1-9001
-Date: 2024-09-02
+Version: 2.0.1-9002
+Date: 2024-09-17
 Title: Base StoX Functions
 Authors@R: c(
   person(given = "Arne Johannes", 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# RstoxData v2.0.1-9002  (2024-09-17)
+* Renamed ReportVariable to TargetVariable and ReportVariableUnit to TargetVariableUnit in ReportSpeciesCategoryCatch() for consistency with other report functions.
+* Added TargetVariable and TargetVariableUnit in ReportPreySpeciesCategoryCatch().
+
+
 # RstoxData v2.0.1-9001  (2024-09-01)
 * Added functions PreySpeciesCategoryCatch and ReportPreySpeciesCategoryCatch.
 * Added the ReportFunction "number", "fractionOfOccurrence" and "fractionOfSum".
@@ -36,7 +41,7 @@
 * Added documentation of ReportFunctions.
 * Added the exported getFunctionArgumentHierarchyForSpcificationParameters() used in stoxFunctionAttributes.
 * Fixed report functions number(), fractionOfOccurrence() and fractionOfSum().
-* Fixed bug where IndividualAge was not avaiable as TargetVariable in reports (due to class integer, which was not accounted for).
+* Fixed bug where IndividualAge was not available as TargetVariable in reports (due to class integer, which was not accounted for).
 
 
 # RstoxBase v1.11.4-9007  (2024-04-19)
@@ -167,7 +172,7 @@
 
 
 # RstoxBase v1.10.3 (2022-11-21)
-* Added the parameter TargetVariableUnit in ReportSuperIndividuals() and ReportQuantity(), DensityUnit in ReportDensity(), and ReportVariableUnit in ReportSpeciesCategoryCatch(), which all acn be used to set the units for the report.
+* Added the parameter TargetVariableUnit in ReportSuperIndividuals() and ReportQuantity(), DensityUnit in ReportDensity(), and ReportVariableUnit in ReportSpeciesCategoryCatch(), which all can be used to set the units for the report.
 
 
 # RstoxBase v1.10.2 (2022-10-31)

diff --git a/R/Report.R b/R/Report.R
@@ -643,8 +643,8 @@ getReportFunctionElementByFunctionName <- function(x, element) {
 #' Reports the sum, mean or other functions on a variable of the \code{\link{SpeciesCategoryCatch}}.
 #' 
 #' @inheritParams ModelData
-#' @param ReportVariable The column to report.
-#' @param ReportVariableUnit The unit to use for the \code{ReportVariable}. See RstoxData::StoxUnits for possible units (look for the appropriate quantity, e.g. "length" for IndividualTotalLength, and use the shortname in the \code{ReportVariableUnit}).
+#' @param TargetVariable The column to report.
+#' @param TargetVariableUnit The unit to use for the \code{TargetVariable}. See RstoxData::StoxUnits for possible units (look for the appropriate quantity, e.g. "length" for IndividualTotalLength, and use the shortname in the \code{TargetVariableUnit}).
 #' 
 #' @details This function is useful to, e.g, sum Biomass for each SpeciesCategory and IndividualTotalLenght, or average IndividualTotalLength for each IndiivdualAge and Stratum.
 #' 
@@ -655,12 +655,12 @@ getReportFunctionElementByFunctionName <- function(x, element) {
 #' 
 ReportSpeciesCategoryCatch <- function(
     SpeciesCategoryCatchData, 
-    ReportVariable = c("TotalCatchNumber", "TotalCatchWeight"), 
-    ReportVariableUnit = character()
+    TargetVariable = c("TotalCatchWeight", "TotalCatchNumber"), 
+    TargetVariableUnit = character()
 ){
 
-    # Get the ReportVariable:
-    ReportVariable <- RstoxData::match_arg_informative(ReportVariable)
+    # Get the TargetVariable:
+    TargetVariable <- RstoxData::match_arg_informative(TargetVariable)
 
     # Warning if there are species categories which are empty string:
     categoryVariable <- getDataTypeDefinition(dataType = "DensityData", elements = "categoryVariable", unlist = TRUE)
@@ -669,18 +669,18 @@ ReportSpeciesCategoryCatch <- function(
         warning("StoX: There are empty strings for the ", categoryVariable, ". These will be included in the column V1 in the SpeciesCategoryCatch table.")
     }
 
-    SpeciesCategoryCatchData[[ReportVariable]] <- setUnitRstoxBase(
-        SpeciesCategoryCatchData[[ReportVariable]], 
+    SpeciesCategoryCatchData[[TargetVariable]] <- setUnitRstoxBase(
+        SpeciesCategoryCatchData[[TargetVariable]], 
         dataType =  "SpeciesCategoryCatchData", 
-        variableName = ReportVariable, 
-        unit = ReportVariableUnit
+        variableName = TargetVariable, 
+        unit = TargetVariableUnit
     )
 
