From eda386039c0b8ec4479e1773bda01a23bc0ec177 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 12 Nov 2024 18:17:22 -0800
Subject: [PATCH 01/29] Updated news to reflect file pathway being added to
 distanceMatrix() function

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 87fef68..77a2971 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -22,6 +22,7 @@ Enhancements:
   * New `convertLotekCDMAFile()` function to prepare lotek txt logs for further analyses (issue [#103](https://github.com/hugomflavio/actel/issues/103)).
   * New `plotDot()` function to help users inspect their spatial.txt files (issue [#55](https://github.com/hugomflavio/actel/issues/55)).
   * Improved internal mechanisms for message/warning/debug/stop reporting. new internal function `event()` replaces the old `appendTo()`, `stopAndReport()`, and `emergencyBreak()` (issue [#135](https://github.com/hugomflavio/actel/issues/135))
+  * Added the ability to specify a file pathway for `distancesMatrix()` if the 'spatial.csv' is not in the main working directory. (issue [#133](https://github.com/hugomflavio/actel/issues/133))
 
 ## actel 1.3.0
 

From a240cad39adaa07204d885bbb78b0b44c4abe7ab Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 12 Nov 2024 18:18:38 -0800
Subject: [PATCH 02/29] Updated documentation code for distanceMatrix() and
 added the ability to specify a file pathway when the spatial.csv is not in
 the main working directory.

Also compressed the function code to 80c limit
---
 R/distances.R | 235 +++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 176 insertions(+), 59 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 912c65e..8e283e2 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -342,26 +342,39 @@ transitionLayer <- function(x, directions = c(16, 8, 4)){
 
 #' Calculate Distances Matrix
 #'
-#' Using a previously created transition layer (see \code{\link{transitionLayer}}), calculates the distances
-#' between spatial points. Adapted from Grant Adams' script "distance to closest mpa". if the argument 'actel'
-#' is set to TRUE (default), an actel-compatible matrix is generated, and the user will be asked if they would
-#' like to save the matrix as 'distances.csv' in the current directory.
-#'
-#' It is highly recommended to read the manual page regarding distances matrices before running this function.
-#' You can find it here: \href{https://hugomflavio.github.io/actel-website/manual-distances.html}{https://hugomflavio.github.io/actel-website/manual-distances.html}
-#'
-#' @param t.layer A TransitionLayer object, generated by \code{\link{transitionLayer}}.
-#' @param starters A data frame with the points from which to start measuring the distance. Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as starters.
-#' @param targets A data frame with the points to which a way must be found. Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as targets.
-#' @param coord.x,coord.y The names of the columns containing the x and y coordinates in the starters and targets. Must be identical in the starters and targets.
-#' @param id.col The name of the column containing the IDs of the points to be used as starters and targets. Must be identical in both files. Ignored if actel = TRUE (default), as the stations' standard names are used.
-#' @param actel Logical: Should the distance matrix be optimized for actel? Defaults to TRUE.
+#' Using a previously created transition layer (see \code{\link{transitionLayer}}), 
+#' calculates the distances between spatial points. Adapted from Grant Adams' 
+#' script "distance to closest mpa". If the argument 'actel' is set to 
+#' TRUE (default), an actel-compatible matrix is generated, and the user will be 
+#' asked if they would like to save the matrix as 'distances.csv' in the current 
+#' directory.
+#'
+#' It is highly recommended to read the manual page regarding distances matrices 
+#' before running this function.
+#' You can find it here:\href{https://hugomflavio.github.io/actel-website/manual-distances.html}{https://hugomflavio.github.io/actel-website/manual-distances.html}
+#'
+#' @param t.layer A TransitionLayer object, generated by 
+#' \code{\link{transitionLayer}}.
+#' @param starters A data frame with the points from which to start measuring 
+#' the distance. Ignored if actel = TRUE (default), as the 'spatial.csv' is 
+#' loaded as starters.
+#' @param targets A data frame with the points to which a way must be found. 
+#' Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as targets.
+#' @param coord.x,coord.y The names of the columns containing the x and y 
+#' coordinates in the starters and targets. Must be identical in the starters 
+#' and targets.
+#' @param id.col The name of the column containing the IDs of the points to 
+#' be used as starters and targets. Must be identical in both files. 
+#' Ignored if actel = TRUE (default), as the stations' standard names are used.
+#' @param file_path Specify the file path to the 'spatial.csv' file if not in 
+#' the main working directory.
+#' @param actel Logical: Should the distance matrix be optimized for actel? 
+#' Defaults to TRUE.
 #'
 #' @examples
 #' \donttest{
 #' # check if R can run the distance functions
-#' aux <- c(
-#'   length(suppressWarnings(packageDescription("raster"))),
+#' aux <- c(length(suppressWarnings(packageDescription("raster"))),
 #'   length(suppressWarnings(packageDescription("gdistance"))),
 #'   length(suppressWarnings(packageDescription("sp"))),
 #'   length(suppressWarnings(packageDescription("terra"))))
@@ -370,8 +383,10 @@ transitionLayer <- function(x, directions = c(16, 8, 4)){
 #'
 #' if (any(missing.packages)) {
 #'   message("Sorry, this function requires packages '",
-#'     paste(c("raster", "gdistance", "sp", "terra")[missing.packages], collapse = "', '"),
-#'     "' to operate. Please install ", ifelse(sum(missing.packages) > 1, "them", "it"),
+#'     paste(c("raster", "gdistance", "sp", "terra")[missing.packages], 
+#'     collapse = "', '"),
+#'     "' to operate. Please install ", ifelse(sum(missing.packages) > 1, 
+#'     "them", "it"),
 #'     " before proceeding.")
 #' } else {
 #'   # move to a temporary directory
@@ -410,7 +425,7 @@ transitionLayer <- function(x, directions = c(16, 8, 4)){
 #' @export
 #'
 distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
-  coord.x = "x", coord.y = "y", id.col = NULL, actel = TRUE){
+  coord.x = "x", coord.y = "y", id.col = NULL, file_path = NULL, actel = TRUE){
   # initial checks on package presence
   aux <- c(
     length(suppressWarnings(packageDescription("raster"))),
@@ -419,41 +434,88 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
     length(suppressWarnings(packageDescription("terra"))))
   missing.packages <- sapply(aux, function(x) x == 1)
   if (any(missing.packages)) {
-    stop(paste0("This function requires packages '", paste(c("raster", "gdistance", "sp", "terra")[missing.packages], collapse = "', '"),
-      "' to operate. Please install ", ifelse(sum(missing.packages) > 1, "them", "it"), " before proceeding.\n"), call. = FALSE)
+    stop(paste0("This function requires packages '", 
+                paste(c("raster", "gdistance", "sp", "terra")[missing.packages], 
+                      collapse = "', '"),
+      "' to operate. Please install ", 
+      ifelse(sum(missing.packages) > 1, "them", "it"), 
+      " before proceeding.\n"), call. = FALSE)
   }
 
   if (!inherits(t.layer, "TransitionLayer"))
-    stop("Could not recognise 't.layer' as a TransitionLayer object. Make sure to compile it using the function transitionLayer.\n", call. = FALSE)
+    stop("Could not recognise 't.layer' as a TransitionLayer object. Make",
+         " sure to compile it using the function transitionLayer.\n", 
+         call. = FALSE)
 
   if (!is.null(id.col) && length(id.col) > 1)
     stop("Please provide only one column name in 'id.col'", call. = FALSE)
   if (!is.null(id.col) && is.numeric(id.col))
-    stop("Please refer to the column name in 'id.col', rather than the column index.\n", call. = FALSE)
+    stop("Please refer to the column name in 'id.col', rather than the column",
+         " index.\n", call. = FALSE)
 
