Enhance coverage features and fix CRAN compliance issues

DESCRIPTION

@@ -1,4 +1,5 @@
 Package: dssd
+Depends: R (>= 3.6.0)
 Imports:
     sf,
     ggplot2,
@@ -27,7 +28,6 @@ Description: Creates survey designs for distance sampling surveys. These
 BugReports: https://github.com/DistanceDevelopment/dssd/issues
 License: GPL (>=2)
 Encoding: UTF-8
-RoxygenNote: 7.3.2
 Collate: 
     'Class.Constructors.R'
     'Coverage.Grid.R'
@@ -63,3 +63,4 @@ Collate:
     'point.coords.as.dataframe.R'
     'run.coverage.R'
     'write.transects.R'
+Config/roxygen2/version: 8.0.0

R/Class.Constructors.R

@@ -68,7 +68,7 @@ make.region <- function(region.name = "region",
     }
     if(length(strata.name) < length(shape) && length(shape) > 1){
       strata.name <- LETTERS[1:length(shape)]
-      warning("Automatically naming strata as insufficient strata names provided. Assigned strata names:", paste(strata.name, collapse = ", "), call. = F, immediate. = T)
+      warning("Automatically naming strata as insufficient strata names provided. Assigned strata names:", paste(strata.name, collapse = ", "), call. = FALSE)
     }else if(length(strata.name) == 0 && length(shape) == 1){
       strata.name <- region.name
     }else if(length(strata.name) > length(shape)){
@@ -99,7 +99,7 @@ make.region <- function(region.name = "region",
   }else if(strata.count != length(strata.name)){
     if(length(sf.shape) <= 26){
       strata.name <- LETTERS[1:length(sf.shape[[sf.column]])]
-      warning("Automatically naming strata as no (or incorrect number of) strata names provided. Assigned strata names: ", paste(strata.name, collapse = ", "), call. = F, immediate. = T)
+      warning("Automatically naming strata as no (or incorrect number of) strata names provided. Assigned strata names: ", paste(strata.name, collapse = ", "), call. = FALSE)
     }else{
       stop("Too many strata (>26) for strata names to be assigned default names, please provide the correct number of strata names.", call. = FALSE)
     }
@@ -375,7 +375,7 @@ make.design <- function(region = make.region(), transect.type = "line", design =
   }else if(transect.type %in% c("Point", "point", "Point Transect", "point transect")){
     # Check line length not supplied
     if(length(line.length) > 0){
-      warning("Argument line.length not applicable to point transect designs.", immediate. = TRUE, call. = FALSE)
+      warning("Argument line.length not applicable to point transect designs.", call. = FALSE)
     }
     #Create point transect object
     design <- new(Class="Point.Transect.Design", region, truncation, design, spacing, samplers, effort.allocation, design.angle, edge.protocol, coverage.grid)
@@ -423,7 +423,7 @@ make.coverage <- function(region = make.region(),
   }
   if(length(spacing) > 0 && length(n.grid.points) > 0){
     if(n.grid.points != 1000){
-      warning("Both spacing and n.grid.points specified, n.grid.point will be disregarded.", call. = FALSE, immediate. = TRUE)
+      warning("Both spacing and n.grid.points specified, n.grid.point will be disregarded.", call. = FALSE)
     }
     n.grid.points <- numeric(0)
   }

R/Coverage.Grid.R

@@ -70,7 +70,7 @@ setMethod(
       sf.column <- attr(x@grid, "sf_column")
       plot(x@grid[[sf.column]], add = add, col = col, pch = pch)
     }else{
-      warning("No grid points to plot", call. = F, immediate. = F)
+      warning("No grid points to plot", call. = FALSE)
     }
     invisible(x)
   }

R/Line.Transect.Design.R

@@ -233,7 +233,7 @@ gt.LT.fun.body <- function(object, quiet, ...){
   #Need to retain transect IDs as well as strata for lines
   if(length(transects) == 0){
     if(!quiet){
-      warning("No samplers generated.", immediate. = T, call. = FALSE)
+      warning("No samplers generated.", call. = FALSE)
     }
     return(NULL)
   }

