Nothing
test_that("x = SpatRaster, features = SpatRaster", {
# import data
sim_pu_raster <- get_sim_pu_raster()
sim_features <- get_sim_features()
# create problem
sim_pu_raster <- terra::setValues(
sim_pu_raster, runif(terra::ncell(sim_pu_raster), -1, 1)
)
sim_features[[1]] <- terra::setValues(
sim_features[[1]], runif(terra::ncell(sim_features[[1]]), -1, 1)
)
expect_warning(x <- problem(sim_pu_raster, sim_features), "negative")
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
suppressMessages(x$print())
suppressMessages(x$show())
suppressMessages(x$repr())
# tests for integer fields
expect_equal(x$feature_names(), names(sim_features))
expect_equal(x$zone_names(), names(sim_pu_raster))
expect_equal(x$number_of_features(), terra::nlyr(sim_features))
expect_equal(
x$number_of_planning_units(),
length(terra::cells(is.na(sim_pu_raster), 0)[[1]])
)
expect_equal(x$number_of_total_units(), terra::ncell(sim_pu_raster))
expect_equal(
x$planning_unit_indices(),
terra::cells(is.na(sim_pu_raster), 0)[[1]]
)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
sim_pu_raster[[1]][!is.na(sim_pu_raster)],
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), names(sim_pu_raster))
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
terra::global(
terra::mask(sim_features, sim_pu_raster), "sum", na.rm = TRUE
)[[1]]
),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
x$zone_names()
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
x$feature_names()
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(terra::global(sim_features, "sum", na.rm = TRUE)[[1]], ncol = 1),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
x$zone_names()
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
x$feature_names()
)
# tests for rij_matrix field
expect_equal(
x$data$rij_matrix,
list(rij_matrix(sim_pu_raster, sim_features)),
ignore_attr = TRUE
)
expect_equal(names(x$data$rij_matrix), x$zone_names())
expect_equal(rownames(x$data$rij_matrix[[1]]), x$feature_names())
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = SpatRaster, features = ZonesSpatRaster", {
# import data
sim_zones_pu_raster <- get_sim_zones_pu_raster()
sim_zones_features <- get_sim_zones_features()
sim_units_mask <- max(!is.na(sim_zones_pu_raster))
# create problem
x <- problem(sim_zones_pu_raster, sim_zones_features)
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), feature_names(sim_zones_features))
expect_equal(x$zone_names(), zone_names(sim_zones_features))
expect_equal(x$number_of_features(), number_of_features(sim_zones_features))
expect_equal(x$number_of_zones(), number_of_zones(sim_zones_features))
expect_equal(
x$number_of_planning_units(),
terra::global(max(!is.na(sim_zones_pu_raster)), "sum", na.rm = TRUE)[[1]]
)
expect_equal(
x$planning_unit_indices(),
terra::cells(min(is.na(sim_zones_pu_raster)), 0)[[1]]
)
expect_equal(x$number_of_total_units(), terra::ncell(sim_zones_pu_raster))
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
sim_zones_pu_raster[min(is.na(sim_zones_pu_raster)) == 0],
ignore_attr = TRUE
)
expect_equal(
colnames(x$planning_unit_costs()),
zone_names(sim_zones_features)
)
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
sapply(seq_len(terra::nlyr(sim_zones_pu_raster)), function(i) {
terra::global(
terra::mask(sim_zones_features[[i]], sim_zones_pu_raster[[i]]),
"sum", na.rm = TRUE
)[[1]]
}),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
zone_names(sim_zones_features)
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
feature_names(sim_zones_features)
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
sapply(seq_len(terra::nlyr(sim_zones_pu_raster)), function(i) {
terra::global(sim_zones_features[[i]], "sum", na.rm = TRUE)[[1]]
}),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
zone_names(sim_zones_features)
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
feature_names(sim_zones_features)
)
# tests for rij_matrix field
expect_equal(
x$data$rij_matrix,
lapply(
seq_len(terra::nlyr(sim_zones_pu_raster)), function(i) {
l <- sim_zones_pu_raster[[i]]
l <- terra::mask(l, sim_units_mask, maskvalues = 0)
l[which(is.na(terra::values(l)[x$planning_unit_indices()]))] <- 0
m <- rij_matrix(l, sim_zones_features[[i]])
rownames(m) <- x$feature_names()
m
}
),
ignore_attr = TRUE
)
expect_equal(names(x$data$rij_matrix), zone_names(sim_zones_features))