   if (actel) {
     message("M: Creating actel-compatible distances matrix."); flush.console()
-    if (!is.null(starters) | !is.null(targets))
-      warning("starters' or 'targets' were set but will be ignored because 'actel' is set to TRUE. Set 'actel' to FALSE to use the 'starters' and 'targets' arguments.", call. = FALSE, immediate. = TRUE)
-    starters <- targets <- loadSpatial()
-    if (!is.null(id.col))
-      warning("id.col' was set but will be ignored because 'actel' is set to TRUE. Set 'actel' to FALSE to use the 'id.col' argument.", call. = FALSE, immediate. = TRUE)
+    if (!is.null(starters) | !is.null(targets)) {
+      warning("starters' or 'targets' were set but will be ignored because", 
+              " 'actel' is set to TRUE. Set 'actel' to FALSE to use the", 
+              " 'starters' and 'targets' arguments.", 
+              call. = FALSE, immediate. = TRUE) 
+    }
+   # Added new check for 'file_path' being specified in function 
+    if(!is.null(file_path)) {
+      
+      # If a 'file path' is specified, the complete file to the 'spatial.csv' is 
+      # constructed
+      new_path <- paste0(file_path,"spatial.csv")
+      
+      # Added check in case 'file_path' did not lead to the 'spatial.csv' with 
+      # stop event
+      if(!file.exists(new_path)) {
+        event(type = "stop",
+              "'File_path' specified to 'spatial.csv' not found in the",
+              " working directory.")
+      }
+  
+      # Specify new file path to 'spatial.csv' and run as normal
+      starters <- targets <- loadSpatial(input = new_path) 
+    } else {
+      
+      # If no file path is specified, then 'spatial.csv' is assumed to be in 
+      # the main working directory
+      starters <- targets <- loadSpatial() 
+    }
+    
+    if (!is.null(id.col)) {
+      warning("id.col' was set but will be ignored because 'actel' is set to", 
+              " TRUE. Set 'actel' to FALSE to use the 'id.col' argument.", 
+              call. = FALSE, immediate. = TRUE) 
+      }
     id.col <- "Standard.name"
   }
 
-  if (!inherits(starters, "data.frame"))
+  if (!inherits(starters, "data.frame")) {
     stop("'starters' must be a data frame.\n", call. = FALSE)
-  if (!inherits(targets, "data.frame"))
+    }
+  if (!inherits(targets, "data.frame")) {
     stop("'targets' must be a data frame.\n", call. = FALSE)
+    }
 
-  if (is.na(match(coord.x, colnames(starters))))
-    stop(paste0("Could not find a column '", coord.x, "' in 'starters'."), call. = FALSE)
-  if (is.na(match(coord.y, colnames(starters))))
-    stop(paste0("Could not find a column '", coord.y, "' in 'starters'."), call. = FALSE)
-  if (is.na(match(coord.x, colnames(targets))))
-    stop(paste0("Could not find a column '", coord.x, "' in 'targets'."), call. = FALSE)
-  if (is.na(match(coord.y, colnames(targets))))
-    stop(paste0("Could not find a column '", coord.y, "' in 'targets'."), call. = FALSE)
+  if (is.na(match(coord.x, colnames(starters)))) {
+    stop(paste0("Could not find a column '", 
+                coord.x, "' in 'starters'."), call. = FALSE)
+    }
+  if (is.na(match(coord.y, colnames(starters)))) {
+    stop(paste0("Could not find a column '", 
+                coord.y, "' in 'starters'."), call. = FALSE)
+    }
+  if (is.na(match(coord.x, colnames(targets)))) {
+    stop(paste0("Could not find a column '", 
+                coord.x, "' in 'targets'."), call. = FALSE)
+    }
+  if (is.na(match(coord.y, colnames(targets)))) {
+    stop(paste0("Could not find a column '", 
+                coord.y, "' in 'targets'."), call. = FALSE)
+    }
 
     starters <- starters[, c(id.col, coord.x, coord.y)]
     colnames(starters) <- c(id.col, "longitude", "latitude")
@@ -465,25 +527,33 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
     if (!is.na(match(id.col, colnames(starters)))) {
       outputRows <- starters[, id.col]
       if (any(duplicated(outputRows))) {
-        warning("The '", id.col, "' column in 'starters' contains duplicated values; skipping row naming.", immediate. = TRUE, call. = FALSE)
+        warning("The '", id.col, 
+                "' column in 'starters' contains duplicated values;",
+                " skipping row naming.", immediate. = TRUE, call. = FALSE)
         row.rename <- FALSE
       } else {
         row.rename <- TRUE
       }
     } else {
-      warning("Could not find a '", id.col, "' column in 'starters'; skipping row naming.", immediate. = TRUE, call. = FALSE)
+      warning("Could not find a '", id.col, 
+              "' column in 'starters'; skipping row naming.", 
+              immediate. = TRUE, call. = FALSE)
       row.rename <- FALSE
     }
     if (!is.na(match(id.col, colnames(targets)))) {
       outputCols <- targets[, id.col]
       if (any(duplicated(outputCols))) {
-        warning("The '", id.col, "' column in 'targets' contains duplicated values; skipping column naming.", immediate. = TRUE, call. = FALSE)
+        warning("The '", id.col, 
+                "' column in 'targets' contains duplicated values;",
+                " skipping column naming.", immediate. = TRUE, call. = FALSE)
         col.rename <- FALSE
       } else {
         col.rename <- TRUE
       }
     } else {
-      warning("Could not find a '", id.col, "' column in 'targets'; skipping column naming.", immediate. = TRUE, call. = FALSE)
+      warning("Could not find a '", id.col, 
+              "' column in 'targets'; skipping column naming.", 
+              immediate. = TRUE, call. = FALSE)
       col.rename <- FALSE
     }
   } else {
@@ -493,45 +563,92 @@ 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
+    # converts the file to a spatialPoints object
+  sp::coordinates(starters) <- ~ longitude + latitude 
+  
+  # sets the crs
+  raster::crs(starters) <- raster::crs(t.layer) 
+
+  # converts the file to a spatialPoints object
+  sp::coordinates(targets) <- ~ longitude + latitude 
   raster::crs(targets) <- raster::crs(t.layer)
 
   # 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 = ...)
+  # 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
   # responding correctly to crs requests (e.g. sf::st_crs)
 
   #### Calculate a matrix of distances to each object
   dist.mat <- data.frame(gdistance::costDistance(t.layer, starters, targets))
   if (any(dist.mat == Inf)) {
-    warning("At least one station is completely blocked off from the remaining stations by land. Filling
-the respective fields with NA. If your animals were expected to travel around the areas present
-in the shape file, consider applying a 'buffer' when calculating the transition layer. This
-will artificially add water space around the shape file.", call. = FALSE)
+    warning("At least one station is completely blocked off from the remaining",
+            " stations by land. Filling the respective fields with NA.", 
+            " If your animals were expected to travel around the areas present", 
+            " in the shape file, consider applying a 'buffer' when calculating", 
+            " the transition layer. This will artificially add water space", 
+            " around the shape file.", call. = FALSE)
     dist.mat[dist.mat == Inf] <- NA
   }
 
-  if (row.rename)
+  if (row.rename) {
     rownames(dist.mat) <- outputRows
+    }
 
