context("add_max_phylo_objective")
test_that("compile (compressed formulation)", {
# generate optimization problem
data(sim_pu_raster, sim_features, sim_phylogeny)
b <- floor(raster::cellStats(sim_pu_raster, "sum")) * 0.25
targ <- unname(floor(raster::cellStats(sim_features, "sum") * 0.25))
p <- problem(sim_pu_raster, sim_features) %>%
add_max_phylo_objective(budget = b, tree = sim_phylogeny) %>%
add_absolute_targets(targ) %>%
add_binary_decision()
o <- compile(p)
# check that objective has been correctly applied
n_pu <- length(sim_pu_raster[[1]][!is.na(sim_pu_raster)])
n_features <- raster::nlayers(sim_features)
n_branches <- nrow(sim_phylogeny$edge)
bm <- branch_matrix(sim_phylogeny)
scaled_costs <- p$planning_unit_costs()
scaled_costs <- scaled_costs * (1e-10 / min(scaled_costs))
expect_equal(o$modelsense(), "max")
expect_equal(o$obj(), c(scaled_costs, rep(1e-10, n_features),
sim_phylogeny$edge.length))
expect_equal(o$sense(), c(rep(">=", n_features), "<=", rep(">=", n_branches)))
expect_equal(o$rhs(), c(rep(0, n_features), b, rep(0, n_branches)))
expect_equal(o$col_ids(), c(rep("pu", n_pu), rep("spp_met", n_features),
rep("branch_met", n_branches)))
expect_equal(o$row_ids(), c(rep("spp_target", n_features), "budget",
rep("branch_target", n_branches)))
expect_true(all(o$A()[seq_len(n_features),
seq_len(n_pu)] == p$data$rij_matrix))
expect_equal(o$A()[n_features + 1, ], c(p$planning_unit_costs(),
rep(0, n_features),
rep(0, n_branches)))
expect_true(all(o$A()[seq_len(n_features), n_pu + seq_len(n_features)] ==
Matrix::sparseMatrix(i = seq_len(n_features), j = seq_len(n_features),
x = (-1 * targ), giveCsparse = FALSE)))
expect_true(all(
o$A()[n_features + 1 + seq_len(n_branches), n_pu + seq_len(n_features)] ==
t(bm)
))
expect_true(all({
a <- o$A()
a[n_features + 1 + seq_len(n_branches),
n_pu + n_features + seq_len(n_branches)] ==
Matrix::sparseMatrix(i = seq_len(n_branches), j = seq_len(n_branches),
x = rep(-1, n_branches))
}))
expect_true(all(o$lb() == 0))
expect_true(all(o$ub() == 1))
})
test_that("solution (compressed formulation)", {
skip_on_cran()
budget <- 4.23
# create data
cost <- raster::raster(matrix(c(1, 2, NA, 4), ncol = 2))
locked_in <- 2
locked_out <- 1
features <- raster::stack(raster::raster(matrix(c(2, 1, 1, 0), ncol = 2)),
raster::raster(matrix(c(10, 10, 10, 10), ncol = 2)),
raster::raster(matrix(c(0, 0, 0, 2), ncol = 2)))
tr <- list(tip.label = c("layer.1", "layer.2", "layer.3"),
edge.length = c(1, 1, 1, 100),
Nnode = 2L,
edge = matrix(c(
4L, 1L,
4L, 5L,
5L, 2L,
5L, 3L
), byrow = TRUE, ncol = 2))
class(tr) <- "phylo"
attr(tr, "order") <- "cladewise"
# create problem
p <- problem(cost, features) %>%
add_max_phylo_objective(budget = budget, tree = tr) %>%
add_absolute_targets(c(2, 12, 2)) %>%
add_locked_in_constraints(locked_in) %>%
add_locked_out_constraints(locked_out) %>%
add_default_solver(time_limit = 5)
# solve problem
s <- solve(p)
# test for correct solution
expect_equal(raster::values(s), c(0, NA, 0, 1))
})
test_that("compile (expanded formulation)", {
# generate optimization problem
data(sim_pu_raster, sim_features, sim_phylogeny)
b <- floor(raster::cellStats(sim_pu_raster, "sum")) * 0.25
targ <- unname(floor(raster::cellStats(sim_features, "sum") * 0.25))
p <- problem(sim_pu_raster, sim_features) %>%
add_max_phylo_objective(budget = b, tree = sim_phylogeny) %>%
add_absolute_targets(targ) %>%
add_binary_decision()
o <- compile(p, compressed_formulation = FALSE)
# run preliminary calculations
n_pu <- length(sim_pu_raster[[1]][!is.na(sim_pu_raster)])