expect_equal(
sapply(x$data$rij_matrix, rownames),
matrix(
feature_names(sim_zones_features),
ncol = number_of_zones(sim_zones_features),
nrow = number_of_features(sim_zones_features)
),
ignore_attr = TRUE
)
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = sf, features = SpatRaster", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_features <- get_sim_features()
# create problem
x <- problem(sim_pu_polygons, sim_features, "cost")
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), names(sim_features))
expect_equal(x$zone_names(), "cost")
expect_equal(x$number_of_features(), terra::nlyr(sim_features))
expect_equal(x$number_of_planning_units(), sum(!is.na(sim_pu_polygons$cost)))
expect_equal(x$planning_unit_indices(), which(!is.na(sim_pu_polygons$cost)))
expect_equal(x$number_of_total_units(), nrow(sim_pu_polygons))
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
matrix(sim_pu_polygons$cost[!is.na(sim_pu_polygons$cost)], ncol = 1),
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), "cost")
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
Matrix::rowSums(x$data$rij_matrix[[1]]),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
"cost"
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
names(sim_features)
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(
colSums(
exactextractr::exact_extract(
sim_features, sim_pu_polygons, "sum", progress = FALSE
)
),
ncol = 1
),
ignore_attr = TRUE,
tolerance = 1e-6
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
"cost"
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
names(sim_features)
)
# tests for rij_matrix field
expect_equal(
x$data$rij_matrix,
list(
rij_matrix(
sim_pu_polygons[!is.na(sim_pu_polygons[[1]]), ], sim_features
)
),
ignore_attr = TRUE
)
expect_equal(names(x$data$rij_matrix), "cost")
expect_equal(rownames(x$data$rij_matrix[[1]]), names(sim_features))
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = sf, features = ZonesSpatRaster", {
# import data
sim_zones_pu_polygons <- get_sim_zones_pu_polygons()
sim_zones_features <- get_sim_zones_features()
# update data
sim_zones_pu_polygons[5, paste0("cost_", 1:3)] <- NA
# create problem
x <- problem(sim_zones_pu_polygons, sim_zones_features, paste0("cost_", 1:3))
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), feature_names(sim_zones_features))
expect_equal(x$zone_names(), zone_names(sim_zones_features))
expect_equal(x$number_of_features(), terra::nlyr(sim_zones_features[[1]]))
expect_equal(x$number_of_planning_units(), nrow(sim_zones_pu_polygons) - 1)
expect_equal(
x$planning_unit_indices(),
c(seq_len(4), seq(6, nrow(sim_zones_pu_polygons)))
)
expect_equal(x$number_of_total_units(), nrow(sim_zones_pu_polygons))
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
as.matrix(
sf::st_drop_geometry(sim_zones_pu_polygons)[-5, paste0("cost_", 1:3)]
),
ignore_attr = TRUE
)
expect_equal(
colnames(x$planning_unit_costs()),
zone_names(sim_zones_features)
)
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
sapply(seq_along(x$data$rij_matrix), function(i) {
pos1 <- x$planning_unit_indices()
pos2 <- which(!is.na(sim_zones_pu_polygons[[paste0("cost_", i)]]))
pos3 <- match(pos2, pos1)
Matrix::rowSums(x$data$rij_matrix[[i]][, pos3, drop = FALSE])
}),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
zone_names(sim_zones_features)
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
feature_names(sim_zones_features)
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
sapply(
lapply(
sim_zones_features,
function(x) {
terra::extract(
x, terra::vect(sim_zones_pu_polygons), "sum", na.rm = TRUE,
ID = FALSE
)
}
),
colSums,
na.rm = TRUE
),
ignore_attr = TRUE,
tolerance = 1e-6
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
zone_names(sim_zones_features)
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
feature_names(sim_zones_features)
)
# tests for rij_matrix field
expect_equal(
x$data$rij_matrix,
lapply(sim_zones_features, function(l) {
m <- rij_matrix(x = sim_zones_pu_polygons[-5, ], y = l)
rownames(m) <- x$feature_names()
m
}),
ignore_attr = TRUE
)
expect_equal(names(x$data$rij_matrix), zone_names(sim_zones_features))
expect_equal(
sapply(x$data$rij_matrix, rownames),
matrix(
feature_names(sim_zones_features),
ncol = number_of_zones(sim_zones_features),
nrow = number_of_features(sim_zones_features)
),
