delete trailing whitespaces

R/CJS.R

@@ -165,20 +165,20 @@ breakMatricesByArray <- function(m, arrays, type = c("peers", "all"), verbose =
   recipient <- list()
   for (i in 1:length(arrays)) {
     if ((type == "peers" & !is.null(arrays[[i]]$after.peers)) | (type == "all" & !is.null(arrays[[i]]$all.after))) {
-      
+
       # find out relevant arrays
       if (type == "peers")
         a.regex <- paste0("^", c(names(arrays)[i], arrays[[i]]$after.peers), "$", collapse = "|")
       else
         a.regex <- paste0("^", c(names(arrays)[i], arrays[[i]]$all.after), "$", collapse = "|")
-      
+
       # grab only relevant arrays
       aux  <- lapply(m, function(m_i) m_i[, which(grepl(a.regex, colnames(m_i))), drop = FALSE])
-      
+
       # Failsafe in case some tags are released at one of the peers
       keep <- unlist(lapply(m, function(m_i) any(grepl(paste0("^", names(arrays)[i], "$"), colnames(m_i)))))
       aux  <- aux[keep]
-      
+
       # Failsafe in case there is only one column left
       keep <- unlist(lapply(aux, ncol)) > 1
       aux  <- aux[keep]
@@ -207,7 +207,7 @@ breakMatricesByArray <- function(m, arrays, type = c("peers", "all"), verbose =
       own.zero.check <- unlist(lapply(aux, function(x) sum(x[, 2]) == 0))
       peer.zero.check <- unlist(lapply(aux, function(x) sum(x$AnyPeer) == 0))
       zero.check <- all(own.zero.check) | all(peer.zero.check)
-      
+
       if (zero.check) {
         if (all(own.zero.check) & verbose) {
           appendTo(c("Screen", "Warning", "Report"), paste0("No tags passed through array ", names(arrays)[i], ". Skipping efficiency estimations for this array."))
@@ -308,7 +308,7 @@ assembleMatrices <- function(spatial, movements, status.df, arrays, paths, dotma
   output <- lapply(temp, function(x) {
     # include transmitters that were never detected
     x <- includeMissing(x = x, status.df = status.df)
-    
+
     # sort the rows by the same order as status.df (I think these two lines are not needed, but leaving them in just in case)
     link <- sapply(status.df$Transmitter, function(i) grep(paste0("^", i, "$"), rownames(x)))
     x <- x[link, ]
@@ -334,7 +334,7 @@ assembleMatrices <- function(spatial, movements, status.df, arrays, paths, dotma
     # If the release sites start in different arrays, trim the matrices as needed
     if (length(unique.release.arrays) > 1) {
       for(i in 1:length(aux)){ # for each matrix, find the corresponding release site.
-        the_release_site <- sapply(spatial$release.sites$Standard.name, function(x) grepl(paste0("\\.", x, "$"), names(aux)[i])) 
+        the_release_site <- sapply(spatial$release.sites$Standard.name, function(x) grepl(paste0("\\.", x, "$"), names(aux)[i]))
         if(sum(the_release_site) > 1) # if there is more than one matching release site, stop.
           stop("Multiple release sites match the matrix name. Make sure that the release sites' names are not contained within the animal groups or within themselves.\n")
         # else, find which is the first column to keep. This is tricky for multi-branch sites...

R/actel.R

@@ -23,10 +23,10 @@
 #' deploys a set of example files following the structure described in the package
 #' vignettes. Namely:
 #' \itemize{
-#' 	\item biometrics.csv
-#' 	\item deployments.csv
-#' 	\item spatial.csv
-#' 	\item detections/ (a folder with .csv files)
+#'   \item biometrics.csv
+#'   \item deployments.csv
+#'   \item spatial.csv
+#'   \item detections/ (a folder with .csv files)
 #' }
 #'
 #' Once the example dataset is created, \code{\link{exampleWorkspace}} also provides
@@ -64,7 +64,7 @@
 #' \code{\link{explore}}, but on top of it, it analyses the animal behaviour.
 #' By selecting the arrays that lead to success, you can define whether or not
 #' your animals survived the migration. Additional plots help you find out if some
-#' animals/tags has been acting odd. Multiple options allow you to tweak the 
+#' animals/tags has been acting odd. Multiple options allow you to tweak the
 #' analysis to fit your study perfectly.
 #'
 #'