n_f <- raster::nlayers(sim_features)
n_b <- nrow(sim_phylogeny$edge)
rij <- rij_matrix(sim_pu_raster, sim_features)
n_rij <- length(rij@x)
bm <- branch_matrix(sim_phylogeny)
scaled_costs <- p$planning_unit_costs()
scaled_costs <- scaled_costs * (1e-10 / min(scaled_costs))
# test that metadata and constraints are correct
expect_equal(o$modelsense(), "max")
expect_equal(o$obj(), c(scaled_costs, rep(1e-10, n_f),
rep(0, n_pu * n_f),
sim_phylogeny$edge.length))
expect_equal(o$sense(), c(rep("<=", n_rij), rep(">=", n_f), "<=",
rep(">=", n_b)))
expect_equal(o$rhs(), c(rep(0, n_rij), rep(0, n_f), b,
rep(0, n_b)))
expect_equal(o$col_ids(), c(rep("pu", n_pu), rep("pu_ij", n_pu * n_f),
rep("spp_met", n_f),
rep("branch_met", n_b)))
expect_equal(o$row_ids(), c(rep("pu_ij", n_rij),
rep("spp_target", n_f), "budget",
rep("branch_target", n_b)))
expect_equal(o$lb(), rep(0, n_pu + (n_f * n_pu) + n_f + n_b))
expect_equal(o$ub(), rep(1, n_pu + (n_f * n_pu) + n_f + n_b))
# test that problem matrix is correct
row <- 0
for (i in seq_len(n_f)) {
for (j in seq_len(n_pu)) {
row <- row + 1
curr_row <- rep(0, n_pu + (n_pu * n_f) + n_f + n_b)
curr_row[j] <- -1
curr_row[n_pu + ( (i - 1) * n_pu) + j] <- 1
expect_equal(o$A()[row, ], curr_row)
}
}
for (i in seq_len(n_f)) {
curr_row <- rep(0, n_pu + (n_pu * n_f) + n_f + n_b)
curr_row[(i * n_pu) + seq_len(n_pu)] <- rij[i, ]
curr_row[n_pu + (n_f * n_pu) + i] <- -1 * targ[i]
expect_equal(o$A()[(n_f * n_pu) + i, ], curr_row)
}
expect_equal(o$A()[(n_pu * n_f) + n_f + 1, ], c(p$planning_unit_costs(),
rep(0, n_f * n_pu),
rep(0, n_f),
rep(0, n_b)))
for (i in seq_len(n_b)) {
curr_row <- rep(0, n_pu + (n_f * n_pu) + n_f + n_b)
curr_row[n_pu + (n_f * n_pu) + which(bm[, i] == 1)] <- 1
curr_row[n_pu + (n_f * n_pu) + n_f + i] <- -1
expect_equal(o$A()[(n_f * n_pu) + n_f + 1 + i, ], curr_row)
}
})
test_that("solution (expanded formulation)", {
skip_on_cran()
# create data
cost <- raster::raster(matrix(c(1, 2, NA, 4), ncol = 2))
budget <- 4.23
locked_in <- 2
locked_out <- 1
features <- raster::stack(raster::raster(matrix(c(2, 1, 1, 0), ncol = 2)),
raster::raster(matrix(c(10, 10, 10, 10), ncol = 2)),
raster::raster(matrix(c(0, 0, 0, 2), ncol = 2)))
tr <- list(tip.label = c("layer.1", "layer.2", "layer.3"),
edge.length = c(1, 1, 1, 100),
Nnode = 2L,
edge = matrix(c(
4L, 1L,
4L, 5L,
5L, 2L,
5L, 3L
), byrow = TRUE, ncol = 2))
class(tr) <- "phylo"
attr(tr, "order") <- "cladewise"
# create problem
p <- problem(cost, features) %>%
add_max_phylo_objective(budget = budget, tree = tr) %>%
add_absolute_targets(c(2, 12, 2)) %>%
add_locked_in_constraints(locked_in) %>%
add_locked_out_constraints(locked_out) %>%
add_default_solver(time_limit = 5)
# solve problem
s <- solve(p, compressed_formulation = FALSE)
# test for correct solution
expect_equal(raster::values(s), c(0, NA, 0, 1))
})
test_that("invalid inputs", {
# check that invalid arguments result in errors
expect_error({
problem(sim_pu_raster, sim_features) %>%
add_max_phylo_objective(budget = -5, sim_phylogeny)
})
expect_error({
problem(sim_pu_raster, sim_features) %>%
add_max_phylo_objective(budget = 0, sim_phylogeny)
})
expect_error({
problem(sim_pu_raster, sim_features) %>%
add_max_phylo_objective(budget = NA, sim_phylogeny)
})
expect_error({
problem(sim_pu_raster, sim_features) %>%
add_max_phylo_objective(budget = Inf, sim_phylogeny)
})
expect_error({
problem(sim_pu_raster, sim_features) %>%
add_max_phylo_objective(budget = 5000,
ape::drop.tip(sim_phylogeny, "layer.1"))
})
})
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