ignore_attr = TRUE
)
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = sf, features = character", {
# create data
sim_pu_polygons <- get_sim_pu_polygons()
# update data
sim_pu_polygons$cost[2] <- NA
sim_pu_polygons$spp1 <- runif(nrow(sim_pu_polygons))
sim_pu_polygons$spp2 <- c(NA, rpois(nrow(sim_pu_polygons) - 1, 5))
# create problem
x <- problem(sim_pu_polygons, c("spp1", "spp2"), "cost")
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), c("spp1", "spp2"))
expect_equal(x$zone_names(), "cost")
expect_equal(x$number_of_features(), 2)
expect_equal(x$number_of_zones(), 1)
expect_equal(x$number_of_planning_units(), nrow(sim_pu_polygons) - 1)
expect_equal(x$planning_unit_indices(), c(1, seq(3, nrow(sim_pu_polygons))))
expect_equal(x$number_of_total_units(), nrow(sim_pu_polygons))
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
matrix(sim_pu_polygons$cost[-2], ncol = 1),
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), "cost")
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
colSums(
sf::st_drop_geometry(sim_pu_polygons)[-2, c("spp1", "spp2")],
na.rm = TRUE
),
ncol = 1
),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
"cost"
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
c("spp1", "spp2")
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(
colSums(
sf::st_drop_geometry(sim_pu_polygons)[, c("spp1", "spp2")],
na.rm = TRUE
),
ncol = 1
),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
"cost"
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
c("spp1", "spp2")
)
# tests for rij_matrix field
rij <- Matrix::sparseMatrix(
i = c(
rep(1, nrow(sim_pu_polygons) - 1),
rep(2, nrow(sim_pu_polygons) - 2)
),
j = c(
seq_len(nrow(sim_pu_polygons) - 1),
seq_len(nrow(sim_pu_polygons) - 1)[-1]
),
x = c(
sim_pu_polygons$spp1[-2],
sim_pu_polygons$spp2[c(-1, -2)]
),
dims = c(2, nrow(sim_pu_polygons) - 1)
)
rij <- list(rij)
expect_true(all(x$data$rij_matrix[[1]] == rij[[1]]))
expect_equal(names(x$data$rij_matrix), "cost")
expect_equal(rownames(x$data$rij_matrix[[1]]), c("spp1", "spp2"))
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = sf, features = ZonesCharacter", {
# create data
sim_zones_pu_polygons <- get_sim_zones_pu_polygons()
# update data
sim_zones_pu_polygons$cost_1[2] <- NA
sim_zones_pu_polygons[3, c("cost_1", "cost_2")] <- NA
sim_zones_pu_polygons$spp1_1 <- runif(nrow(sim_zones_pu_polygons))
sim_zones_pu_polygons$spp2_1 <-
c(NA, rpois(nrow(sim_zones_pu_polygons) - 1, 5))
sim_zones_pu_polygons$spp1_2 <- runif(nrow(sim_zones_pu_polygons))
sim_zones_pu_polygons$spp2_2 <- runif(nrow(sim_zones_pu_polygons))
sim_zones_pu_polygons <- sim_zones_pu_polygons[1:5, ]
# create problem
x <- problem(
sim_zones_pu_polygons,
zones(
c("spp1_1", "spp2_1"), c("spp1_2", "spp2_2"),
zone_names = c("z1", "z2"),
feature_names = c("spp1", "spp2")),
c("cost_1", "cost_2")
)
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), c("spp1", "spp2"))
expect_equal(x$zone_names(), c("z1", "z2"))
expect_equal(x$number_of_features(), 2)
expect_equal(x$number_of_zones(), 2)
expect_equal(x$number_of_planning_units(), nrow(sim_zones_pu_polygons) - 1)
expect_equal(
x$planning_unit_indices(),
c(c(1, 2), seq(4, nrow(sim_zones_pu_polygons)))
)
expect_equal(x$number_of_total_units(), nrow(sim_zones_pu_polygons))
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
as.matrix(
sf::st_drop_geometry(sim_zones_pu_polygons)[-3, c("cost_1", "cost_2")]
),
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), c("z1", "z2"))
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
c(
sum(
sim_zones_pu_polygons$spp1_1[!is.na(sim_zones_pu_polygons$cost_1)],
na.rm = TRUE
),
sum(
sim_zones_pu_polygons$spp2_1[!is.na(sim_zones_pu_polygons$cost_1)],
na.rm = TRUE
),
sum(
sim_zones_pu_polygons$spp1_2[!is.na(sim_zones_pu_polygons$cost_2)],
na.rm = TRUE
),
sum(
sim_zones_pu_polygons$spp2_2[!is.na(sim_zones_pu_polygons$cost_2)],
na.rm = TRUE
)
),
ncol = 2,
dimnames = list(x$feature_names(), x$zone_names())
),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
c("z1", "z2")
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
c("spp1", "spp2")
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(
colSums(
sf::st_drop_geometry(sim_zones_pu_polygons)[,
c("spp1_1", "spp2_1", "spp1_2", "spp2_2")
],
na.rm = TRUE
),
ncol = 2
),
ignore_attr = TRUE
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