R/Line.Transect.R

@@ -91,7 +91,7 @@ setMethod(
       #}
       plot(x@samplers[[sf.column.samps]], add = add, col = col, lwd = lwd)
     }else{
-      warning("No samplers to plot", call. = F, immediate. = F)
+      warning("No samplers to plot", call. = FALSE)
     }
     invisible(x)
   }
@@ -113,45 +113,45 @@ setMethod(
       title <- paste("\n   Strata ", strata.names[strat], ":", sep = "")
       len.title <- nchar(title)
       underline <- paste("   ", paste(rep("_", (len.title-3)), collapse = ""), sep = "")
-      cat(title, fill = T)
-      cat(underline, fill = T)
+      cat(title, fill = TRUE)
+      cat(underline, fill = TRUE)
       design <- switch(object@design[strat],
                        "random" = "randomly located transects",
                        "systematic" = "systematically spaced parallel transects",
                        "eszigzag" = "equal spaced zigzag",
                        "eszigzagcom" = "complementaty equal spaced zigzags",
                        "segmentedgrid" = "segmented grid")
-      cat("Design: ", design, fill = T)
+      cat("Design: ", design, fill = TRUE)
       if(object@design[strat] %in% c("systematic", "eszigzag", "eszigzagcom", "segmentedgrid")){
-        cat("Spacing: ", object@spacing[strat], fill = T)
+        cat("Spacing: ", object@spacing[strat], fill = TRUE)
       }
-      cat("Line length:", object@line.length[strat], fill = T)
+      cat("Line length:", object@line.length[strat], fill = TRUE)
       if(object@design[strat] == "segmentedgrid"){
-        cat("Segment length: ", object@seg.length[strat], fill = T)
-        cat("Segment threshold: ", object@seg.threshold[strat], fill = T)
+        cat("Segment length: ", object@seg.length[strat], fill = TRUE)
+        cat("Segment threshold: ", object@seg.threshold[strat], fill = TRUE)
       }
-      cat("Trackline length:", object@trackline[strat], fill = T)
-      cat("Cyclic trackline length:", object@cyclictrackline[strat], fill = T)
-      cat("Number of samplers: ", object@samp.count[strat], fill = T)
-      cat("Design angle: ", object@design.angle[strat], fill = T)
-      cat("Edge protocol: ", object@edge.protocol[strat], fill = T)
-      cat("Covered area: ", object@cov.area[strat], fill = T)
-      cat("Strata coverage: ", round((object@cov.area[strat]/object@strata.area[strat])*100,2), "%", fill = T, sep = "")
-      cat("Strata area: ", object@strata.area[strat], fill = T)
+      cat("Trackline length:", object@trackline[strat], fill = TRUE)
+      cat("Cyclic trackline length:", object@cyclictrackline[strat], fill = TRUE)
+      cat("Number of samplers: ", object@samp.count[strat], fill = TRUE)
+      cat("Design angle: ", object@design.angle[strat], fill = TRUE)
+      cat("Edge protocol: ", object@edge.protocol[strat], fill = TRUE)
+      cat("Covered area: ", object@cov.area[strat], fill = TRUE)
+      cat("Strata coverage: ", round((object@cov.area[strat]/object@strata.area[strat])*100,2), "%", fill = TRUE, sep = "")
+      cat("Strata area: ", object@strata.area[strat], fill = TRUE)
     }
     #Now print totals
-    cat("\n   Study Area Totals:", fill = T)
-    cat("   _________________", fill = T)
-    cat("Line length:", sum(object@line.length, na.rm = T), fill = T)
-    cat("Trackline length:", sum(object@trackline, na.rm = T), fill = T)
-    cat("Cyclic trackline length:", sum(object@cyclictrackline, na.rm = T), fill = T)
-    cat("Number of samplers: ", sum(object@samp.count, na.rm = T), fill = T)
+    cat("\n   Study Area Totals:", fill = TRUE)
+    cat("   _________________", fill = TRUE)
+    cat("Line length:", sum(object@line.length, na.rm = TRUE), fill = TRUE)
+    cat("Trackline length:", sum(object@trackline, na.rm = TRUE), fill = TRUE)
+    cat("Cyclic trackline length:", sum(object@cyclictrackline, na.rm = TRUE), fill = TRUE)
+    cat("Number of samplers: ", sum(object@samp.count, na.rm = TRUE), fill = TRUE)
     if(length(object@effort.allocation) > 0){
-      cat("Effort allocation: ", paste(object@effort.allocation*100, collapse = "%, "), "%", fill = T, sep = "")
+      cat("Effort allocation: ", paste(object@effort.allocation*100, collapse = "%, "), "%", fill = TRUE, sep = "")
     }
-    cat("Covered area: ", sum(object@cov.area, na.rm = T), fill = T)
+    cat("Covered area: ", sum(object@cov.area, na.rm = TRUE), fill = TRUE)
     index <- which(!is.na(object@cov.area))
-    cat("Average coverage: ", round((sum(object@cov.area[index])/sum(object@strata.area))*100,2), "%", fill = T, sep = "")
+    cat("Average coverage: ", round((sum(object@cov.area[index])/sum(object@strata.area))*100,2), "%", fill = TRUE, sep = "")
     invisible(object)
   }
 )

