tests/testthat/test_distancesMatrix_functions.R
In hugomflavio/actel: Acoustic Telemetry Data Analysis
skip_on_cran()
aux <- c(
length(suppressWarnings(packageDescription("raster"))),
length(suppressWarnings(packageDescription("gdistance"))),
length(suppressWarnings(packageDescription("sp"))),
length(suppressWarnings(packageDescription("terra"))))
missing.packages <- sapply(aux, function(x) x == 1)
if (any(missing.packages)) {
test_that("shapeToRaster, transitionLayer and distancesMatrix stop due to missing dependencies", {
expect_error(shapeToRaster(),
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"), fixed = TRUE)
expect_error(transitionLayer(),
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"), fixed = TRUE)
expect_error(distancesMatrix(),
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"), fixed = TRUE)
})
} else {
if (suppressWarnings(require("gdistance"))) {
tests.home <- getwd()
setwd(tempdir())
shape.path <- paste0(tests.home, "/aux_transitionLayer.shp")
test_that("shapeToRaster complains if coord.y or coord.x are given and spatial.csv is not present", {
expect_warning(shapeToRaster(shape = shape.path,
size = 10, coord.x = "x.32632", coord.y = "y.32632"),
"Could not find a spatial.csv file in the current working directory. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path,
size = 10, coord.x = "x.32632"),
"'coord.x' was set but 'coord.y' was not. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path,
size = 10, coord.y = "x.32632"),
"'coord.y' was set but 'coord.x' was not. Skipping range check.", fixed = TRUE)
})
xspatial <- example.spatial[8:11, ]
xspatial$x.32632 <- c(453568, 453400, 453047, 452975)
xspatial$y.32632 <- c(6242912, 6242630, 6242387, 6242169)
write.csv(xspatial, "spatial.csv", row.names = FALSE)
test_that("shapeToRaster complains if coord.y or coord.x are not valid column names", {
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "test", coord.y = "y.32632", type = "water"),
"Could not find column 'test' in the spatial data frame. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "x.32632", coord.y = "test"),
"Could not find column 'test' in the spatial data frame. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "test2", coord.y = "test"),
"Could not find columns 'test2' and 'test' in the spatial data frame. Skipping range check.", fixed = TRUE)
})
test_that("shapeToRaster only allows valid buffers", {
expect_error(shapeToRaster(shape = shape.path, size = 10, buffer = "a"),
"'buffer' must be numeric (in metres or degrees, depending on the shape coordinate system).", fixed = TRUE)
expect_error(shapeToRaster(shape = shape.path, size = 10, buffer = 1:2),
"'buffer' must either contain one value (applied to all four corners), or four values (applied to xmin, xmax, ymin and ymax, respectively)", fixed = TRUE)
expect_error(shapeToRaster(shape = shape.path, size = 10, buffer = -1),
"'buffer' values cannot be negative.", fixed = TRUE)
tryCatch(shapeToRaster(shape = shape.path, size = 10, buffer = 100),
warning = function(w) stop(paste("A warning was issued where it should not have been. This was the warning:", w)))
tryCatch(base.raster <<- shapeToRaster(shape = paste0(tests.home, "/aux_transitionLayer.shp"), size = 10, buffer = c(50, 100, 200, 250)),
warning = function(w) stop(paste("A warning was issued where it should not have been. This was the warning:", w)))
})
test_that("shapeToRaster stops if shape is not present or is not .shp", {
expect_error(shapeToRaster(shape = "test/test.shp", size = 10, buffer = 100),
"Could not find file 'test/test.shp'.", fixed = TRUE)
expect_error(shapeToRaster(shape = "test.shp", size = 10, buffer = 100),
"Could not find file 'test.shp'.", fixed = TRUE)
write.table(1, "test.txt")
expect_error(shapeToRaster(shape = "test.txt", size = 10, buffer = 100),
"'shape' must be a .shp file.", fixed = TRUE)
file.remove("test.txt")
})
test_that("transitionLayer is working properly", {
tryCatch(t.layer <- transitionLayer(base.raster),
warning = function(w) stop(paste("A warning was issued where it should not have been. This was the warning:", w)))
expect_equal(as.character(class(t.layer)), "TransitionLayer")
})