     # Create the table with species categories in the columns:
     ReportSpeciesCategoryCatchData <- data.table::dcast(
         SpeciesCategoryCatchData, 
         formula = Haul ~ get(categoryVariable), 
-        value.var = ReportVariable, 
+        value.var = TargetVariable, 
         fun.aggregate = sum
     )
 
@@ -699,8 +699,8 @@ ReportSpeciesCategoryCatch <- function(
         by = "Haul"
     )
 
-    if(RstoxData::hasUnit(SpeciesCategoryCatchData[[ReportVariable]], property = "shortname")) {
-        unit <- RstoxData::getUnit(SpeciesCategoryCatchData[[ReportVariable]], property = "shortname")
+    if(RstoxData::hasUnit(SpeciesCategoryCatchData[[TargetVariable]], property = "shortname")) {
+        unit <- RstoxData::getUnit(SpeciesCategoryCatchData[[TargetVariable]], property = "shortname")
         ReportSpeciesCategoryCatchData <- cbind(ReportSpeciesCategoryCatchData, Unit = unit)
     }
 
@@ -817,7 +817,6 @@ filterTable <- function(table, filter = character()) {
 #' 
 #' @inheritParams ModelData
 #' @inheritParams general_report_arguments
-#' @param TotalPreyCatchWeightUnit The unit to use for the \code{TotalPreyCatchWeight}. Run the following in R for possible units: subset(RstoxData::StoxUnits, quantity == "mass", select = "shortname").
 #' 
 #' @return
 #' A \code{\link{ReportPreySpeciesCategoryCatchData}} object.
@@ -826,8 +825,10 @@ filterTable <- function(table, filter = character()) {
 #' 
 ReportPreySpeciesCategoryCatch <- function(
     PreySpeciesCategoryCatchData, 
-    TotalPreyCatchWeightUnit = character(), 
-    #TargetVariable = character(), 
+    # No longer hard coding this to weight:
+    #TotalPreyCatchWeightUnit = character(), 
+    TargetVariable = c("TotalPreyCatchWeight", "TotalPreyCatchNumber"), 
+    TargetVariableUnit = character(),
     ReportFunction = getReportFunctions(use = "Baseline"), 
     GroupingVariables = character(), 
     InformationVariables = character(), 
@@ -839,8 +840,9 @@ ReportPreySpeciesCategoryCatch <- function(
     FractionOverVariable = character()
 ) 
 {
-    # Only Density is relevant here:
-    TargetVariable <- "TotalPreyCatchWeight"
+    # No longer hard coding this to weight:
+    ## Only Density is relevant here:
+    #TargetVariable <- "TotalPreyCatchWeight"
 
     # Issue a warning if RemoveMissingValues = TRUE:
     if(isTRUE(RemoveMissingValues) && any(is.na(PreySpeciesCategoryCatchData[[TargetVariable]]))) {
@@ -851,7 +853,7 @@ ReportPreySpeciesCategoryCatch <- function(
         PreySpeciesCategoryCatchData[[TargetVariable]], 
         dataType =  "PreySpeciesCategoryCatchData", 
         variableName = TargetVariable, 
-        unit = TotalPreyCatchWeightUnit
+        unit = TargetVariableUnit
     )
 
     output <- aggregateBaselineDataOneTable(

diff --git a/R/Spatial.R b/R/Spatial.R
@@ -806,7 +806,7 @@ polygonArea_accurate <- function(stratumPolygon, useLonLatCentroid = TRUE) {
     # Re-project for equal area projection, using the centroid of the multipolygon:
 
     # rgeos is retiring, so we use sf instead to get the centroid:
-    centroid <- getCentroid(stratumPolygon, iterativeCentroidCalculation = !useLonLatCentroid) 
+    centroid <- getCentroid(stratumPolygon, iterativeCentroidCalculation = !useLonLatCentroid)
 
     #centroid <- rgeos::gCentroid(stratumPolygon)@coords
     laea.CRS <- paste0(

diff --git a/R/backwardCompatibility.R b/R/backwardCompatibility.R
@@ -364,6 +364,13 @@ backwardCompatibility_RstoxBase <- list(
             functionName = "ReportQuantity", 
             modelName = "report", 
             parameterName = "FractionOverVariable"
+        ), 
+        list(
+            changeVersion = "2.0.1-9002", 
+            functionName = "ReportPreySpeciesCategoryCatch", 
+            modelName = "report", 
+            parameterName = "TargetVariable", 
+            parameterValue = "TotalPreyCatchWeight"
         )
     ),  
 