R/distances.R

@@ -29,7 +29,7 @@
 #'   length(suppressWarnings(packageDescription("gdistance"))),
 #'   length(suppressWarnings(packageDescription("sp"))),
 #'   length(suppressWarnings(packageDescription("terra"))))
-#' 
+#'
 #' missing.packages <- sapply(aux, function(x) x == 1)
 #'
 #' if (any(missing.packages)) {
@@ -121,12 +121,12 @@ shapeToRaster <- function(shape, size, spatial = "spatial.csv",
   } else {
     stop("'shape' must be a .shp file.\n", call. = FALSE)
   }
-  
+
   # extend ranges with the buffer
   if (!is.null(buffer)) {
     OriEx <- terra::ext(shape)
     # terra does xmin, xmax, ymin, ymax
-    
+
     if (length(buffer) == 1){
       NewEx <- terra::ext(OriEx[1] - buffer, #xmin
                           OriEx[2] + buffer, #xmax
@@ -199,7 +199,7 @@ shapeToRaster <- function(shape, size, spatial = "spatial.csv",
   message(paste("M: Chosen pixel size:", size, "\nM: Resulting pixel dimensions:"))
   message(paste0(capture.output(print(pixel.res)), collapse = "\n"), "\n")
 
-  ras <- terra::rast(nrows = pixel.res[2], 
+  ras <- terra::rast(nrows = pixel.res[2],
                     ncols = pixel.res[1],
                     xmin = NewEx[1],
                     xmax = NewEx[2],
@@ -240,16 +240,16 @@ shapeToRaster <- function(shape, size, spatial = "spatial.csv",
 
 
 #' DEPRECATED
-#' 
+#'
 #' Please use shapeToRaster instead.
-#' 
+#'
 #' @inheritParams shapeToRaster
 #'
 #' @examples
 #' \donttest{
 #'  message("This function is deprecated, please use shapeToRaster instead.")
 #' }
-#' 
+#'
 #' @return A raster object.
 #'
 #' @export
@@ -288,7 +288,7 @@ loadShape <- function(shape, size, spatial = "spatial.csv",
 #'   length(suppressWarnings(packageDescription("gdistance"))),
 #'   length(suppressWarnings(packageDescription("sp"))),
 #'   length(suppressWarnings(packageDescription("terra"))))
-#' 
+#'
 #' missing.packages <- sapply(aux, function(x) x == 1)
 #'
 #' if (any(missing.packages)) {
@@ -365,7 +365,7 @@ transitionLayer <- function(x, directions = c(16, 8, 4)){
 #'   length(suppressWarnings(packageDescription("gdistance"))),
 #'   length(suppressWarnings(packageDescription("sp"))),
 #'   length(suppressWarnings(packageDescription("terra"))))
-#' 
+#'
 #' missing.packages <- sapply(aux, function(x) x == 1)
 #'
 #' if (any(missing.packages)) {
@@ -460,7 +460,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
 
     targets <- targets[, c(id.col, coord.x, coord.y)]
     colnames(targets) <- c(id.col, "longitude", "latitude")
-    
+
   if (!is.null(id.col)) {
     if (!is.na(match(id.col, colnames(starters)))) {
       outputRows <- starters[, id.col]
@@ -495,15 +495,15 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
   #### Create starters and targets spatial dataframes
   sp::coordinates(starters) <- ~ longitude + latitude # converts the file to a spatialPoints object
   raster::crs(starters) <- raster::crs(t.layer) # sets the crs
-  
+
   sp::coordinates(targets) <- ~ longitude + latitude # converts the file to a spatialPoints object
   raster::crs(targets) <- raster::crs(t.layer)
 
-  # NOTE: THE LINES ABOVE COULD BE CHANGED ONCE gdistance'S 
+  # NOTE: THE LINES ABOVE COULD BE CHANGED ONCE gdistance'S
   # FUNCTIONS START LIKING SF OBJECTS LAYER
   # starters <- sf::st_as_sf(starters, coords = c("longitude","latitude"), crs = ...)
   # targets <- sf::st_as_sf(targets, coords = c("longitude","latitude"), crs = ...)
-  # NOTE: currently, transition layer objects are not 
+  # NOTE: currently, transition layer objects are not
   # responding correctly to crs requests (e.g. sf::st_crs)
 