R/Point.Transect.Design.R

@@ -166,7 +166,7 @@ setMethod(
     }
     if(length(transects) == 0){
       if(!quiet){
-        warning("No samplers generated.", immediate. = T, call. = FALSE)
+        warning("No samplers generated.", call. = FALSE)
       }
       index <- numeric(0)
     }else{

R/Point.Transect.R

@@ -66,7 +66,7 @@ setMethod(
     if(length(x@samplers) > 0){
       plot(x@samplers[[sf.column]], add = add, col = col, pch = pch)
     }else{
-      warning("No samplers to plot", call. = F, immediate. = F)
+      warning("No samplers to plot", call. = FALSE)
     }
     invisible(x)
   }
@@ -87,32 +87,32 @@ setMethod(
       title <- paste("\n   Strata ", strata.names[strat], ":", sep = "")
       len.title <- nchar(title)
       underline <- paste("   ", paste(rep("_", (len.title-3)), collapse = ""), sep = "")
-      cat(title, fill = T)
-      cat(underline, fill = T)
+      cat(title, fill = TRUE)
+      cat(underline, fill = TRUE)
       design <- switch(object@design[strat],
                        "random" = "randomly located transects",
                        "systematic" = "systematically spaced transects")
-      cat("Design: ", design, fill = T)
+      cat("Design: ", design, fill = TRUE)
       if(object@design[strat] == "systematic"){
-        cat("Spacing: ", object@spacing[strat], fill = T)
+        cat("Spacing: ", object@spacing[strat], fill = TRUE)
       }
-      cat("Number of samplers: ", object@samp.count[strat], fill = T)
-      cat("Design angle: ", object@design.angle[strat], fill = T)
-      cat("Edge protocol: ", object@edge.protocol[strat], fill = T)
-      cat("Covered area: ", object@cov.area[strat], fill = T)
-      cat("Strata coverage: ", round((object@cov.area[strat]/object@strata.area[strat])*100,2), "%", fill = T, sep = "")
-      cat("Strata area: ", object@strata.area[strat], fill = T)
+      cat("Number of samplers: ", object@samp.count[strat], fill = TRUE)
+      cat("Design angle: ", object@design.angle[strat], fill = TRUE)
+      cat("Edge protocol: ", object@edge.protocol[strat], fill = TRUE)
+      cat("Covered area: ", object@cov.area[strat], fill = TRUE)
+      cat("Strata coverage: ", round((object@cov.area[strat]/object@strata.area[strat])*100,2), "%", fill = TRUE, sep = "")
+      cat("Strata area: ", object@strata.area[strat], fill = TRUE)
     }
     #Now print totals
-    cat("\n   Study Area Totals:", fill = T)
-    cat("   _________________", fill = T)
-    cat("Number of samplers: ", sum(object@samp.count, na.rm = T), fill = T)
+    cat("\n   Study Area Totals:", fill = TRUE)
+    cat("   _________________", fill = TRUE)
+    cat("Number of samplers: ", sum(object@samp.count, na.rm = TRUE), fill = TRUE)
     if(length(object@effort.allocation) > 0){
-      cat("Effort allocation: ", paste(object@effort.allocation*100, collapse = "%, "), "%", fill = T, sep = "")
+      cat("Effort allocation: ", paste(object@effort.allocation*100, collapse = "%, "), "%", fill = TRUE, sep = "")
     }
-    cat("Covered area: ", sum(object@cov.area, na.rm = T), fill = T)
+    cat("Covered area: ", sum(object@cov.area, na.rm = TRUE), fill = TRUE)
     index <- which(!is.na(object@cov.area))
-    cat("Average coverage: ", round((sum(object@cov.area[index])/sum(object@strata.area))*100,2), "%", fill = T, sep = "")
+    cat("Average coverage: ", round((sum(object@cov.area[index])/sum(object@strata.area))*100,2), "%", fill = TRUE, sep = "")
     invisible(object)
   }
 )