base.raster <- shapeToRaster(shape = shape.path, size = 5,
coord.x = "x.32632", coord.y = "y.32632")
t.layer <- transitionLayer(base.raster)
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),
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)
expect_error(distancesMatrix(t.layer = t.layer, id.col = 2),
"Please refer to the column name in 'id.col', rather than the column index.", fixed = TRUE)
expect_error(distancesMatrix(t.layer = "test"),
"Could not recognise 't.layer' as a TransitionLayer object. Make sure to compile it using the function transitionLayer.\n", fixed = TRUE)
write.table(1, "test.txt")
expect_error(distancesMatrix(t.layer = t.layer,
coord.x = "x.32632", coord.y = "y.32632", starters = "test.txt", actel = FALSE),
"'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", 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
# n
base.raster <- shapeToRaster(shape = shape.path, size = 5,
coord.x = "x.32632", coord.y = "y.32632", buffer = 100)
t.layer <- transitionLayer(base.raster)
test_that("distancesMatrix handles bad data correctly pt2", {
expect_warning(distancesMatrix(t.layer = t.layer,
coord.x = "x.32632", coord.y = "y.32632", starters = loadSpatial(), id.col = "Array", actel = FALSE),
"The 'Array' column in 'starters' contains duplicated values; skipping row naming.", fixed = TRUE)
expect_warning(distancesMatrix(t.layer = t.layer,
coord.x = "x.32632", coord.y = "y.32632", starters = loadSpatial(), id.col = "Array", actel = FALSE),
"The 'Array' column in 'targets' contains duplicated values; skipping column naming.", fixed = TRUE)
colnames(xspatial)[ncol(xspatial)] <- "test"
write.csv(xspatial, "spatial2.csv", row.names = FALSE)
expect_error(distancesMatrix(t.layer = t.layer,
coord.x = "test", coord.y = "y.32632", starters = loadSpatial(), targets = loadSpatial("spatial2.csv"), actel = FALSE),
"Could not find a column 'test' in 'starters'.", fixed = TRUE)
expect_error(distancesMatrix(t.layer = t.layer,
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 = "."))
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))
})
# n
xspatial <- example.spatial[8:11, ]
xspatial$x.32632 <- c(454568, 453400, 452047, 452975)
xspatial$y.32632 <- c(6243912, 6242630, 6242387, 6241169)
test_that("shapeToRaster expands the grid range if the spatial objects are outside the shape range.", {
expect_message(shapeToRaster(shape = shape.path, size = 10,
coord.x = "x.32632", coord.y = "y.32632", spatial = xspatial),
"Extending the shape ranges with open water to ensure the stations fit inside it.", fixed = TRUE)
})
xspatial <- example.spatial[8:11, ]
xspatial$x.32632 <- c(453500, 453400, 452047, 452975)
xspatial$y.32632 <- c(6242800, 6242630, 6242387, 6241169)
test_that("shapeToRaster expands the grid range if the spatial objects are outside the shape range.", {
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "x.32632", coord.y = "y.32632", spatial = xspatial),
"Station 'Station 7' is not placed in water! This can cause several problems.", fixed = TRUE)
})
file.remove("spatial.csv")
setwd(tests.home)
rm(list = ls())
}
}
# n
# n
# n
# n
# ------------------------
# Manual functions
tests.home <- getwd()
setwd(tempdir())
test_that("emptyMatrix stops if the required file are not present.", {
expect_error(emptyMatrix(), "Could not find file 'spatial.csv'.", fixed = TRUE)
})
test_that("emptyMatrix creates a distances matrix with the correct structure", {
dist.mat <<- emptyMatrix(paste0(system.file(package = "actel")[1], "/example_spatial.csv"))
expect_equal(ncol(dist.mat), nrow(dist.mat))
expect_true(sum(is.na(dist.mat)) == (ncol(dist.mat) ^ 2) - ncol(dist.mat))
})
for(i in 2:ncol(dist.mat)) {
for(j in 1:(i - 1)) {
dist.mat[j, i] <- i + j
}
}
test_that("completeMatrix works as expected", {
expect_error(completeMatrix("a"), "The input must be a matrix", fixed = TRUE)
expect_error(completeMatrix(matrix(ncol = 2, nrow = 3)), "The matrix does not contain the same number of columns and rows. Aborting.", fixed = TRUE)
output <- completeMatrix(dist.mat)
for(i in 2:ncol(output)) {
for(j in 1:(i - 1)) {
expect_equal(output[i, j], i + j)
}
}
})
setwd(tests.home)
rm(list = ls())
hugomflavio/actel documentation built on June 11, 2025, 5:02 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