-  if (col.rename)
+  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) ",
+    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"))
+    
     if (decision == "y") {
-      if (file.exists('distances.csv')) {
-        warning("A file 'distances.csv' is already present in the current directory.", call. = FALSE, immediate. = TRUE)
-        decision <- userInput("Continuing will overwrite this file. Would you like to continue?(y/n) ", choices = c("y", "n"))
+      
+      if(!is.null(file_path)) {
+        
+        # If a 'file_path' has been specified, a new path is created where 
+        # 'distances.csv' will be saved
+        new_path <- paste0(file_path,"distances.csv")
+        
+        # Checks if 'distances.csv' is already in the file path specified
+        if (file.exists(new_path)) {
+          
+          warning("A file 'distances.csv' is already present in the current",
+                  " directory.", call. = FALSE, immediate. = TRUE)
+          
+          decision <- userInput("Continuing will overwrite this file. Would",
+                                " you like to continue?(y/n) ", 
+                                choices = c("y", "n"))
+        }
+        
+        if (decision == "y") {
+          
+          write.csv(round(dist.mat, 0), new_path, row.names = TRUE)
+          
+          }
+      } else {
+        # If no 'file_path' specified, then 'distances.csv' is saved to the 
+        # current working directory
+        if (file.exists('distances.csv')) {
+          warning("A file 'distances.csv' is already present in the current",
+                  " directory.", call. = FALSE, immediate. = TRUE)
+          
+          decision <- userInput("Continuing will overwrite this file. Would",
+                                " you like to continue?(y/n) ", 
+                                choices = c("y", "n"))
       }
-      if (decision == "y")
+      if (decision == "y") {
         write.csv(round(dist.mat, 0), "distances.csv", row.names = TRUE)
+        }
+      }
+      
+      
     }
   } # nocov end
   return(round(dist.mat, 0))

From e35192decc0f8769487d05dd64022dc8e55ae3f1 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 12 Nov 2024 18:19:01 -0800
Subject: [PATCH 03/29] Updated documentation for distanceMatrix() function

---
 man/distancesMatrix.Rd | 49 ++++++++++++++++++++++++++++--------------
 1 file changed, 33 insertions(+), 16 deletions(-)

diff --git a/man/distancesMatrix.Rd b/man/distancesMatrix.Rd
index 5a1beab..eb4b8f9 100644
--- a/man/distancesMatrix.Rd
+++ b/man/distancesMatrix.Rd
@@ -11,40 +11,55 @@ distancesMatrix(
   coord.x = "x",
   coord.y = "y",
   id.col = NULL,
+  file_path = NULL,
   actel = TRUE
 )
 }
 \arguments{
-\item{t.layer}{A TransitionLayer object, generated by \code{\link{transitionLayer}}.}
+\item{t.layer}{A TransitionLayer object, generated by
+\code{\link{transitionLayer}}.}
 
-\item{starters}{A data frame with the points from which to start measuring the distance. Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as starters.}
+\item{starters}{A data frame with the points from which to start measuring
+the distance. Ignored if actel = TRUE (default), as the 'spatial.csv' is
+loaded as starters.}
 
-\item{targets}{A data frame with the points to which a way must be found. Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as targets.}
+\item{targets}{A data frame with the points to which a way must be found.
+Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as targets.}
 
-\item{coord.x, coord.y}{The names of the columns containing the x and y coordinates in the starters and targets. Must be identical in the starters and targets.}
+\item{coord.x, coord.y}{The names of the columns containing the x and y
+coordinates in the starters and targets. Must be identical in the starters
+and targets.}
 
-\item{id.col}{The name of the column containing the IDs of the points to be used as starters and targets. Must be identical in both files. Ignored if actel = TRUE (default), as the stations' standard names are used.}
+\item{id.col}{The name of the column containing the IDs of the points to
+be used as starters and targets. Must be identical in both files.
+Ignored if actel = TRUE (default), as the stations' standard names are used.}
 
-\item{actel}{Logical: Should the distance matrix be optimized for actel? Defaults to TRUE.}
+\item{file_path}{Specify the file path to the 'spatial.csv' file if not in
+the main working directory.}
+
+\item{actel}{Logical: Should the distance matrix be optimized for actel?
+Defaults to TRUE.}
 }
 \value{
 A matrix with the distances between each pair of points.
 }
 \description{
-Using a previously created transition layer (see \code{\link{transitionLayer}}), calculates the distances
-between spatial points. Adapted from Grant Adams' script "distance to closest mpa". if the argument 'actel'
-is set to TRUE (default), an actel-compatible matrix is generated, and the user will be asked if they would
-like to save the matrix as 'distances.csv' in the current directory.
+Using a previously created transition layer (see \code{\link{transitionLayer}}),
+calculates the distances between spatial points. Adapted from Grant Adams'
+script "distance to closest mpa". If the argument 'actel' is set to
+TRUE (default), an actel-compatible matrix is generated, and the user will be
+asked if they would like to save the matrix as 'distances.csv' in the current
+directory.
 }
 \details{
-It is highly recommended to read the manual page regarding distances matrices before running this function.
-You can find it here: \href{https://hugomflavio.github.io/actel-website/manual-distances.html}{https://hugomflavio.github.io/actel-website/manual-distances.html}
+It is highly recommended to read the manual page regarding distances matrices
+before running this function.
+You can find it here:\href{https://hugomflavio.github.io/actel-website/manual-distances.html}{https://hugomflavio.github.io/actel-website/manual-distances.html}
 }
 \examples{
 \donttest{
 # check if R can run the distance functions
-aux <- c(
-  length(suppressWarnings(packageDescription("raster"))),
+aux <- c(length(suppressWarnings(packageDescription("raster"))),
   length(suppressWarnings(packageDescription("gdistance"))),
   length(suppressWarnings(packageDescription("sp"))),
   length(suppressWarnings(packageDescription("terra"))))
@@ -53,8 +68,10 @@ missing.packages <- sapply(aux, function(x) x == 1)
 
 if (any(missing.packages)) {
   message("Sorry, this function requires packages '",
-    paste(c("raster", "gdistance", "sp", "terra")[missing.packages], collapse = "', '"),
-    "' to operate. Please install ", ifelse(sum(missing.packages) > 1, "them", "it"),
+    paste(c("raster", "gdistance", "sp", "terra")[missing.packages], 
+    collapse = "', '"),
+    "' to operate. Please install ", ifelse(sum(missing.packages) > 1, 
+    "them", "it"),
     " before proceeding.")
 } else {
   # move to a temporary directory

From 50fd11b471fb92d9b227c589f7b4cca72905dbbc Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 12 Nov 2024 18:19:49 -0800
Subject: [PATCH 04/29] Had to adjust distanceMatrix() test since compressing
 to 80c changed how a check operated when looking for a warning.