R/Region.R

@@ -50,7 +50,7 @@ setMethod(
       if(!is.na(tmp)){
         if(is.null(tmp$units)){
           units <- units
-          warning("Coordinate reference system detected but no units can be found. Has this shape been projected - shapefiles must be projected on to a flat plane before surveys are designed. dssd is unstable and may generate errors when working with unprojected regions.", call. = FALSE, immediate. = TRUE)
+          warning("Coordinate reference system detected but no units can be found. Has this shape been projected - shapefiles must be projected on to a flat plane before surveys are designed. dssd is unstable and may generate errors when working with unprojected regions.", call. = FALSE)
         }else
           units <- tmp$units
       }else{
@@ -137,7 +137,7 @@ setMethod(
   definition=function(x, y, main = "", region.col = "default", strata = "all", line.col = gray(.2), legend.params = list()){
     # Warn of depreications
     if(length(legend.params) > 0){
-      warning("legend.params argument is deprecated since version 0.2.3", immediate. = TRUE, call. = FALSE)
+      warning("legend.params argument is deprecated since version 0.2.3", call. = FALSE)
     }
     # Tidy up space to keep ggplot happy
     suppressWarnings(invisible(gc()))
@@ -213,7 +213,7 @@ setMethod(
   definition=function(x, y, main = "", region.col = "default", strata = "all", line.col = gray(.2), col = "blue", lwd = 1, covered.area = FALSE, legend.params = list()){
     # Warn of depreications
     if(length(legend.params) > 0){
-      warning("legend.params argument is deprecated since version 0.2.3", immediate. = TRUE, call. = FALSE)
+      warning("legend.params argument is deprecated since version 0.2.3", call. = FALSE)
     }
     # Tidy up space to keep ggplot happy
     suppressWarnings(invisible(gc()))

R/Survey.Design.R

@@ -148,54 +148,54 @@ setMethod(
       title <- paste("\n   Strata ", strata.names[strat], ":", sep = "")
       len.title <- nchar(title)
       underline <- paste("   ", paste(rep("_", (len.title-3)), collapse = ""), sep = "")
-      cat(title, fill = T)
-      cat(underline, fill = T)
+      cat(title, fill = TRUE)
+      cat(underline, fill = TRUE)
       design <- switch(object@design[strat],
                        "random" = "randomly located transects",
                        "systematic" = "systematically spaced transects",
                        "eszigzag" = "equal spaced zigzag",
                        "eszigzagcom" = "complementaty equal spaced zigzags",
                        "segmentedgrid" = "segmented grid")
-      cat("Design: ", design, fill = T)
+      cat("Design: ", design, fill = TRUE)
       if(object@design[strat] %in% c("systematic", "eszigzag", "eszigzagcom", "segmentedgrid")){
-        cat("Spacing: ", object@spacing[strat], fill = T)
+        cat("Spacing: ", object@spacing[strat], fill = TRUE)
       }
       if(length(object@samplers) == 1){
-        cat("Number of samplers: ", object@samplers, " (shared across strata)", fill = T)
+        cat("Number of samplers: ", object@samplers, " (shared across strata)", fill = TRUE)
       }else{
-        cat("Number of samplers: ", object@samplers[strat], fill = T)
+        cat("Number of samplers: ", object@samplers[strat], fill = TRUE)
       }
       line.length <- try(object@line.length, silent = TRUE)
       if(!inherits(line.length, "try-error")){
         if(length(line.length) == 1){
-          cat("Line length: ", line.length, " (shared across strata)", fill = T)
+          cat("Line length: ", line.length, " (shared across strata)", fill = TRUE)
         }else if(length(line.length) == length(strata.names)){
-          cat("Line length: ", line.length[strat], fill = T)
+          cat("Line length: ", line.length[strat], fill = TRUE)
         }else{
-          cat("Line length: NA", fill = T)
+          cat("Line length: NA", fill = TRUE)
         }
       }
       if(object@design[strat] %in% c("segmentedgrid")){
-        cat("Segment length: ", object@seg.length[strat], fill = T)
-        cat("Segment threshold: ", object@seg.threshold[strat], fill = T)
+        cat("Segment length: ", object@seg.length[strat], fill = TRUE)
+        cat("Segment threshold: ", object@seg.threshold[strat], fill = TRUE)
       }
-      cat("Design angle: ", object@design.angle[strat], fill = T)
-      cat("Edge protocol: ", object@edge.protocol[strat], fill = T)
+      cat("Design angle: ", object@design.angle[strat], fill = TRUE)
+      cat("Edge protocol: ", object@edge.protocol[strat], fill = TRUE)
     }
     dp <- ifelse(any(object@region@area < 10), 3, 0)
-    cat("\nStrata areas: ", paste(round(object@region@area, dp), collapse = ", "), fill = T)
+    cat("\nStrata areas: ", paste(round(object@region@area, dp), collapse = ", "), fill = TRUE)
     if(length(object@region@units) > 0){
       if(!inherits(line.length, "try-error")){
-        cat("Region and effort units: ", object@region@units, fill = T)
+        cat("Region and effort units: ", object@region@units, fill = TRUE)
       }else{
-        cat("Region units: ", object@region@units, fill = T)
+        cat("Region units: ", object@region@units, fill = TRUE)
       }
     }
     if(length(object@effort.allocation) > 0){
-      cat("Effort allocation across strata: ", paste(object@effort.allocation*100, collapse = "%, "), "%", sep = "", fill = T)
+      cat("Effort allocation across strata: ", paste(object@effort.allocation*100, collapse = "%, "), "%", sep = "", fill = TRUE)
     }
     if(length(object@coverage.scores) > 0){
-      cat("Coverage Simulation repetitions: ", object@coverage.reps, fill = T)
+      cat("Coverage Simulation repetitions: ", object@coverage.reps, fill = TRUE)
     }
 