   #### Calculate a matrix of distances to each object
@@ -515,13 +515,13 @@ in the shape file, consider applying a 'buffer' when calculating the transition
 will artificially add water space around the shape file.", call. = FALSE)
     dist.mat[dist.mat == Inf] <- NA
   }
-  
+
   if (row.rename)
     rownames(dist.mat) <- outputRows
-  
+
   if (col.rename)
     colnames(dist.mat) <- outputCols
-  
+
   if (interactive() & actel) { # nocov start
     decision <- userInput("Would you like to save an actel-compatible distances matrix as 'distances.csv' in the current work directory?(y/n) ",
                           choices = c("y", "n"))
@@ -620,4 +620,4 @@ completeMatrix <- function(x){
   return(x)
 }
 
- 
+

R/explore.R

@@ -56,7 +56,7 @@
 #' @param override A vector of signals for which the user intends to manually
 #'  define which movement events are valid and invalid.
 #' @param detections.y.axis The type of y axis desired for the individual
-#'  detection plots. While the argument defaults to "auto", it can be hard-set 
+#'  detection plots. While the argument defaults to "auto", it can be hard-set
 #'  to one of "stations" or "arrays".
 #' @param print.releases Logical: Should the release sites be printed in the
 #'  study area diagrams?
@@ -161,7 +161,7 @@ explore <- function(
   GUI = c("needed", "always", "never"),
   save.tables.locally = FALSE,
   print.releases = TRUE,
-  detections.y.axis = c("auto", "stations", "arrays")) 
+  detections.y.axis = c("auto", "stations", "arrays"))
 {
 
 # check deprecated argument
@@ -188,10 +188,10 @@ explore <- function(
     checkToken(token = attributes(datapack)$actel.token,
                timestamp = attributes(datapack)$timestamp)
 
-  if (length(min.per.event) > 1) 
+  if (length(min.per.event) > 1)
     appendTo(c('screen', 'warning', 'report'),
       'explore() only has array movements but two values were set for min.per.event. Disregarding second value.')
-  
+
   aux <- checkArguments(dp = datapack,
                         tz = tz,
                         min.total.detections = min.total.detections,
@@ -377,7 +377,7 @@ explore <- function(
       output <- checkMinimumN(movements = movements[[tag]], tag = tag, min.total.detections = min.total.detections,
                                min.per.event = min.per.event[1], n = counter)
 
-      output <- checkImpassables(movements = output, tag = tag, bio = bio, detections = detections.list[[tag]], n = counter, 
+      output <- checkImpassables(movements = output, tag = tag, bio = bio, detections = detections.list[[tag]], n = counter,
                                  spatial = spatial, dotmat = dotmat, GUI = GUI, save.tables.locally = save.tables.locally)
 
       output <- checkJumpDistance(movements = output, bio = bio, tag = tag, dotmat = dotmat, paths = paths, arrays = arrays,
@@ -387,8 +387,8 @@ explore <- function(
       if (do.checkSpeeds) {
         temp.valid.movements <- simplifyMovements(movements = output, tag = tag, bio = bio, discard.first = discard.first,
                                                   speed.method = speed.method, dist.mat = dist.mat)
-        output <- checkSpeeds(movements = output, tag = tag, detections = detections.list[[tag]], n = counter, 
-                              valid.movements = temp.valid.movements, speed.warning = speed.warning, 
+        output <- checkSpeeds(movements = output, tag = tag, detections = detections.list[[tag]], n = counter,
+                              valid.movements = temp.valid.movements, speed.warning = speed.warning,
                               speed.error = speed.error, GUI = GUI, save.tables.locally = save.tables.locally)
         rm(temp.valid.movements)
       }
@@ -397,9 +397,9 @@ explore <- function(
         output <- checkInactiveness(movements = output, tag = tag, detections = detections.list[[tag]], n = counter,
                                     inactive.warning = inactive.warning, inactive.error = inactive.error,
                                     dist.mat = dist.mat, GUI = GUI, save.tables.locally = save.tables.locally)
-      }  
+      }
     } else { # nocov start
-      output <- overrideValidityChecks(moves = movements[[tag]], tag = tag, detections = detections.list[[tag]], 
+      output <- overrideValidityChecks(moves = movements[[tag]], tag = tag, detections = detections.list[[tag]],
                                        GUI = GUI, save.tables.locally = save.tables.locally, n = counter)
     } # nocov end
     return(output)
@@ -417,7 +417,7 @@ explore <- function(
 
   aux <- list(valid.movements = valid.movements,
               spatial = spatial,
-              rsp.info = list(bio = bio, 
+              rsp.info = list(bio = bio,
                               analysis.type = "explore"))
   times <- getTimes(input = aux, move.type = "array", event.type = "arrival", n.events = "first")
   rm(aux)
@@ -434,7 +434,7 @@ explore <- function(
   deployments <- do.call(rbind.data.frame, deployments)
 