c("z1", "z2")
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
c("spp1", "spp2")
)
# tests for rij_matrix field
r1 <- Matrix::sparseMatrix(
i = c(
rep(1, nrow(sim_zones_pu_polygons) - 1),
rep(2, nrow(sim_zones_pu_polygons) - 2)
),
j = c(
seq_len(nrow(sim_zones_pu_polygons) - 1),
seq_len(nrow(sim_zones_pu_polygons) - 1)[-1]
),
x = c(
sim_zones_pu_polygons$spp1_1[-3],
sim_zones_pu_polygons$spp2_1[c(-1, -3)]
),
dims = c(2, nrow(sim_zones_pu_polygons) - 1)
)
r2 <- Matrix::sparseMatrix(
i = c(
rep(1, nrow(sim_zones_pu_polygons) - 1),
rep(2, nrow(sim_zones_pu_polygons) - 1)),
j = c(
seq_len(nrow(sim_zones_pu_polygons) - 1),
seq_len(nrow(sim_zones_pu_polygons) - 1)
),
x = c(
sim_zones_pu_polygons$spp1_2[-3],
sim_zones_pu_polygons$spp2_2[-3]
),
dims = c(2, nrow(sim_zones_pu_polygons) - 1)
)
rij <- list(r1, r2)
expect_equal(names(x$data$rij_matrix), c("z1", "z2"))
expect_true(all(x$data$rij_matrix[[1]] == rij[[1]]))
expect_true(all(x$data$rij_matrix[[2]] == rij[[2]]))
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = data.frame, features = character", {
# create data
pu <- data.frame(
id = seq_len(10), cost = c(runif(1), NA, runif(8)),
spp1 = runif(10), spp2 = c(rpois(9, 4), NA)
)
# create problem
x <- problem(pu, c("spp1", "spp2"), "cost")
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), c("spp1", "spp2"))
expect_equal(x$zone_names(), "cost")
expect_equal(x$number_of_features(), 2)
expect_equal(x$number_of_zones(), 1)
expect_equal(x$number_of_planning_units(), 9)
expect_equal(x$planning_unit_indices(), which(!is.na(pu$cost)))
expect_equal(x$number_of_total_units(), 10)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
matrix(pu$cost[-2], ncol = 1),
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), "cost")
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(colSums(pu[-2, c("spp1", "spp2")], na.rm = TRUE), ncol = 1),
ignore_attr = TRUE
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
c("spp1", "spp2")
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
c("cost")
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(colSums(pu[, c("spp1", "spp2")], na.rm = TRUE), ncol = 1),
ignore_attr = TRUE
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
c("spp1", "spp2")
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
c("cost")
)
# tests for rij_matrix field
expect_equal(
x$data$rij_matrix[[1]],
Matrix::sparseMatrix(
i = c(rep(1, 9), rep(2, 8)),
j = c(1:9, 1:8),
x = c(pu$spp1[-2], pu$spp2[c(-2, -10)]),
dims = c(2, 9),
dimnames = list(x$feature_names(), NULL)
),
ignore_attr = TRUE
)
expect_equal(names(x$data$rij_matrix), "cost")
expect_equal(rownames(x$data$rij_matrix[[1]]), c("spp1", "spp2"))
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x=data.frame, features=ZonesCharacter", {
# create data
pu <- data.frame(
id = seq_len(10),
cost_1 = c(NA, NA, runif(8)), cost_2 = c(0.3, NA, runif(8)),
spp1_1 = runif(10), spp2_1 = c(rpois(9, 4), NA),
spp1_2 = runif(10), spp2_2 = runif(10)
)
# create problem
x <- problem(
pu, zones(c("spp1_1", "spp2_1"), c("spp1_2", "spp2_2")),
c("cost_1", "cost_2")
)
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), c("1", "2"))
expect_equal(x$zone_names(), c("1", "2"))
expect_equal(x$number_of_features(), 2)
expect_equal(x$number_of_zones(), 2)
expect_equal(x$number_of_planning_units(), 9)
expect_equal(x$planning_unit_indices(), c(1, seq(3, nrow(pu))))
expect_equal(x$number_of_total_units(), 10)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
`colnames<-`(as.matrix(pu[-2, 2:3]), x$zone_names())
)
expect_equal(colnames(x$planning_unit_costs()), c("1", "2"))
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
c(
sum(pu$spp1_1[!is.na(pu$cost_1)], na.rm = TRUE),
sum(pu$spp2_1[!is.na(pu$cost_1)], na.rm = TRUE),
sum(pu$spp1_2[!is.na(pu$cost_2)], na.rm = TRUE),
sum(pu$spp2_2[!is.na(pu$cost_2)], na.rm = TRUE)
),
ncol = 2,
dimnames = list(x$feature_names(), x$zone_names())
)
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
c("1", "2")
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
c("1", "2")
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(colSums(pu[, 4:7], na.rm = TRUE), ncol = 2),
ignore_attr = TRUE
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
c("1", "2")
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
c("1", "2")
)