---
 tests/testthat/test_distancesMatrix_functions.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test_distancesMatrix_functions.R b/tests/testthat/test_distancesMatrix_functions.R
index 4029393..c309365 100644
--- a/tests/testthat/test_distancesMatrix_functions.R
+++ b/tests/testthat/test_distancesMatrix_functions.R
@@ -103,10 +103,12 @@ if (any(missing.packages)) {
 		test_that("distancesMatrix produces a warning when there are no viable passages between stations", {
 			expect_warning(dist.mat <- distancesMatrix(t.layer = t.layer,
 		  		coord.x = "x.32632", coord.y = "y.32632", actel = TRUE),
-			"At least one station is completely blocked off from the remaining stations by land. Filling
-the respective fields with NA. If your animals were expected to travel around the areas present
-in the shape file, consider applying a 'buffer' when calculating the transition layer. This
-will artificially add water space around the shape file.", fixed = TRUE)
+		  		paste0("At least one station is completely blocked off from the remaining",
+		  		" stations by land. Filling the respective fields with NA.", 
+		  		" If your animals were expected to travel around the areas present", 
+		  		" in the shape file, consider applying a 'buffer' when calculating", 
+		  		" the transition layer. This will artificially add water space", 
+		  		" around the shape file."), fixed = TRUE)
 		})
 		# n
 

From 852f215e316c0e22ff2c9a6c629d474288529dd5 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Wed, 13 Nov 2024 13:17:19 -0800
Subject: [PATCH 05/29] Minor updates to allow checks to pass

---
 R/distances.R | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 8e283e2..029d94b 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -472,8 +472,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
       # stop event
       if(!file.exists(new_path)) {
         event(type = "stop",
-              "'File_path' specified to 'spatial.csv' not found in the",
-              " working directory.")
+              "'spatial.csv' not found in the 'file_path' specified")
       }
   
       # Specify new file path to 'spatial.csv' and run as normal
@@ -603,9 +602,9 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
     }
 
   if (interactive() & actel) { # nocov start
-    decision <- userInput("Would you like to save an actel-compatible", 
+    decision <- userInput(paste0("Would you like to save an actel-compatible", 
                           " distances matrix as 'distances.csv' in the",
-                          " current work directory?(y/n) ",
+                          " current work directory?(y/n) "),
                           choices = c("y", "n"))
     
     if (decision == "y") {
@@ -622,8 +621,8 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
           warning("A file 'distances.csv' is already present in the current",
                   " directory.", call. = FALSE, immediate. = TRUE)
           
-          decision <- userInput("Continuing will overwrite this file. Would",
-                                " you like to continue?(y/n) ", 
+          decision <- userInput(paste0("Continuing will overwrite this file.",
+                                "  Would you like to continue?(y/n) "), 
                                 choices = c("y", "n"))
         }
         
@@ -639,8 +638,8 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
           warning("A file 'distances.csv' is already present in the current",
                   " directory.", call. = FALSE, immediate. = TRUE)
           
-          decision <- userInput("Continuing will overwrite this file. Would",
-                                " you like to continue?(y/n) ", 
+          decision <- userInput(paste0("Continuing will overwrite this file.",
+                                " Would you like to continue?(y/n) "), 
                                 choices = c("y", "n"))
       }
       if (decision == "y") {

From 42325f8d0acf2bb85ee1ca43aaf6bd2330908bca Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Wed, 13 Nov 2024 13:18:25 -0800
Subject: [PATCH 06/29] added new checks to test `distanceMatrix()` 'file_path'
 addition.

---
 .../testthat/test_distancesMatrix_functions.R | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/tests/testthat/test_distancesMatrix_functions.R b/tests/testthat/test_distancesMatrix_functions.R
index c309365..05912b4 100644
--- a/tests/testthat/test_distancesMatrix_functions.R
+++ b/tests/testthat/test_distancesMatrix_functions.R
@@ -112,6 +112,12 @@ if (any(missing.packages)) {
 		})
 		# n
 
+		test_that("distancesMatrix handles missing sptial.csv when file_path used", {
+		  expect_error(output <- distancesMatrix(t.layer = t.layer, coord.x = "x.32632", 
+		                            coord.y = "y.32632", file_path = "file_test"),
+		               "'spatial.csv' not found in the 'file_path' specified")
+		})
+		
 		test_that("distancesMatrix handles bad data correctly pt1", {
 			expect_error(distancesMatrix(t.layer = t.layer, id.col = 1:2),
 				"Please provide only one column name in 'id.col'", fixed = TRUE)
@@ -165,6 +171,23 @@ if (any(missing.packages)) {
 			"Could not find a column 'test' in 'targets'.", fixed = TRUE)
 		})
 
+		dir.create("file_test")
+		
+		write.csv(xspatial, "file_test/spatial.csv", row.names = FALSE)
+		
+		test_that("distancesMatrix output is as expected when file_path used", {
+		  output <- distancesMatrix(t.layer = t.layer, coord.x = "x.32632",
+		                            coord.y = "y.32632", file_path = "file_test/")
+		  expect_equal(colnames(output), paste("St", 1:4, sep = "."))
+		  expect_equal(rownames(output), paste("St", 1:4, sep = "."))
+		  expect_equal(output[, 1], c(   0, 586, 934, 1154))
+		  expect_equal(output[, 2], c( 586,   0, 490,  656))
+		  expect_equal(output[, 3], c( 934, 490,   0,  237))
+		  expect_equal(output[, 4], c(1154, 656, 237,    0))
+		})
+		
+		unlink("file_test", recursive = TRUE)
+		
 		test_that("distancesMatrix output is as expected", {
 		 output <- distancesMatrix(t.layer = t.layer, coord.x = "x.32632", coord.y = "y.32632")
 		 expect_equal(colnames(output), paste("St", 1:4, sep = "."))

From 14290a8df3ce67cfdea25c1e15f596961c4c8a91 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 19 Nov 2024 12:28:36 -0800
Subject: [PATCH 07/29] Updated news description based on changes made to
 'distancesMatrix()'

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 77a2971..b836340 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -22,7 +22,7 @@ Enhancements:
   * New `convertLotekCDMAFile()` function to prepare lotek txt logs for further analyses (issue [#103](https://github.com/hugomflavio/actel/issues/103)).
   * New `plotDot()` function to help users inspect their spatial.txt files (issue [#55](https://github.com/hugomflavio/actel/issues/55)).
   * Improved internal mechanisms for message/warning/debug/stop reporting. new internal function `event()` replaces the old `appendTo()`, `stopAndReport()`, and `emergencyBreak()` (issue [#135](https://github.com/hugomflavio/actel/issues/135))
-  * Added the ability to specify a file pathway for `distancesMatrix()` if the 'spatial.csv' is not in the main working directory. (issue [#133](https://github.com/hugomflavio/actel/issues/133))
+  * Added the ability to use output of `loadSpatial()` as 'starters' for `distancesMatrix()` when 'actel' is 'TRUE'. This allows a user to input their spatial.csv if located in a separate working directory (issue [#133](https://github.com/hugomflavio/actel/issues/133))
 
 ## actel 1.3.0
 

From ec35ecc9b266a26ddff8438b865ba79c68f973a9 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 19 Nov 2024 12:29:53 -0800
Subject: [PATCH 08/29] Updated help documentation for 'distancesMatrix()'
 where the output of 'loadSpatial()' can now be used in place of starters when
 actel == TRUE

---
 man/distancesMatrix.Rd | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/man/distancesMatrix.Rd b/man/distancesMatrix.Rd
index eb4b8f9..8e3ca16 100644
--- a/man/distancesMatrix.Rd
+++ b/man/distancesMatrix.Rd
@@ -7,11 +7,10 @@
 distancesMatrix(
   t.layer,
   starters = NULL,
-  targets = starters,
+  targets = NULL,
   coord.x = "x",
   coord.y = "y",
   id.col = NULL,
-  file_path = NULL,
   actel = TRUE
 )
 }
@@ -20,11 +19,9 @@ distancesMatrix(
 \code{\link{transitionLayer}}.}
 
 \item{starters}{A data frame with the points from which to start measuring
-the distance. Ignored if actel = TRUE (default), as the 'spatial.csv' is
-loaded as starters.}
+the distance or the output of \code{loadSpatial()}.}
 
-\item{targets}{A data frame with the points to which a way must be found.
-Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as targets.}
+\item{targets}{A data frame with the points to which a way must be found.}
 
 \item{coord.x, coord.y}{The names of the columns containing the x and y
 coordinates in the starters and targets. Must be identical in the starters
@@ -34,9 +31,6 @@ and targets.}
 be used as starters and targets. Must be identical in both files.
 Ignored if actel = TRUE (default), as the stations' standard names are used.}
 
-\item{file_path}{Specify the file path to the 'spatial.csv' file if not in
-the main working directory.}
-
 \item{actel}{Logical: Should the distance matrix be optimized for actel?
 Defaults to TRUE.}
 }

From 46d5e7852efd8a4076722c0c828577a7506090f1 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 19 Nov 2024 12:30:46 -0800
Subject: [PATCH 09/29] Some minor check fixes to address new
 'distancesMatrix()' changes. Removed old checks related to file_path and
 removed checks which checked for errors or warning no longer present.