   # extra info for potential RSP analysis
-  rsp.info <- list(analysis.type = "explore", analysis.time = the.time, 
+  rsp.info <- list(analysis.type = "explore", analysis.time = the.time,
                    bio = bio, tz = tz, actel.version = utils::packageVersion("actel"))
 
   if (!is.null(override))
@@ -457,7 +457,7 @@ explore <- function(
   }
 
   if (interactive()) { # nocov start
-    decision <- userInput(paste0("Would you like to save a copy of the results to ", resultsname, "?(y/n) "), 
+    decision <- userInput(paste0("Would you like to save a copy of the results to ", resultsname, "?(y/n) "),
                           choices = c("y", "n"), hash = "# save results?")
   } else { # nocov end
     decision <- "n"
@@ -466,10 +466,10 @@ explore <- function(
   if (decision == "y") { # nocov start
     appendTo(c("Screen", "Report"), paste0("M: Saving results as '", resultsname, "'."))
     if (attributes(dist.mat)$valid)
-      save(bio, detections, valid.detections, spatial, deployments, arrays, 
+      save(bio, detections, valid.detections, spatial, deployments, arrays,
         movements, valid.movements, times, rsp.info, dist.mat, file = resultsname)
     else
-      save(bio, detections, valid.detections, spatial, deployments, arrays, 
+      save(bio, detections, valid.detections, spatial, deployments, arrays,
         movements, valid.movements, times, rsp.info, file = resultsname)
   } else {
     appendTo(c("Screen", "Report"), paste0("M: Skipping saving of the results."))
@@ -494,24 +494,24 @@ explore <- function(
 
     biometric.fragment <- printBiometrics(bio = bio)
 
-    printDot(dot = dot, 
-             spatial = spatial, 
+    printDot(dot = dot,
+             spatial = spatial,
              print.releases = print.releases)
 
-    individual.plots <- printIndividuals(detections.list = detections, 
+    individual.plots <- printIndividuals(detections.list = detections,
                                          movements = movements,
                                          valid.movements = valid.movements,
                                          spatial = spatial,
                                          rsp.info = rsp.info,
                                          y.axis = detections.y.axis)
 
-    circular.plots <- printCircular(times = timesToCircular(times), 
+    circular.plots <- printCircular(times = timesToCircular(times),
                                     bio = bio)
 
     if (any(sapply(valid.detections, function(x) any(!is.na(x$Sensor.Value))))) {
-      sensor.plots <- printSensorData(detections = valid.detections, 
+      sensor.plots <- printSensorData(detections = valid.detections,
                                       spatial = spatial,
-                                      rsp.info = rsp.info, 
+                                      rsp.info = rsp.info,
                                       colour.by = detections.y.axis)
     } else {
       sensor.plots <- NULL
@@ -582,7 +582,7 @@ explore <- function(
   jobname <- paste0(gsub(" |:", ".", as.character(Sys.time())), ".actel.log.txt")
 
   if (interactive() & !report) { # nocov start
-    decision <- userInput(paste0("Would you like to save a copy of the analysis log to ", jobname, "?(y/n) "), 
+    decision <- userInput(paste0("Would you like to save a copy of the analysis log to ", jobname, "?(y/n) "),
                           choices = c("y", "n"), hash = "# save job log?")
   } else { # nocov end
     decision <- "n"
@@ -593,14 +593,14 @@ explore <- function(
   } # nocov end
 
   output <- list(bio = bio,
-                 detections = detections, 
-                 valid.detections = valid.detections, 
-                 spatial = spatial, 
-                 deployments = deployments, 
+                 detections = detections,
+                 valid.detections = valid.detections,
+                 spatial = spatial,
+                 deployments = deployments,
                  arrays = arrays,
-                 movements = movements, 
-                 valid.movements = valid.movements, 
-                 times = times, 
+                 movements = movements,
+                 valid.movements = valid.movements,
+                 times = times,
                  rsp.info = rsp.info)
 
   if (attributes(dist.mat)$valid)