     design.stats <- object@design.statistics
@@ -208,31 +208,31 @@ setMethod(
                      "line.length" = "Line length:",
                      "trackline" = "Trackline length:",
                      "cyclictrackline" = "Cyclic trackline length:")
-     cat("\n   ", title, fill = T)
+     cat("\n   ", title, fill = TRUE)
      underline <- paste(rep("", (nchar(title)-3)), collapse = "")
-     cat("   ", underline, fill = T)
+     cat("   ", underline, fill = TRUE)
      print(design.stats[[i]])
     }
     if(!all(is.na(object@coverage.scores))){
       title <- "Coverage Score Summary:"
-      cat("\n   ", title, fill = T)
+      cat("\n   ", title, fill = TRUE)
       underline <- paste(rep("", (nchar(title)-3)), collapse = "")
-      cat("   ", underline, fill = T)
+      cat("   ", underline, fill = TRUE)
       cov.scores <- array(NA, dim = c(5, (length(strata.names)+1)), dimnames = list(c("Minimum", "Mean", "Median", "Maximum", "sd"), c(strata.names, "Total")))
       for(i in seq(along = strata.names)){
         cov.strat <- get.coverage(object, i)
-        cov.scores["Minimum",i] <- min(cov.strat, na.rm = T)
-        cov.scores["Mean",i] <- mean(cov.strat, na.rm = T)
-        cov.scores["Median",i] <- median(cov.strat, na.rm = T)
-        cov.scores["Maximum",i] <- max(cov.strat, na.rm = T)
-        cov.scores["sd",i] <- sd(cov.strat, na.rm = T)
+        cov.scores["Minimum",i] <- min(cov.strat, na.rm = TRUE)
+        cov.scores["Mean",i] <- mean(cov.strat, na.rm = TRUE)
+        cov.scores["Median",i] <- median(cov.strat, na.rm = TRUE)
+        cov.scores["Maximum",i] <- max(cov.strat, na.rm = TRUE)
+        cov.scores["sd",i] <- sd(cov.strat, na.rm = TRUE)
       }
       #Add in total column
-      cov.scores["Minimum","Total"] <- min(object@coverage.scores, na.rm = T)
-      cov.scores["Mean","Total"] <- mean(object@coverage.scores, na.rm = T)
-      cov.scores["Median","Total"] <- median(object@coverage.scores, na.rm = T)
-      cov.scores["Maximum","Total"] <- max(object@coverage.scores, na.rm = T)
-      cov.scores["sd","Total"] <- sd(object@coverage.scores, na.rm = T)
+      cov.scores["Minimum","Total"] <- min(object@coverage.scores, na.rm = TRUE)
+      cov.scores["Mean","Total"] <- mean(object@coverage.scores, na.rm = TRUE)
+      cov.scores["Median","Total"] <- median(object@coverage.scores, na.rm = TRUE)
+      cov.scores["Maximum","Total"] <- max(object@coverage.scores, na.rm = TRUE)
+      cov.scores["sd","Total"] <- sd(object@coverage.scores, na.rm = TRUE)
       print(cov.scores)
     }
   }