---
 .../testthat/test_distancesMatrix_functions.R | 22 +++++--------------
 1 file changed, 5 insertions(+), 17 deletions(-)

diff --git a/tests/testthat/test_distancesMatrix_functions.R b/tests/testthat/test_distancesMatrix_functions.R
index 05912b4..fbd24c4 100644
--- a/tests/testthat/test_distancesMatrix_functions.R
+++ b/tests/testthat/test_distancesMatrix_functions.R
@@ -111,12 +111,6 @@ if (any(missing.packages)) {
 		  		" around the shape file."), fixed = TRUE)
 		})
 		# n
-
-		test_that("distancesMatrix handles missing sptial.csv when file_path used", {
-		  expect_error(output <- distancesMatrix(t.layer = t.layer, coord.x = "x.32632", 
-		                            coord.y = "y.32632", file_path = "file_test"),
-		               "'spatial.csv' not found in the 'file_path' specified")
-		})
 		
 		test_that("distancesMatrix handles bad data correctly pt1", {
 			expect_error(distancesMatrix(t.layer = t.layer, id.col = 1:2),
@@ -134,13 +128,9 @@ if (any(missing.packages)) {
 				"'starters' must be a data frame.", fixed = TRUE)
 
 			file.remove("test.txt")
-			
-			expect_warning(distancesMatrix(t.layer =  t.layer,
-		  		coord.x = "x.32632", coord.y = "y.32632", starters = "test", id.col = "test", actel = TRUE),
-			"starters' or 'targets' were set but will be ignored because 'actel' is set to TRUE. Set 'actel' to FALSE to use the 'starters' and 'targets' arguments.", fixed = TRUE)
 
 			expect_warning(distancesMatrix(t.layer =  t.layer,
-		  		coord.x = "x.32632", coord.y = "y.32632", starters = "test", id.col = "test", actel = TRUE),
+		  		coord.x = "x.32632", coord.y = "y.32632", id.col = "test", actel = TRUE),
 			"id.col' was set but will be ignored because 'actel' is set to TRUE. Set 'actel' to FALSE to use the 'id.col' argument.", fixed = TRUE)
 		})
 		# n
@@ -170,14 +160,12 @@ if (any(missing.packages)) {
 		  		coord.x = "x.32632", coord.y = "test", starters = loadSpatial("spatial2.csv"), targets = loadSpatial(), actel = FALSE),
 			"Could not find a column 'test' in 'targets'.", fixed = TRUE)
 		})
-
-		dir.create("file_test")
 		
-		write.csv(xspatial, "file_test/spatial.csv", row.names = FALSE)
+		test_loadspatial <- loadSpatial()
 		
-		test_that("distancesMatrix output is as expected when file_path used", {
+		test_that("distancesMatrix output is as expected when output of loadSpatial() is used", {
 		  output <- distancesMatrix(t.layer = t.layer, coord.x = "x.32632",
-		                            coord.y = "y.32632", file_path = "file_test/")
+		                            coord.y = "y.32632", starters = test_loadspatial)
 		  expect_equal(colnames(output), paste("St", 1:4, sep = "."))
 		  expect_equal(rownames(output), paste("St", 1:4, sep = "."))
 		  expect_equal(output[, 1], c(   0, 586, 934, 1154))
@@ -186,7 +174,7 @@ if (any(missing.packages)) {
 		  expect_equal(output[, 4], c(1154, 656, 237,    0))
 		})
 		
-		unlink("file_test", recursive = TRUE)
+		rm(test_loadspatial)
 		
 		test_that("distancesMatrix output is as expected", {
 		 output <- distancesMatrix(t.layer = t.layer, coord.x = "x.32632", coord.y = "y.32632")

From 4b74870660f8177498d4a2a881a891e70569acc7 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Tue, 19 Nov 2024 12:32:37 -0800
Subject: [PATCH 10/29] Modified 'distancesMatrix()' function to allow starters
 and targets to be specified when actel == TRUE. This also allows
 'loadSpatial()' to be used in starters to specify if the 'spatial.csv' is in
 a different working directory. Also updated code to allow 'distances.csv' to
 be saved to a specific folder if the user desires.

---
 R/distances.R | 114 ++++++++++++++++++++++++++++++++++----------------
 1 file changed, 77 insertions(+), 37 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 029d94b..12cb3dd 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -356,18 +356,14 @@ transitionLayer <- function(x, directions = c(16, 8, 4)){
 #' @param t.layer A TransitionLayer object, generated by 
 #' \code{\link{transitionLayer}}.
 #' @param starters A data frame with the points from which to start measuring 
-#' the distance. Ignored if actel = TRUE (default), as the 'spatial.csv' is 
-#' loaded as starters.
+#' the distance or the output of `loadSpatial()`.
 #' @param targets A data frame with the points to which a way must be found. 
-#' Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as targets.
 #' @param coord.x,coord.y The names of the columns containing the x and y 
 #' coordinates in the starters and targets. Must be identical in the starters 
 #' and targets.
 #' @param id.col The name of the column containing the IDs of the points to 
 #' be used as starters and targets. Must be identical in both files. 
 #' Ignored if actel = TRUE (default), as the stations' standard names are used.
-#' @param file_path Specify the file path to the 'spatial.csv' file if not in 
-#' the main working directory.
 #' @param actel Logical: Should the distance matrix be optimized for actel? 
 #' Defaults to TRUE.
 #'
@@ -424,8 +420,8 @@ transitionLayer <- function(x, directions = c(16, 8, 4)){
 #'
 #' @export
 #'
-distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
-  coord.x = "x", coord.y = "y", id.col = NULL, file_path = NULL, actel = TRUE){
+distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
+  coord.x = "x", coord.y = "y", id.col = NULL, actel = TRUE){
   # initial checks on package presence
   aux <- c(
     length(suppressWarnings(packageDescription("raster"))),
@@ -455,35 +451,44 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
 
   if (actel) {
     message("M: Creating actel-compatible distances matrix."); flush.console()
-    if (!is.null(starters) | !is.null(targets)) {
-      warning("starters' or 'targets' were set but will be ignored because", 
-              " 'actel' is set to TRUE. Set 'actel' to FALSE to use the", 
-              " 'starters' and 'targets' arguments.", 
-              call. = FALSE, immediate. = TRUE) 
-    }
-   # Added new check for 'file_path' being specified in function 
-    if(!is.null(file_path)) {
-      
-      # If a 'file path' is specified, the complete file to the 'spatial.csv' is 
-      # constructed
-      new_path <- paste0(file_path,"spatial.csv")
-      
-      # Added check in case 'file_path' did not lead to the 'spatial.csv' with 
-      # stop event
-      if(!file.exists(new_path)) {
-        event(type = "stop",
-              "'spatial.csv' not found in the 'file_path' specified")
+    
+    if(!is.null(starters) | !is.null(targets)) {
+      # distancesMatrix() crashes if actel = TRUE and starters/targets were 
+      # supplied but do not contain a column called "Standard.name"
+      if(!is.null(starters) & !any(grepl(c("Standard.name"), 
+                                         colnames(starters)))) {
+        event("'starters' is missing column called 'Standard.name'",
+              type = "stop")
       }
-  
-      # Specify new file path to 'spatial.csv' and run as normal
-      starters <- targets <- loadSpatial(input = new_path) 
-    } else {
       