skip_on_cran()
aux <- c(
length(suppressWarnings(packageDescription("raster"))),
length(suppressWarnings(packageDescription("gdistance"))),
length(suppressWarnings(packageDescription("sp"))),
length(suppressWarnings(packageDescription("terra"))))
missing.packages <- sapply(aux, function(x) x == 1)
if (any(missing.packages)) {
test_that("shapeToRaster, transitionLayer and distancesMatrix stop due to missing dependencies", {
expect_error(shapeToRaster(),
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"), fixed = TRUE)
expect_error(transitionLayer(),
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"), fixed = TRUE)
expect_error(distancesMatrix(),
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"), fixed = TRUE)
})
} else {
if (suppressWarnings(require("gdistance"))) {
tests.home <- getwd()
setwd(tempdir())
shape.path <- paste0(tests.home, "/aux_transitionLayer.shp")
test_that("shapeToRaster complains if coord.y or coord.x are given and spatial.csv is not present", {
expect_warning(shapeToRaster(shape = shape.path,
size = 10, coord.x = "x.32632", coord.y = "y.32632"),
"Could not find a spatial.csv file in the current working directory. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path,
size = 10, coord.x = "x.32632"),
"'coord.x' was set but 'coord.y' was not. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path,
size = 10, coord.y = "x.32632"),
"'coord.y' was set but 'coord.x' was not. Skipping range check.", fixed = TRUE)
})
xspatial <- example.spatial[8:11, ]
xspatial$x.32632 <- c(453568, 453400, 453047, 452975)
xspatial$y.32632 <- c(6242912, 6242630, 6242387, 6242169)
write.csv(xspatial, "spatial.csv", row.names = FALSE)
test_that("shapeToRaster complains if coord.y or coord.x are not valid column names", {
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "test", coord.y = "y.32632", type = "water"),
"Could not find column 'test' in the spatial data frame. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "x.32632", coord.y = "test"),
"Could not find column 'test' in the spatial data frame. Skipping range check.", fixed = TRUE)
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "test2", coord.y = "test"),
"Could not find columns 'test2' and 'test' in the spatial data frame. Skipping range check.", fixed = TRUE)
})
test_that("shapeToRaster only allows valid buffers", {
expect_error(shapeToRaster(shape = shape.path, size = 10, buffer = "a"),
"'buffer' must be numeric (in metres or degrees, depending on the shape coordinate system).", fixed = TRUE)
expect_error(shapeToRaster(shape = shape.path, size = 10, buffer = 1:2),
"'buffer' must either contain one value (applied to all four corners), or four values (applied to xmin, xmax, ymin and ymax, respectively)", fixed = TRUE)
expect_error(shapeToRaster(shape = shape.path, size = 10, buffer = -1),
"'buffer' values cannot be negative.", fixed = TRUE)
tryCatch(shapeToRaster(shape = shape.path, size = 10, buffer = 100),
warning = function(w) stop(paste("A warning was issued where it should not have been. This was the warning:", w)))
tryCatch(base.raster <<- shapeToRaster(shape = paste0(tests.home, "/aux_transitionLayer.shp"), size = 10, buffer = c(50, 100, 200, 250)),
warning = function(w) stop(paste("A warning was issued where it should not have been. This was the warning:", w)))
})
test_that("shapeToRaster stops if shape is not present or is not .shp", {
expect_error(shapeToRaster(shape = "test/test.shp", size = 10, buffer = 100),
"Could not find file 'test/test.shp'.", fixed = TRUE)
expect_error(shapeToRaster(shape = "test.shp", size = 10, buffer = 100),
"Could not find file 'test.shp'.", fixed = TRUE)
write.table(1, "test.txt")
expect_error(shapeToRaster(shape = "test.txt", size = 10, buffer = 100),
"'shape' must be a .shp file.", fixed = TRUE)
file.remove("test.txt")
})
test_that("transitionLayer is working properly", {
tryCatch(t.layer <- transitionLayer(base.raster),
warning = function(w) stop(paste("A warning was issued where it should not have been. This was the warning:", w)))
expect_equal(as.character(class(t.layer)), "TransitionLayer")
})
base.raster <- shapeToRaster(shape = shape.path, size = 5,