# tests for rij_matrix field
expect_equal(names(x$data$rij_matrix), c("1", "2"))
expect_true(
all(
x$data$rij_matrix[[1]] ==
Matrix::sparseMatrix(
i = c(rep(1, 9), rep(2, 8)),
j = c(1:9, 1:8),
x = c(pu$spp1_1[-2], pu$spp2_1[c(-2, -10)]),
dims = c(2, 9)
)
)
)
expect_true(
all(
x$data$rij_matrix[[2]] ==
Matrix::sparseMatrix(
i = c(rep(1, 9), rep(2, 9)),
j = c(1:9, 1:9),
x = c(pu$spp1_2[-2], pu$spp2_2[-2]),
dims = c(2, 9)
)
)
)
expect_equal(names(x$data$rij_matrix), c("1", "2"))
expect_equal(rownames(x$data$rij_matrix[[1]]), c("1", "2"))
expect_equal(rownames(x$data$rij_matrix[[2]]), c("1", "2"))
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = data.frame, features = data.frame (single zone)", {
# create data
pu <- data.frame(id = seq_len(10), cost = c(0.1, NA, runif(8)))
species <- data.frame(id = seq_len(5), name = letters[1:5], targets = 0.5)
rij <- expand.grid(pu = seq_len(9), species = seq_len(5))
rij$amount <- runif(nrow(rij))
# create problem
x <- problem(pu, species, rij, "cost")
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), letters[1:5])
expect_equal(x$zone_names(), "cost")
expect_equal(x$number_of_features(), 5)
expect_equal(x$number_of_zones(), 1)
expect_equal(x$number_of_planning_units(), 9)
expect_equal(x$planning_unit_indices(), which(!is.na(pu$cost)))
expect_equal(x$number_of_total_units(), 10)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
matrix(pu$cost[-2], ncol = 1),
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), "cost")
# tests for feature_abundances_in_planning_units field
rij2 <- rij[rij$pu != 2, ]
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
Matrix::rowSums(
Matrix::sparseMatrix(
i = rij2[[2]],
j = rij2[[1]],
x = rij2[[3]]
)
),
dimnames = list(x$feature_names(), x$zone_names())
)
)
expect_equal(rownames(x$feature_abundances_in_planning_units()), letters[1:5])
expect_equal(colnames(x$feature_abundances_in_planning_units()), "cost")
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(
Matrix::rowSums(
Matrix::sparseMatrix(
i = rij[[2]],
j = rij[[1]],
x = rij[[3]]
)
),
dimnames = list(x$feature_names(), x$zone_names())
)
)
expect_equal(rownames(x$feature_abundances_in_total_units()), letters[1:5])
expect_equal(colnames(x$feature_abundances_in_total_units()), "cost")
# tests for rij_matrix field
rij2 <- rij[rij$pu != 2, ]
rij2$pu <- match(rij2$pu, pu$id[-2])
expect_equal(
x$data$rij_matrix[[1]],
Matrix::sparseMatrix(
i = rij2[[2]],
j = rij2[[1]],
x = rij2[[3]],
dims = c(5, 9),
dimnames = list(x$feature_names(), NULL)
)
)
expect_equal(names(x$data$rij_matrix), "cost")
expect_equal(rownames(x$data$rij_matrix[[1]]), letters[1:5])
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = data.frame, features = data.frame (factor, single zone)", {
# create data
pu <- data.frame(id = seq_len(10), cost = c(0.1, NA, runif(8)))
species <- data.frame(
id = seq_len(5), name = factor(letters[1:5]), targets = 0.5
)
rij <- expand.grid(pu = seq_len(9), species = seq_len(5))
rij$amount <- runif(nrow(rij))
# create problem
x <- problem(pu, species, rij, "cost")
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), letters[1:5])
expect_equal(x$zone_names(), "cost")
expect_equal(x$number_of_features(), 5)
expect_equal(x$number_of_zones(), 1)
expect_equal(x$number_of_planning_units(), 9)
expect_equal(x$planning_unit_indices(), which(!is.na(pu$cost)))
expect_equal(x$number_of_total_units(), 10)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
matrix(pu$cost[-2], ncol = 1),
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), "cost")
# tests for feature_abundances_in_planning_units field
rij2 <- rij[rij$pu != 2, ]
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
Matrix::rowSums(
Matrix::sparseMatrix(
i = rij2[[2]],
j = rij2[[1]],
x = rij2[[3]]
)
),
dimnames = list(x$feature_names(), x$zone_names())
)
)
expect_equal(rownames(x$feature_abundances_in_planning_units()), letters[1:5])
expect_equal(colnames(x$feature_abundances_in_planning_units()), "cost")
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(
Matrix::rowSums(
Matrix::sparseMatrix(
i = rij[[2]],
j = rij[[1]],
x = rij[[3]]
)
),
dimnames = list(x$feature_names(), x$zone_names())
)
)
expect_equal(rownames(x$feature_abundances_in_total_units()), letters[1:5])
expect_equal(colnames(x$feature_abundances_in_total_units()), "cost")
# tests for rij_matrix field
rij2 <- rij[rij$pu != 2, ]
