diff --git a/NEWS.md b/NEWS.md
index 2305313..a4d45a4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -23,6 +23,7 @@ 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 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
diff --git a/R/distances.R b/R/distances.R
index 912c65e..446016c 100644
--- a/R/distances.R
+++ b/R/distances.R
@@ -342,26 +342,35 @@ 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 or the output of `loadSpatial()`.
+#' @param targets A data frame with the points to which a way must be found.
+#' @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.
#'
#' @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 +379,10 @@ 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
@@ -409,7 +420,7 @@ transitionLayer <- function(x, directions = c(16, 8, 4)){
#'
#' @export
#'
-distancesMatrix <- function(t.layer, starters = NULL, targets = starters,
+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(
@@ -419,41 +430,105 @@ 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("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)) {
+ # 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))) {
+ stop("'starters' is missing column called 'Standard.name'",
+ call. = FALSE)
+ }
+
+ if (!is.null(targets) && !("Standard.name" %in% colnames(targets))) {
+ stop("'targets' is missing column called 'Standard.name'",
+ call. = FALSE)
+ }
+ }
+
+ if (!is.null(starters) & !is.null(targets)) {
+ message("M: 'starters' and 'targets' were specified.",
+ " Using 'starters' and 'targets' for distances.",
+ call. = FALSE, immediate. = TRUE)
+ }
+
+ if (!is.null(starters) & is.null(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)) {
+ 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()
+ }
+
+ 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"
}
+
+ # Failsafe from old way code worked where targets used starters by default
+ # when actel == FALSE
+ 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)
+ }
+ }
- 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 +540,33 @@ 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 +576,110 @@ 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(paste0("Would you like to save an actel-compatible",
+ " distances matrix as 'distances.csv'?(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"))
+ 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(dir_decision == "n") {
+
+ # If a different directory has been specified, a new path is created
+ # where 'distances.csv' will be saved
+ path <- paste0(target_dir, "/distances.csv")
+
+ } 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)) {
+
+ 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), path, row.names = TRUE)
+
}
- if (decision == "y")
- write.csv(round(dist.mat, 0), "distances.csv", row.names = TRUE)
}
} # nocov end
return(round(dist.mat, 0))
diff --git a/man/distancesMatrix.Rd b/man/distancesMatrix.Rd
index 5a1beab..8e3ca16 100644
--- a/man/distancesMatrix.Rd
+++ b/man/distancesMatrix.Rd
@@ -7,7 +7,7 @@
distancesMatrix(
t.layer,
starters = NULL,
- targets = starters,
+ targets = NULL,
coord.x = "x",
coord.y = "y",
id.col = NULL,
@@ -15,36 +15,45 @@ distancesMatrix(
)
}
\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 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 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{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 +62,10 @@ 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
diff --git a/tests/testthat/test_distancesMatrix_functions.R b/tests/testthat/test_distancesMatrix_functions.R
index 4029393..fbd24c4 100644
--- a/tests/testthat/test_distancesMatrix_functions.R
+++ b/tests/testthat/test_distancesMatrix_functions.R
@@ -103,13 +103,15 @@ 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
-
+
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)
@@ -126,13 +128,9 @@ will artificially add water space around the shape file.", fixed = TRUE)
"'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
@@ -162,7 +160,22 @@ will artificially add water space around the shape file.", fixed = TRUE)
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)
})
-
+
+ test_loadspatial <- loadSpatial()
+
+ 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", 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))
+ 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))
+ })
+
+ rm(test_loadspatial)
+
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 = "."))