coord.x = "x.32632", coord.y = "y.32632")
t.layer <- transitionLayer(base.raster)
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),
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)
expect_error(distancesMatrix(t.layer = t.layer, id.col = 2),
"Please refer to the column name in 'id.col', rather than the column index.", fixed = TRUE)
expect_error(distancesMatrix(t.layer = "test"),
"Could not recognise 't.layer' as a TransitionLayer object. Make sure to compile it using the function transitionLayer.\n", fixed = TRUE)
write.table(1, "test.txt")
expect_error(distancesMatrix(t.layer = t.layer,
coord.x = "x.32632", coord.y = "y.32632", starters = "test.txt", actel = FALSE),
"'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", 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
# n
base.raster <- shapeToRaster(shape = shape.path, size = 5,
coord.x = "x.32632", coord.y = "y.32632", buffer = 100)
t.layer <- transitionLayer(base.raster)
test_that("distancesMatrix handles bad data correctly pt2", {
expect_warning(distancesMatrix(t.layer = t.layer,
coord.x = "x.32632", coord.y = "y.32632", starters = loadSpatial(), id.col = "Array", actel = FALSE),
"The 'Array' column in 'starters' contains duplicated values; skipping row naming.", fixed = TRUE)
expect_warning(distancesMatrix(t.layer = t.layer,
coord.x = "x.32632", coord.y = "y.32632", starters = loadSpatial(), id.col = "Array", actel = FALSE),
"The 'Array' column in 'targets' contains duplicated values; skipping column naming.", fixed = TRUE)
colnames(xspatial)[ncol(xspatial)] <- "test"
write.csv(xspatial, "spatial2.csv", row.names = FALSE)
expect_error(distancesMatrix(t.layer = t.layer,
coord.x = "test", coord.y = "y.32632", starters = loadSpatial(), targets = loadSpatial("spatial2.csv"), actel = FALSE),
"Could not find a column 'test' in 'starters'.", fixed = TRUE)
expect_error(distancesMatrix(t.layer = t.layer,
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 = "."))
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))
})
# n
xspatial <- example.spatial[8:11, ]
xspatial$x.32632 <- c(454568, 453400, 452047, 452975)
xspatial$y.32632 <- c(6243912, 6242630, 6242387, 6241169)
test_that("shapeToRaster expands the grid range if the spatial objects are outside the shape range.", {
expect_message(shapeToRaster(shape = shape.path, size = 10,
coord.x = "x.32632", coord.y = "y.32632", spatial = xspatial),
"Extending the shape ranges with open water to ensure the stations fit inside it.", fixed = TRUE)
})
xspatial <- example.spatial[8:11, ]
xspatial$x.32632 <- c(453500, 453400, 452047, 452975)
xspatial$y.32632 <- c(6242800, 6242630, 6242387, 6241169)
test_that("shapeToRaster expands the grid range if the spatial objects are outside the shape range.", {
expect_warning(shapeToRaster(shape = shape.path, size = 10,
coord.x = "x.32632", coord.y = "y.32632", spatial = xspatial),
"Station 'Station 7' is not placed in water! This can cause several problems.", fixed = TRUE)
})
file.remove("spatial.csv")
setwd(tests.home)
rm(list = ls())
}
}
# n
# n
# n
# n
# ------------------------
# Manual functions
tests.home <- getwd()
setwd(tempdir())
test_that("emptyMatrix stops if the required file are not present.", {
expect_error(emptyMatrix(), "Could not find file 'spatial.csv'.", fixed = TRUE)
})
test_that("emptyMatrix creates a distances matrix with the correct structure", {
dist.mat <<- emptyMatrix(paste0(system.file(package = "actel")[1], "/example_spatial.csv"))
expect_equal(ncol(dist.mat), nrow(dist.mat))
expect_true(sum(is.na(dist.mat)) == (ncol(dist.mat) ^ 2) - ncol(dist.mat))
})
for(i in 2:ncol(dist.mat)) {
for(j in 1:(i - 1)) {
dist.mat[j, i] <- i + j
}
}
test_that("completeMatrix works as expected", {
expect_error(completeMatrix("a"), "The input must be a matrix", fixed = TRUE)
expect_error(completeMatrix(matrix(ncol = 2, nrow = 3)), "The matrix does not contain the same number of columns and rows. Aborting.", fixed = TRUE)
output <- completeMatrix(dist.mat)
for(i in 2:ncol(output)) {
for(j in 1:(i - 1)) {
expect_equal(output[i, j], i + j)
}
}
})
setwd(tests.home)
rm(list = ls())
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