rij2$pu <- match(rij2$pu, pu$id[-2])
expect_equal(
x$data$rij_matrix[[1]],
Matrix::sparseMatrix(
i = rij2[[2]],
j = rij2[[1]],
x = rij2[[3]],
dims = c(5, 9),
dimnames = list(x$feature_names(), NULL)
)
)
expect_equal(names(x$data$rij_matrix), "cost")
expect_equal(rownames(x$data$rij_matrix[[1]]), letters[1:5])
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x=data.frame, features=data.frame (multiple zones)", {
# create data
pu <- data.frame(
id = seq_len(10),
cost_1 = c(0.1, NA, runif(8)), cost_2 = c(NA, NA, runif(8))
)
species <- data.frame(id = seq_len(5), name = letters[1:5], targets = 0.5)
rij <- expand.grid(pu = seq_len(9), species = seq_len(5), zone = 1:2)
rij$amount <- runif(nrow(rij))
z <- data.frame(id = 1:2, name = c("z1", "z2"))
# create problem
x <- problem(pu, species, rij, c("cost_1", "cost_2"), z)
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), letters[1:5])
expect_equal(x$zone_names(), c("z1", "z2"))
expect_equal(x$number_of_features(), 5)
expect_equal(x$number_of_zones(), 2)
expect_equal(x$number_of_planning_units(), 9)
expect_equal(x$planning_unit_indices(), c(1, seq(3, nrow(pu))))
expect_equal(x$number_of_total_units(), 10)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
`colnames<-`(as.matrix(pu[-2, 2:3]), x$zone_names())
)
expect_equal(colnames(x$planning_unit_costs()), c("z1", "z2"))
# tests for feature_abundances_in_planning_units field
rij2 <- rij
rij2 <- rij2[!(rij2$pu %in% pu$id[is.na(pu$cost_1)] & rij2$zone == 1), ]
rij2 <- rij2[!(rij2$pu %in% pu$id[is.na(pu$cost_2)] & rij2$zone == 2), ]
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
aggregate(rij2[[4]], by = list(rij2[[2]], rij2[[3]]), sum)[[3]],
ncol = 2
),
ignore_attr = TRUE
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
letters[1:5]
)
expect_equal(
colnames(x$feature_abundances_in_planning_units()),
c("z1", "z2")
)
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(
aggregate(rij[[4]], by = list(rij[[2]], rij[[3]]), sum)[[3]],
ncol = 2
),
ignore_attr = TRUE
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
letters[1:5]
)
expect_equal(
colnames(x$feature_abundances_in_total_units()),
c("z1", "z2")
)
# tests for rij_matrix field
rij2 <- rij[rij$pu != 2, ]
rij2$pu <- match(rij2$pu, sort(unique(rij2$pu)))
expect_equal(names(x$data$rij_matrix), c("z1", "z2"))
expect_equal(
x$data$rij_matrix[[1]],
Matrix::sparseMatrix(
i = rij2[[2]][rij2[[3]] == 1],
j = rij2[[1]][rij2[[3]] == 1],
x = rij2[[4]][rij2[[3]] == 1],
dims = c(5, 9),
dimnames = list(x$feature_names(), NULL)
)
)
expect_equal(
x$data$rij_matrix[[2]],
Matrix::sparseMatrix(
i = rij2[[2]][rij2[[3]] == 2],
j = rij2[[1]][rij2[[3]] == 2],
x = rij2[[4]][rij2[[3]] == 2],
dims = c(5, 9),
dimnames = list(x$feature_names(), NULL)
)
)
expect_equal(rownames(x$data$rij_matrix[[1]]), letters[1:5])
expect_equal(rownames(x$data$rij_matrix[[2]]), letters[1:5])
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = numeric, features = data.frame, rij_matrix = matrix", {
# create data
pu <- data.frame(
id = seq_len(10), cost = c(0.2, NA, runif(8)),
spp1 = runif(10), spp2 = c(rpois(9, 4), NA)
)
# create problem
x <- problem(
pu$cost, data.frame(id = seq_len(2), name = c("spp1", "spp2")),
as.matrix(t(pu[, 3:4]))
)
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), c("spp1", "spp2"))
expect_equal(x$zone_names(), "1")
expect_equal(x$number_of_features(), 2)
expect_equal(x$number_of_zones(), 1)
expect_equal(x$number_of_planning_units(), 9)
expect_equal(x$planning_unit_indices(), which(!is.na(pu$cost)))
expect_equal(x$number_of_total_units(), 10)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
matrix(pu$cost[-2], ncol = 1),
ignore_attr = TRUE
)
expect_equal(colnames(x$planning_unit_costs()), "1")
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
rowSums(t(pu[-2, 3:4]), na.rm = TRUE),
ignore_attr = TRUE
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
c("spp1", "spp2")
)
expect_equal(colnames(x$feature_abundances_in_planning_units()), "1")
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(
rowSums(t(pu[, 3:4]), na.rm = TRUE),
dimnames = list(x$feature_names(), x$zone_names())
)
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
c("spp1", "spp2")
)
expect_equal(colnames(x$feature_abundances_in_total_units()), "1")
# tests for rij_matrix field
expect_equal(names(x$data$rij_matrix), "1")