-      # If no file path is specified, then 'spatial.csv' is assumed to be in 
-      # the main working directory
-      starters <- targets <- loadSpatial() 
+      if(!is.null(targets) & !any(grepl(c("Standard.name"), 
+                                         colnames(targets)))) {
+        event("'targets' is missing column called 'Standard.name'",
+              type = "stop")
+      }
+    }
+    
+    if (!is.null(starters) & !is.null(targets)) {
+      warning("'starters' and 'targets' were specified while 'actel'",
+              " is set to TRUE. Using 'starters' and 'targets' for distances.", 
+              call. = FALSE, immediate. = TRUE) 
     }
     
+    if (!is.null(starters) & is.null(targets)) {
+        warning("'starters' were specified but 'targets' were not while 'actel'",
+              " is set to TRUE. Using 'starters' for 'targets'.", 
+              call. = FALSE, immediate. = TRUE) 
+      
+        targets <- starters
+        }
+    
+    if (is.null(starters) & is.null(targets)) {
+        warning("'starters' and 'targets' were not set while 'actel' is set to",
+              " TRUE. Creating 'starters' and 'targets' from 'spatial.csv' ",
+              " in working directory." , call. = FALSE, immediate. = TRUE)
+        starters <- targets <- loadSpatial() 
+        }
+    
     if (!is.null(id.col)) {
       warning("id.col' was set but will be ignored because 'actel' is set to", 
               " TRUE. Set 'actel' to FALSE to use the 'id.col' argument.", 
@@ -491,6 +496,14 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
       }
     id.col <- "Standard.name"
   }
+  
+  # Failsafe from old way code worked where targets used starters by default 
+  # when actel == FALSE
+  if(!actel) {
+    if(is.null(targets)) {
+      targets <- starters
+    }
+  }
 
   if (!inherits(starters, "data.frame")) {
     stop("'starters' must be a data frame.\n", call. = FALSE)
@@ -603,17 +616,44 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
 
   if (interactive() & actel) { # nocov start
     decision <- userInput(paste0("Would you like to save an actel-compatible", 
-                          " distances matrix as 'distances.csv' in the",
-                          " current work directory?(y/n) "),
+                                 " distances matrix as 'distances.csv'?(y/n)"),
                           choices = c("y", "n"))
-    
+    if (decision == "y") {
+       dir_decision <- userInput(paste0("Would you like 'distances.csv' saved in",
+                                    " the current working directory?(y/n)"),
+                          choices = c("y", "n"))
+       if (dir_decision == "n") {
+         
+         target_dir <- ""
+
+         while(!dir.exists(target_dir)){
+           target_dir <- readline(paste0("Specify the folder to save 'distances.csv'",
+                                         " to. Hit enter to skip."))
+           if(nchar(target_dir) == 0) {
+             dir_decision <- "y"
+             {break}
+           } 
+           
+           if(!dir.exists(target_dir)) {
+             dir_decision <- userInput(paste0("Directory specified not found.",
+                                              " Do you want to continue?(y/n)"),
+                       choices = c("y", "n"))
+             if(dir_decision == "n") {
+               dir_decision <- "y"
+               {break}
+             }
+           }
+         }
+       }
+    }
+   
     if (decision == "y") {
       
-      if(!is.null(file_path)) {
+      if(dir_decision == "n") {
         
         # If a 'file_path' has been specified, a new path is created where 
         # 'distances.csv' will be saved
-        new_path <- paste0(file_path,"distances.csv")
+        new_path <- paste(target_dir,"distances.csv", sep = "/")
         
         # Checks if 'distances.csv' is already in the file path specified
         if (file.exists(new_path)) {

From 127d326852610e882e5188a8378509558c6ed991 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Thu, 5 Dec 2024 10:33:20 -0800
Subject: [PATCH 11/29] Removed curly brackets from break. Condensed write.csv
 and check for distances.csv existing. Fixed a bracket space.

---
 R/distances.R | 59 +++++++++++++++++++++------------------------------
 1 file changed, 24 insertions(+), 35 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 12cb3dd..b774928 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -626,12 +626,12 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
          
          target_dir <- ""
 
-         while(!dir.exists(target_dir)){
+         while(!dir.exists(target_dir)) {
            target_dir <- readline(paste0("Specify the folder to save 'distances.csv'",
                                          " to. Hit enter to skip."))
            if(nchar(target_dir) == 0) {
              dir_decision <- "y"
-             {break}
+             break
            } 
            
            if(!dir.exists(target_dir)) {
@@ -640,54 +640,43 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
                        choices = c("y", "n"))
              if(dir_decision == "n") {
                dir_decision <- "y"
-               {break}
+               break
              }
            }
          }
        }
-    }
+     }
    
     if (decision == "y") {
       
       if(dir_decision == "n") {
         
-        # If a 'file_path' has been specified, a new path is created where 
-        # 'distances.csv' will be saved
-        new_path <- paste(target_dir,"distances.csv", sep = "/")
+        # If a different directory has been specified, a new path is created  
+        # where 'distances.csv' will be saved
+        path <- paste(target_dir,"distances.csv", sep = "/")
+        
+        } else {
+        # If no 'path' specified, then 'distances.csv' is saved to the 
+        # current working directory
+        
+        path <- paste("distances.csv", sep = "/")
         
-        # Checks if 'distances.csv' is already in the file path specified
-        if (file.exists(new_path)) {
-          
-          warning("A file 'distances.csv' is already present in the current",
-                  " directory.", call. = FALSE, immediate. = TRUE)
-          
-          decision <- userInput(paste0("Continuing will overwrite this file.",
-                                "  Would you like to continue?(y/n) "), 
-                                choices = c("y", "n"))
         }
+      # Checks if 'distances.csv' is already in the file path specified
+      if (file.exists(path)) {
         
-        if (decision == "y") {
-          
-          write.csv(round(dist.mat, 0), new_path, row.names = TRUE)
-          
-          }
-      } else {
-        # If no 'file_path' specified, then 'distances.csv' is saved to the 
-        # current working directory
-        if (file.exists('distances.csv')) {
-          warning("A file 'distances.csv' is already present in the current",
-                  " directory.", call. = FALSE, immediate. = TRUE)
-          
-          decision <- userInput(paste0("Continuing will overwrite this file.",
-                                " Would you like to continue?(y/n) "), 
-                                choices = c("y", "n"))
+        warning("A file 'distances.csv' is already present in the current",
+                " directory.", call. = FALSE, immediate. = TRUE)
+        
+        decision <- userInput(paste0("Continuing will overwrite this file.",
+                                     "  Would you like to continue?(y/n) "), 
+                              choices = c("y", "n"))
       }
       if (decision == "y") {
-        write.csv(round(dist.mat, 0), "distances.csv", row.names = TRUE)
-        }
+        
+        write.csv(round(dist.mat, 0), path, row.names = TRUE)
+        
       }
-      
-      
     }
   } # nocov end
   return(round(dist.mat, 0))

From 549c3062fd0614423848897835c02ecb8151599d Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:18:20 -0800
Subject: [PATCH 12/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

accepted Hugo's change

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index b774928..746d491 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -655,13 +655,13 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
         # where 'distances.csv' will be saved
         path <- paste(target_dir,"distances.csv", sep = "/")
         
-        } else {
+      } else {
         # If no 'path' specified, then 'distances.csv' is saved to the 
         # current working directory
         
         path <- paste("distances.csv", sep = "/")
         
-        }
+      }
       # Checks if 'distances.csv' is already in the file path specified
       if (file.exists(path)) {
         

From 4ca4199249ec0c367c8a4ad58b42738125b2b43f Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:19:02 -0800
Subject: [PATCH 13/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Removal of paste0() as per Hugo's requested change.

