Testing

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RstoxBase
 Version: 2.2.0-9009
-Date: 2026-01-12
+Date: 2026-01-24
 Title: Base StoX Functions
 Authors@R: c(
   person(given = "Arne Johannes", 
@@ -47,7 +47,7 @@ Imports:
     jsonlite (>= 1.6),
     lwgeom (>= 0.2-0),
     maps (>= 0.2-0),
-    RstoxData (>= 2.2.0-9010),
+    RstoxData (>= 2.2.0-9011),
     sf (>= 0.9.0),
     stringi (>= 1.4.0),
     units (>= 0.7),

NAMESPACE

@@ -39,6 +39,7 @@ export(RelativeLengthDistribution)
 export(ReportDensity)
 export(ReportQuantity)
 export(ReportSpeciesCategoryCatch)
+export(ReportStationsAlongTransectDesign)
 export(ReportSuperIndividuals)
 export(ReportTransectDesign)
 export(SpeciesCategoryCatch)

NEWS.md

@@ -1,6 +1,11 @@
 # RstoxBase v2.2.0-9009  (2026-01-12)
+* Added the new function ReportStationsAlongTransectDesign().
+* Fixed bug in PlotTransectDesign() where TrackPointColor did not work.
+* Re-organized arguments of TransectDesign() to have SurveyDistance before SurveyTime, since SurveyDistance has precedence over SurveyTime.
 * Fixed bug in the drop down list of DensityUnit in ReportDensity(), where only the area number density units were shown even when DensityType was "AreaWeightDensity" (by introducing the column variableType in dataTypeUnits).
 * Fixed bug where ReplaceLevel and ReplaceStratumLayerIndividual were not reset in ImputeSuperIndividuals, so that values from a previous such process remained in the output.
+* Removed the argument EqualEffort from TransectDesign(), as this is better accomplished using a common Coverage for all Strata.
+* Fixed bug where Coverage was not calculated.
 
 # RstoxBase v2.2.0-9008  (2025-11-12)
 * Added names to stations in output from WriteStationsAlongTransectDesign() in the form Station_01, Station_02, etc.

R/Data.R

@@ -212,7 +212,7 @@ NULL
 #' General stratum plotting parameters of RstoxBase
 #' 
 #' @param ShowStratumPolygon Logical: If TRUE include the stratumPolygon. in the plot.
-#' @param StratumPolygonColor Character: The color palette to use for the strata. The default ("hue") is the default HUE color used by ggplot2. See the \code{Palettes} section in \code{\link[ggplot2]{scale_fill_brewer}} for a list of options (both Diverging, Qualitative and Sequential color palettes are possible).
+#' @param StratumPolygonColor Character: The color palette to use for the strata. The default ("hue") is the default HUE color used by ggplot2. See the \code{Palettes} section in \code{\link[ggplot2]{scale_fill_brewer}} for a list of options (both Diverging, Qualitative and Sequential color palettes are possible). A color blind firendly palette is "viridis".
 #' @param StratumPolygonBorderColor Character: The single color to use for the polygon borders.
 #' @param StratumPolygonBorderLineWidth Numeric: The line width of the polygon borders.
 #' 
@@ -265,6 +265,7 @@ NULL
 #' @param WriteTransectDesignData The \code{\link{WriteTransectDesignData}} data.
 #' @param PlotTransectDesignData The \code{\link{PlotTransectDesignData}} data.
 #' @param StationsAlongTransectDesignData The \code{\link{StationsAlongTransectDesignData}} data.
+#' @param ReportStationsAlongTransectDesignData The \code{\link{ReportStationsAlongTransectDesignData}} data.
 #' @param WriteStationsAlongTransectDesignData The \code{\link{WriteStationsAlongTransectDesignData}} data.
 #' @param NASCData The \code{\link{NASCData}} data.
 #' @param SumNASCData The \code{\link{SumNASCData}} data.
@@ -635,6 +636,18 @@ NULL
 #' 
 NULL
 
+##################################################
+##################################################
+#' Report stations along transect design
+#' 
+#' The ReportStationsAlongTransectDesignData model data is a table with the columns Stratum, giving the Stratum name, and NumberOfStationssegments, giving the number of stations in each Stratum, contained in the \code{\link{StationsAlongTransectDesignData}}.
+#' 
+#' @seealso This data type is produced by \code{\link{ReportStationsAlongTransectDesign}}. See \code{\link{DataTypes}} for a list of all StoX data types produced by \code{\link{RstoxBase}}.
+#' 
+#' @name ReportStationsAlongTransectDesignData
+#' 
+NULL
+
 ##################################################
 ##################################################
 #' Stations along transect design as GPX 

R/Plot.R

@@ -731,8 +731,7 @@ plot_lon_lat <- function(
             plotspec$data <- trackData
         }
 
-
-
+        # If the color.track.point and size are given as the name of a column in the data, plot color and size as a function of these columns:
         if(length(color.track.point) && color.track.point %in% names(trackData) && length(size) && size %in% names(trackData)) {
             # Fix the stroke to the strokeToPointFactor times the size.max (multiply by 1.5 since this seems to be needed in ggplot2:
             strokeWidth <- 1.5 * size.max * strokeToPointFactor
@@ -744,6 +743,7 @@ plot_lon_lat <- function(
                 stroke = strokeWidth
             )
         }
+        # If only the color.track.point is given as the name of a column in the data, plot color as a function of this column, whereas size is assumed to be a numeric:
         else if(length(color.track.point) && color.track.point %in% names(trackData)) {
             mapping <- ggplot2::aes_string(
                 x = lon_name, 
@@ -752,6 +752,7 @@ plot_lon_lat <- function(
             )
             plotspec$size <- size
         }
+        # If only the size is given as the name of a column in the data, plot size as a function of this column, whereas color.track.point is assumed to be a valid color:
         else if(length(size) && size %in% names(trackData)) {
             # Fix the stroke to the strokeToPointFactor times the size.max (multiply by 1.5 since this seems to be needed in ggplot2:
             strokeWidth <- 1.5 * size.max * strokeToPointFactor
@@ -764,6 +765,7 @@ plot_lon_lat <- function(
 
             plotspec$color <- color.track.point
         }
+        # Otherwise, use the size as a numeric and color.track.point as a valid color:
         else {
             mapping <- ggplot2::aes_string(
                 x = lon_name, 

R/Spatial.R

@@ -524,7 +524,7 @@ getStratumPolygonList <- function(StratumPolygon) {
 #' @details
 #' The area output is given in international square nautical miles. 
 #' 
-#' The \code{AreaMethod} "Accurate" calculates each stratum are using the function \code{\link[sf]{st_area}} with the stratum transformed to Cartesian coordinates using the WGS84 Lambert Azimuthal Equal Area projection with origin at the centroid of the stratum as calculated from the geographical coordinates (longitude, latitude).
+#' The \code{AreaMethod} "Accurate" calculates each stratum using the function \code{\link[sf]{st_area}} with the stratum transformed to Cartesian coordinates using the WGS84 Lambert Azimuthal Equal Area projection with origin at the centroid of the stratum as calculated from the geographical coordinates (longitude, latitude).
 #' 
 #' The \code{AreaMethod} "Simple" is used in StoX 2.7 and earlier versions and kept for backwards compatibility.
 #'