expect_equal(
x$data$rij_matrix[[1]],
{
m <- as(t(pu[-2, 3:4]), "sparseMatrix")
rownames(m) <- x$feature_names()
colnames(m) <- NULL
m@x[is.na(m@x)] <- 0
Matrix::drop0(m)
}
)
expect_equal(rownames(x$data$rij_matrix[[1]]), c("spp1", "spp2"))
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = matrix, features = data.frame, rij_matrix = matrix", {
# create data
pu <- data.frame(
id = seq_len(10),
cost_1 = c(NA, NA, runif(8)), cost_2 = c(0.3, NA, runif(8)),
spp1_1 = runif(10), spp2_1 = c(rpois(9, 4), NA),
spp1_2 = runif(10), spp2_2 = runif(10)
)
# create problem
x <- problem(
as.matrix(pu[, 2:3]),
data.frame(id = seq_len(2), name = c("spp1", "spp2")),
list(as.matrix(t(pu[, 4:5])), as.matrix(t(pu[, 6:7])))
)
# verify that object can be printed
suppressMessages(print(x))
suppressMessages(summary(x))
suppressMessages(x)
# tests for integer fields
expect_equal(x$feature_names(), c("spp1", "spp2"))
expect_equal(x$zone_names(), c("1", "2"))
expect_equal(x$number_of_features(), 2)
expect_equal(x$number_of_zones(), 2)
expect_equal(x$number_of_planning_units(), 9)
expect_equal(x$planning_unit_indices(), c(1, seq(3, nrow(pu))))
expect_equal(x$number_of_total_units(), 10)
# tests for planning_unit_costs field
expect_equal(
x$planning_unit_costs(),
{
m <- as.matrix(pu[-2, 2:3])
colnames(m) <- x$zone_names()
rownames(m) <- NULL
m
}
)
expect_equal(colnames(x$planning_unit_costs()), c("1", "2"))
# tests for feature_abundances_in_planning_units field
expect_equal(
x$feature_abundances_in_planning_units(),
matrix(
c(
sum(pu$spp1_1[!is.na(pu$cost_1)], na.rm = TRUE),
sum(pu$spp2_1[!is.na(pu$cost_1)], na.rm = TRUE),
sum(pu$spp1_2[!is.na(pu$cost_2)], na.rm = TRUE),
sum(pu$spp2_2[!is.na(pu$cost_2)], na.rm = TRUE)
),
ncol = 2,
dimnames = list(x$feature_names(), x$zone_names())
)
)
expect_equal(
rownames(x$feature_abundances_in_planning_units()),
c("spp1", "spp2")
)
expect_equal(colnames(x$feature_abundances_in_planning_units()), c("1", "2"))
# tests for feature_abundances_in_total_units field
expect_equal(
x$feature_abundances_in_total_units(),
matrix(colSums(pu[, 4:7], na.rm = TRUE), ncol = 2),
ignore_attr = TRUE
)
expect_equal(
rownames(x$feature_abundances_in_total_units()),
c("spp1", "spp2")
)
expect_equal(colnames(x$feature_abundances_in_total_units()), c("1", "2"))
# tests for rij_matrix field
expect_equal(names(x$data$rij_matrix), c("1", "2"))
expect_equal(
x$data$rij_matrix[[1]],
{
m <- as(t(pu[-2, 4:5]), "sparseMatrix")
colnames(m) <- NULL
rownames(m) <- x$feature_names()
m@x[is.na(m@x)] <- 0
Matrix::drop0(m)
}
)
expect_equal(
x$data$rij_matrix[[2]],
{
m <- as(t(pu[-2, 6:7]), "sparseMatrix")
colnames(m) <- NULL
rownames(m) <- x$feature_names()
m@x[is.na(m@x)] <- 0
Matrix::drop0(m)
}
)
expect_equal(rownames(x$data$rij_matrix[[1]]), c("spp1", "spp2"))
expect_equal(rownames(x$data$rij_matrix[[2]]), c("spp1", "spp2"))
# test that calling targets before they have been initialized throws error
expect_error(x$feature_targets())
})
test_that("x = matrix, features = data.frame, rij_matrix = dgCMatrix", {
# create data
pu <- data.frame(
id = seq_len(10),
cost_1 = c(NA, NA, runif(8)), cost_2 = c(0.3, NA, runif(8)),
spp1_1 = runif(10), spp2_1 = c(rpois(9, 4), NA),
spp1_2 = runif(10), spp2_2 = runif(10)
)
rij <- list(as.matrix(t(pu[, 4:5])), as.matrix(t(pu[, 6:7])))
# create problem
x1 <- problem(
as.matrix(pu[, 2:3]),
data.frame(id = seq_len(2), name = c("spp1", "spp2")),
rij_matrix = rij
)
x2 <- problem(
as.matrix(pu[, 2:3]),
data.frame(id = seq_len(2), name = c("spp1", "spp2")),
rij_matrix = lapply(rij, as_Matrix, "dgCMatrix")
)
# verify that object can be printed
suppressMessages(print(x1))
suppressMessages(x1)
suppressMessages(print(x2))
suppressMessages(x2)
# tests
expect_equal(x1$data, x2$data)
})
test_that("invalid problem inputs (invalid input class)", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_pu_polygons$spp_1 <- runif(nrow(sim_pu_polygons))
sim_pu_raster <- get_sim_pu_raster()
sim_features <- get_sim_features()
# tests
expect_tidy_error(problem("a", sim_features))
expect_tidy_error(problem(c(sim_pu_raster, sim_pu_raster), sim_features))
expect_tidy_error(
problem(
sim_pu_polygons,
c("spp_1", attr(sim_pu_polygons, "sf_column")),
"cost"
),
"geometry data"
)
})
test_that("invalid problem inputs (all planning units have NA costs)", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_pu_raster <- get_sim_pu_raster()