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 746d491..e0e07da 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -430,12 +430,12 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
     length(suppressWarnings(packageDescription("terra"))))
   missing.packages <- sapply(aux, function(x) x == 1)
   if (any(missing.packages)) {
-    stop(paste0("This function requires packages '", 
-                paste(c("raster", "gdistance", "sp", "terra")[missing.packages], 
-                      collapse = "', '"),
-      "' to operate. Please install ", 
-      ifelse(sum(missing.packages) > 1, "them", "it"), 
-      " before proceeding.\n"), call. = FALSE)
+    stop("This function requires packages '", 
+         paste(c("raster", "gdistance", "sp", "terra")[missing.packages], 
+               collapse = "', '"),
+         "' to operate. Please install ", 
+         ifelse(sum(missing.packages) > 1, "them", "it"), 
+         " before proceeding.\n", call. = FALSE)
   }
 
   if (!inherits(t.layer, "TransitionLayer"))

From e2e51e39b7f6148d46e59248357eda128b8d75aa Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:19:49 -0800
Subject: [PATCH 14/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Acceptance of Hugo;s change of & to &&

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index e0e07da..c139d61 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -455,8 +455,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
     if(!is.null(starters) | !is.null(targets)) {
       # distancesMatrix() crashes if actel = TRUE and starters/targets were 
       # supplied but do not contain a column called "Standard.name"
-      if(!is.null(starters) & !any(grepl(c("Standard.name"), 
-                                         colnames(starters)))) {
+      if(!is.null(starters) && !("Standard.name" %in% colnames(starters))) {
         event("'starters' is missing column called 'Standard.name'",
               type = "stop")
       }

From 7a9ef9b61c6b768146afe3af3f2139b41a65f905 Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:20:19 -0800
Subject: [PATCH 15/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Retention of stop() instead of event()

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index c139d61..a9b6160 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -456,8 +456,8 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
       # distancesMatrix() crashes if actel = TRUE and starters/targets were 
       # supplied but do not contain a column called "Standard.name"
       if(!is.null(starters) && !("Standard.name" %in% colnames(starters))) {
-        event("'starters' is missing column called 'Standard.name'",
-              type = "stop")
+        stop("'starters' is missing column called 'Standard.name'",
+             call. = FALSE)
       }
       
       if(!is.null(targets) & !any(grepl(c("Standard.name"), 

From 21a97c0faa1a126e17a06b0a2fe608ec02f48dbb Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:20:49 -0800
Subject: [PATCH 16/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Retention of stop() instead of event()

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index a9b6160..4ac9d73 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -462,8 +462,8 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
       
       if(!is.null(targets) & !any(grepl(c("Standard.name"), 
                                          colnames(targets)))) {
-        event("'targets' is missing column called 'Standard.name'",
-              type = "stop")
+        stop("'targets' is missing column called 'Standard.name'",
+             call. = FALSE)
       }
     }
     

From a838e9bd81c775a04cd1654896f53c6691cd7d6a Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:21:40 -0800
Subject: [PATCH 17/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Compression of code

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 4ac9d73..8fb1dab 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -626,8 +626,9 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
          target_dir <- ""
 
          while(!dir.exists(target_dir)) {
-           target_dir <- readline(paste0("Specify the folder to save 'distances.csv'",
-                                         " to. Hit enter to skip."))
+           target_dir <- readline(paste0("Specify the folder to save",
+                                         " 'distances.csv' to.",
+                                         " Hit enter to skip."))
            if(nchar(target_dir) == 0) {
              dir_decision <- "y"
              break

From 86ac9d5008149dc3e5dcab8ad0c197418abb6011 Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:22:06 -0800
Subject: [PATCH 18/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Addition of missing space

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/distances.R b/R/distances.R
index 8fb1dab..cff38dd 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -629,7 +629,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
            target_dir <- readline(paste0("Specify the folder to save",
                                          " 'distances.csv' to.",
                                          " Hit enter to skip."))
-           if(nchar(target_dir) == 0) {
+           if (nchar(target_dir) == 0) {
              dir_decision <- "y"
              break
            } 

From 2db30e95377958bd82f5e0849fe30b5962af1b9a Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:22:23 -0800
Subject: [PATCH 19/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Format changes

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index cff38dd..b1529ac 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -634,11 +634,11 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
              break
            } 
            
-           if(!dir.exists(target_dir)) {
+           if (!dir.exists(target_dir)) {
              dir_decision <- userInput(paste0("Directory specified not found.",
                                               " Do you want to continue?(y/n)"),
-                       choices = c("y", "n"))
-             if(dir_decision == "n") {
+                                       choices = c("y", "n"))
+             if (dir_decision == "n") {
                dir_decision <- "y"
                break
              }

From 4ec30af73e9520519552e2609279a5cfd264d163 Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:22:50 -0800
Subject: [PATCH 20/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Use of paste0() instead of paste()

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/distances.R b/R/distances.R
index b1529ac..3dd756e 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -653,7 +653,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
         
         # If a different directory has been specified, a new path is created  
         # where 'distances.csv' will be saved
-        path <- paste(target_dir,"distances.csv", sep = "/")
+        path <- paste0(target_dir, "/distances.csv")
         
       } else {
         # If no 'path' specified, then 'distances.csv' is saved to the 

From 19e8731deb1636c6149a784f99db5a608480802b Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:23:18 -0800
Subject: [PATCH 21/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Format changes

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 3dd756e..5a544c3 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -514,11 +514,11 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
   if (is.na(match(coord.x, colnames(starters)))) {
     stop(paste0("Could not find a column '", 
                 coord.x, "' in 'starters'."), call. = FALSE)
-    }
+  }
   if (is.na(match(coord.y, colnames(starters)))) {
     stop(paste0("Could not find a column '", 
                 coord.y, "' in 'starters'."), call. = FALSE)
-    }
+  }
   if (is.na(match(coord.x, colnames(targets)))) {
     stop(paste0("Could not find a column '", 
                 coord.x, "' in 'targets'."), call. = FALSE)
@@ -526,7 +526,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
   if (is.na(match(coord.y, colnames(targets)))) {
     stop(paste0("Could not find a column '", 
                 coord.y, "' in 'targets'."), call. = FALSE)
-    }
+  }
 
     starters <- starters[, c(id.col, coord.x, coord.y)]
     colnames(starters) <- c(id.col, "longitude", "latitude")

From 866c8ea81795227334a0703b4fe8c542eed7743e Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:23:43 -0800
Subject: [PATCH 22/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

minor format changes

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/distances.R b/R/distances.R
index 5a544c3..6ffb53b 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -574,7 +574,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
 