@@ -416,6 +423,27 @@ backwardCompatibility_RstoxBase <- list(
             modelName = "baseline", 
             parameterName = "AbundanceData",
             newParameterName = "QuantityData"
+        ), 
+        list(
+            changeVersion = "2.0.1-9002", 
+            functionName = "ReportSpeciesCategoryCatch", 
+            modelName = "report", 
+            parameterName = "ReportVariable",
+            newParameterName = "TargetVariable"
+        ), 
+        list(
+            changeVersion = "2.0.1-9002", 
+            functionName = "ReportSpeciesCategoryCatch", 
+            modelName = "report", 
+            parameterName = "ReportVariableUnit",
+            newParameterName = "TargetVariableUnit"
+        ), 
+        list(
+            changeVersion = "2.0.1-9002", 
+            functionName = "ReportPreySpeciesCategoryCatch", 
+            modelName = "report", 
+            parameterName = "TotalPreyCatchWeightUnit",
+            newParameterName = "TargetVariableUnit"
         )
     ),  
 

diff --git a/R/stoxFunctionAttributes.R b/R/stoxFunctionAttributes.R
@@ -1343,6 +1343,13 @@ stoxFunctionAttributes <- list(
                 getFunctionArgumentHierarchyForSpcificationParameters(
                     use = "Baseline", 
                     functionName = "ReportFunction"
+                ), 
+                list(
+                    TargetVariableUnit = list(
+                        ReportFunction = function(functionArguments) {
+                            !startsWith(functionArguments$ReportFunction, "fractionOf")
+                        }
+                    )
                 )
             )
         ), 
@@ -1369,6 +1376,13 @@ stoxFunctionAttributes <- list(
                 getFunctionArgumentHierarchyForSpcificationParameters(
                     use = "Baseline", 
                     functionName = "ReportFunction"
+                ), 
+                list(
+                    TargetVariableUnit = list(
+                        ReportFunction = function(functionArguments) {
+                            !startsWith(functionArguments$ReportFunction, "fractionOf")
+                        }
+                    )
                 )
             )
         ), 
@@ -1395,6 +1409,13 @@ stoxFunctionAttributes <- list(
                 getFunctionArgumentHierarchyForSpcificationParameters(
                     use = "Baseline", 
                     functionName = "ReportFunction"
+                ), 
+                list(
+                    DensityUnit = list(
+                        ReportFunction = function(functionArguments) {
+                            !startsWith(functionArguments$ReportFunction, "fractionOf")
+                        }
+                    )
                 )
             )
         ), 
@@ -1408,7 +1429,7 @@ stoxFunctionAttributes <- list(
         functionCategory = "report", 
         functionOutputDataType = "ReportSpeciesCategoryCatchData", 
         functionParameterFormat = list(
-            ReportVariableUnit = "reportVariableUnit_ReportSpeciesCategoryCatch"
+            TargetVariableUnit = "targetVariableUnit_ReportSpeciesCategoryCatch"
         )
     ), 
 
@@ -1431,6 +1452,13 @@ stoxFunctionAttributes <- list(
                 getFunctionArgumentHierarchyForSpcificationParameters(
                     use = "Baseline", 
                     functionName = "ReportFunction"
+                ), 
+                list(
+                    TargetVariableUnit = list(
+                        ReportFunction = function(functionArguments) {
+                            !startsWith(functionArguments$ReportFunction, "fractionOf")
+                        }
+                    )
                 )
             )
         ), 
@@ -2344,14 +2372,14 @@ processPropertyFormats <- list(
 
 
 
-    reportVariableUnit_ReportSpeciesCategoryCatch = list(
+    targetVariableUnit_ReportSpeciesCategoryCatch = list(
         class = "single", 
-        title = "Select unit for the ReportVariable", 
-        possibleValues = function(ReportVariable) {
+        title = "Select unit for the TargetVariable", 
+        possibleValues = function(TargetVariable) {
             dataType <- "SpeciesCategoryCatchData"
-            quantity <- getBaseUnit(dataType = dataType, variableName = ReportVariable, element = "quantity")
+            quantity <- getBaseUnit(dataType = dataType, variableName = TargetVariable, element = "quantity")
             if(!length(quantity) || is.na(quantity)) {
-                warning("StoX: No units defined for the variable ", ReportVariable, " of datatype ", dataType)
+                warning("StoX: No units defined for the variable ", TargetVariable, " of datatype ", dataType)
                 list()
             }
             else {

diff --git a/inst/extdata/functionArguments.rds b/inst/extdata/functionArguments.rds
diff --git a/man/ReportPreySpeciesCategoryCatch.Rd b/man/ReportPreySpeciesCategoryCatch.Rd
diff --git a/man/ReportSpeciesCategoryCatch.Rd b/man/ReportSpeciesCategoryCatch.Rd