sim_features <- get_sim_features()
# update data
sim_pu_polygons$cost <- NA_real_
sim_pu_raster <- raster::setValues(sim_pu_raster, NA_real_)
sim_pu_polygons$spp_1 <- runif(nrow(sim_pu_polygons))
sim_pu_polygons$spp_2 <- runif(nrow(sim_pu_polygons))
# tests
expect_tidy_error(
problem(sim_pu_raster, sim_features),
"missing"
)
expect_tidy_error(
problem(sim_pu_polygons, sim_features, "cost"),
"missing"
)
expect_tidy_error(
problem(sim_pu_polygons, c("spp_1", "spp_2"), "cost"),
"missing"
)
expect_tidy_error(
problem(sf::st_drop_geometry(sim_pu_polygons), c("spp_1", "spp_2"), "cost"),
"missing"
)
})
test_that("problematic problem inputs (planning units with negative values)", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_pu_raster <- get_sim_pu_raster()
sim_features <- get_sim_features()
# update feature data
sim_pu_raster <- sim_pu_raster * -1
sim_pu_polygons$cost <- runif(nrow(sim_pu_polygons)) * -1
sim_pu_polygons$spp_1 <- runif(nrow(sim_pu_polygons))
sim_pu_polygons$spp_2 <- runif(nrow(sim_pu_polygons))
# tests
expect_warning(
problem(sim_pu_raster, sim_features),
"has negative values"
)
expect_warning(
problem(sim_pu_polygons, sim_features, "cost"),
"has negative values"
)
expect_warning(
problem(sim_pu_polygons, c("spp_1", "spp_2"), "cost"),
"has negative values"
)
expect_warning(
problem(sim_pu_polygons, c("spp_1", "spp_2"), "cost"),
"has negative values"
)
expect_warning(
problem(sf::st_drop_geometry(sim_pu_polygons), c("spp_1", "spp_2"), "cost"),
"has negative values"
)
})
test_that("problematic problem inputs (feature contains negative values)", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_pu_raster <- get_sim_pu_raster()
sim_features <- get_sim_features()
# update feature data
sim_features <- sim_features * -1
sim_pu_polygons$cost <- runif(nrow(sim_pu_polygons))
sim_pu_polygons$spp_1 <- runif(nrow(sim_pu_polygons)) * -1
sim_pu_polygons$spp_2 <- runif(nrow(sim_pu_polygons))
# tests
expect_warning(
problem(sim_pu_raster, sim_features),
"has negative values"
)
expect_warning(
problem(sim_pu_polygons, sim_features, "cost"),
"has negative values"
)
expect_warning(
problem(sim_pu_polygons, c("spp_1", "spp_2"), "cost"),
"has negative values"
)
expect_warning(
problem(sim_pu_polygons, c("spp_1", "spp_2"), "cost"),
"has negative values"
)
expect_warning(
problem(sf::st_drop_geometry(sim_pu_polygons), c("spp_1", "spp_2"), "cost"),
"has negative values"
)
})
test_that("problematic problem inputs (feature contains only zero values)", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_pu_raster <- get_sim_pu_raster()
sim_features <- get_sim_features()
# update feature data
sim_features[[1]] <- sim_features[[1]] * 0
sim_pu_polygons$cost <- runif(nrow(sim_pu_polygons))
sim_pu_polygons$spp_1 <- 0
sim_pu_polygons$spp_2 <- runif(nrow(sim_pu_polygons))
# tests
expect_warning(
problem(sim_pu_raster, sim_features),
"has only zero values"
)
expect_warning(
problem(sim_pu_polygons, sim_features, "cost"),
"has only zero values"
)
expect_warning(
problem(sim_pu_polygons, c("spp_1", "spp_2"), "cost"),
"has only zero values"
)
expect_warning(
problem(sim_pu_polygons, c("spp_1", "spp_2"), "cost"),
"has only zero values"
)
expect_warning(
problem(sf::st_drop_geometry(sim_pu_polygons), c("spp_1", "spp_2"), "cost"),
"has only zero values"
)
})
test_that("inheritance", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_features <- get_sim_features()
# create problem
p1 <- problem(sim_pu_polygons, sim_features, "cost")
# create a modified copy of the problem
p2 <- p1 %>% add_locked_in_constraints("locked_in")
# test that the original problem remains unchanged
expect_length(p1$constraints, 0)
expect_length(p2$constraints, 1)
})
test_that("warnings on overriding components", {
# import data
sim_pu_polygons <- get_sim_pu_polygons()
sim_features <- get_sim_features()
# create problem
p <-
problem(sim_pu_polygons, sim_features, "cost") %>%
add_min_set_objective() %>%
add_binary_decisions() %>%
add_default_solver() %>%
add_shuffle_portfolio()
# tests
expect_warning(
add_min_set_objective(p),
"objective"
)
expect_warning(
add_binary_decisions(p),
"decision"
)
expect_warning(
add_default_solver(p),
"solver"
)
expect_warning(
add_shuffle_portfolio(p),
"portfolio"
)
})
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