 
   #### Create starters and targets spatial dataframes
-    # converts the file to a spatialPoints object
+  # converts the file to a spatialPoints object
   sp::coordinates(starters) <- ~ longitude + latitude 
   
   # sets the crs

From e3fdca4afb0c48600705f2a270c836238f653b06 Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:24:00 -0800
Subject: [PATCH 23/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

minor format changes

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/distances.R b/R/distances.R
index 6ffb53b..087265b 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -611,7 +611,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
 
   if (col.rename) {
     colnames(dist.mat) <- outputCols
-    }
+  }
 
   if (interactive() & actel) { # nocov start
     decision <- userInput(paste0("Would you like to save an actel-compatible", 

From 1c6354722c2d153fd77e0e606cf65268cdab1a9b Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:24:21 -0800
Subject: [PATCH 24/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

code compression

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 087265b..5f7fd9f 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -618,9 +618,10 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
                                  " distances matrix as 'distances.csv'?(y/n)"),
                           choices = c("y", "n"))
     if (decision == "y") {
-       dir_decision <- userInput(paste0("Would you like 'distances.csv' saved in",
-                                    " the current working directory?(y/n)"),
-                          choices = c("y", "n"))
+       dir_decision <- userInput(paste0("Would you like 'distances.csv'",
+                                        " saved in the current working",
+                                        " directory?(y/n)"),
+                                 choices = c("y", "n"))
        if (dir_decision == "n") {
          
          target_dir <- ""

From 6c5fd8a43a191348b0aba74ae8684806e4953857 Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:24:37 -0800
Subject: [PATCH 25/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

addition of missing space

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/distances.R b/R/distances.R
index 5f7fd9f..61c894f 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -626,7 +626,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
          
          target_dir <- ""
 
-         while(!dir.exists(target_dir)) {
+         while (!dir.exists(target_dir)) {
            target_dir <- readline(paste0("Specify the folder to save",
                                          " 'distances.csv' to.",
                                          " Hit enter to skip."))

From 750815a7964bd8baa5351408a264c2a275a224d4 Mon Sep 17 00:00:00 2001
From: Devon Smith <79339504+dsmith-unbc@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:24:55 -0800
Subject: [PATCH 26/29] Update R/distances.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

format changes

Co-authored-by: Hugo Flávio <40389021+hugomflavio@users.noreply.github.com>
---
 R/distances.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/distances.R b/R/distances.R
index 61c894f..4f0e17c 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -607,7 +607,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
 
   if (row.rename) {
     rownames(dist.mat) <- outputRows
-    }
+  }
 
   if (col.rename) {
     colnames(dist.mat) <- outputCols

From 6882a8b368ea0a3ef5ba82cf5a7cffaec95a3e2a Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Thu, 5 Dec 2024 17:00:12 -0800
Subject: [PATCH 27/29] Removed actel = TRUE from warnings, changes warnings to
 messages, and added message about starters being used for targets when actel
 = FALSE

---
 R/distances.R | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index 4f0e17c..fb501d0 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -452,7 +452,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
   if (actel) {
     message("M: Creating actel-compatible distances matrix."); flush.console()
     
-    if(!is.null(starters) | !is.null(targets)) {
+    if (!is.null(starters) | !is.null(targets)) {
       # distancesMatrix() crashes if actel = TRUE and starters/targets were 
       # supplied but do not contain a column called "Standard.name"
       if(!is.null(starters) && !("Standard.name" %in% colnames(starters))) {
@@ -460,7 +460,7 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
              call. = FALSE)
       }
       
-      if(!is.null(targets) & !any(grepl(c("Standard.name"), 
+      if (!is.null(targets) & !any(grepl(c("Standard.name"), 
                                          colnames(targets)))) {
         stop("'targets' is missing column called 'Standard.name'",
              call. = FALSE)
@@ -468,22 +468,22 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
     }
     
     if (!is.null(starters) & !is.null(targets)) {
-      warning("'starters' and 'targets' were specified while 'actel'",
-              " is set to TRUE. Using 'starters' and 'targets' for distances.", 
+      message("M: 'starters' and 'targets' were specified.",
+              " Using 'starters' and 'targets' for distances.", 
               call. = FALSE, immediate. = TRUE) 
     }
     
     if (!is.null(starters) & is.null(targets)) {
-        warning("'starters' were specified but 'targets' were not while 'actel'",
-              " is set to TRUE. Using 'starters' for 'targets'.", 
+        message("M: 'starters' were specified but 'targets' were not.",
+                " Using 'starters' for 'targets'.", 
               call. = FALSE, immediate. = TRUE) 
       
         targets <- starters
         }
     
     if (is.null(starters) & is.null(targets)) {
-        warning("'starters' and 'targets' were not set while 'actel' is set to",
-              " TRUE. Creating 'starters' and 'targets' from 'spatial.csv' ",
+        message("M: 'starters' and 'targets' were not specified.",
+              " Creating 'starters' and 'targets' from 'spatial.csv' ",
               " in working directory." , call. = FALSE, immediate. = TRUE)
         starters <- targets <- loadSpatial() 
         }
@@ -492,15 +492,19 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
       warning("id.col' was set but will be ignored because 'actel' is set to", 
               " TRUE. Set 'actel' to FALSE to use the 'id.col' argument.", 
               call. = FALSE, immediate. = TRUE) 
-      }
+        }
     id.col <- "Standard.name"
   }
   
   # Failsafe from old way code worked where targets used starters by default 
   # when actel == FALSE
-  if(!actel) {
-    if(is.null(targets)) {
+  if (!actel) {
+    if (is.null(targets)) {
       targets <- starters
+        message("M: 'starters' were specified but 'targets' were not.",
+                " Using 'starters' for 'targets'.", 
+                call. = FALSE, immediate. = TRUE) 
+      }
     }
   }
 

From 4ab77490008c9b0fdac300b9f92a1c190a26f7ef Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Thu, 5 Dec 2024 17:02:12 -0800
Subject: [PATCH 28/29] minor fix to if statement

---
 R/distances.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/distances.R b/R/distances.R
index fb501d0..237ab41 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -455,13 +455,12 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
     if (!is.null(starters) | !is.null(targets)) {
       # distancesMatrix() crashes if actel = TRUE and starters/targets were 
       # supplied but do not contain a column called "Standard.name"
-      if(!is.null(starters) && !("Standard.name" %in% colnames(starters))) {
+      if (!is.null(starters) && !("Standard.name" %in% colnames(starters))) {
         stop("'starters' is missing column called 'Standard.name'",
              call. = FALSE)
       }
       
-      if (!is.null(targets) & !any(grepl(c("Standard.name"), 
-                                         colnames(targets)))) {
+      if (!is.null(targets) && !("Standard.name" %in% colnames(targets))) {
         stop("'targets' is missing column called 'Standard.name'",
              call. = FALSE)
       }

From 4f022f9fada4a7e4b79bc364c414ff86428fc4b5 Mon Sep 17 00:00:00 2001
From: Devon Smith <devon-smith-1@hotmail.com>
Date: Fri, 6 Dec 2024 11:05:10 -0800
Subject: [PATCH 29/29] fixed bracket issue causing checks to fail.

---
 R/distances.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/distances.R b/R/distances.R
index 237ab41..446016c 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -505,7 +505,6 @@ distancesMatrix <- function(t.layer, starters = NULL, targets = NULL,
                 call. = FALSE, immediate. = TRUE) 
       }
     }
-  }
 
   if (!inherits(starters, "data.frame")) {
     stop("'starters' must be a data frame.\n", call. = FALSE)