tests/testthat/test-POST_FATE.graphic_validationStatistics.R
In MayaGueguen/RFate: Vegetation modelling with the FATE model
library(RFate)
context("POST_FATE.graphic_validationStatistics() function")
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with missing data", {
expect_error(POST_FATE.graphic_validationStatistics()
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(NA)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(NULL)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : name.simulation", {
expect_error(POST_FATE.graphic_validationStatistics(1)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics("a")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(factor(1))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : folders", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation/")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
dir.create("FATE_simulation/PARAM_SIMUL/")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "`name.simulation` does not exist or does not contain a RESULTS/ folder")
dir.create("FATE_simulation/RESULTS/")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "`name.simulation` does not exist or does not contain a DATA/ folder")
dir.create("FATE_simulation/DATA/")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : file.simulParam", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST file.simulParam : correct content
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = NULL)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = NA)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
## TEST file.simulParam : correct value
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "toto")
, "`FATE_simulation/PARAM_SIMUL/toto` does not exist")
file.create("FATE_simulation/PARAM_SIMUL/ParamSimul.txt")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : years", {
## TEST years : integer
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt")
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = "a")
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor("a"))
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor(1))
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NULL)
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NA)
, "`years` must be an integer > 0")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : mat.PFG.obs", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/PARAM_SIMUL/ParamSimul.txt")
## TEST mat.PFG.obs : data.frame
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = NA)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = NULL)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = "")
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = 1)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = factor(1))
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = matrix(1))
, "`mat.PFG.obs` must be a data.frame")
## TEST mat.PFG.obs : correct number of rows and columns
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame())
, "`mat.PFG.obs` does not have the appropriate number of rows (>0) or columns (PFG, X, Y, obs)"
, fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(1))
, "`mat.PFG.obs` does not have the appropriate number of rows (>0) or columns (PFG, X, Y, obs)"
, fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(1,2,3,4,5))
, "`mat.PFG.obs` does not have the appropriate number of rows (>0) or columns (PFG, X, Y, obs)"
, fixed = TRUE)
## TEST mat.PFG.obs : correct names of columns
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(1,2,3,4))
, "Column names of `mat.PFG.obs` must be `PFG`, `X`, `Y` and `obs`"
, fixed = TRUE)
## TEST mat.PFG.obs$PFG : length > 0
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = "", X = 1, Y = 1, obs =0))
, "`mat.PFG.obs$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.obs$X : numeric values
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = NA, Y = 1, obs = 0))
, "Missing data!\n Too many NA values. Please check.", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = "a", Y = 1, obs = 0))
, "`mat.PFG.obs$X` must contain numeric values", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = factor(1), Y = 1, obs = 0))
, "`mat.PFG.obs$X` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.obs$Y : numeric values
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = NA, obs = 0))
, "Missing data!\n Too many NA values. Please check.", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = "a", obs = 0))
, "`mat.PFG.obs$Y` must contain numeric values", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = factor(1), obs = 0))
, "`mat.PFG.obs$Y` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.obs$obs : correct values
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = 1, obs = -1))
, "`mat.PFG.obs$obs` must be either `0` or `1`", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = 1, obs = 1.5))
, "`mat.PFG.obs$obs` must be either `0` or `1`", fixed = TRUE)
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : rasters", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
library(raster)
map_mask = raster(nrows = 5, ncols = 5)
map_mask[] = 1
writeRaster(map_mask, filename = "FATE_simulation/DATA/MASK/map_mask.tif", overwrite = TRUE)
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 6
, required.no_strata = 5
, required.simul_duration = 100
, required.seeding_duration = 10
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000)
PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG", 1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)))
PRE_FATE.params_simulParameters(name.simulation = "FATE_simulation"
, name.MASK = "map_mask.tif")
dir.create("FATE_simulation/RESULTS/SIMUL_V1")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/LIGHT")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/SOIL")
## TEST PFG names
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = 1, obs = 1))
, "The names of PFG within `mat.PFG.obs` is different from the names of PFG contained from FATE_simulation/DATA/PFGS/SUCC/")
## TEST RESULTS folder
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = "PFG1", X = 1, Y = 1, obs = 1))
, "The folder FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/ does not contain adequate files")
file.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/Abund_YEAR_1_PFG1_STRATA_all.tif")
# expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
# , years = 1
# , mat.PFG.obs = data.frame(PFG = "PFG1", X = 1, Y = 1, obs = 1))
# , "Cannot create a RasterLayer object from this file.")
})
## OUTPUTS
test_that("POST_FATE.graphic_validationStatistics gives correct outputs : warnings", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
library(raster)
map_0 = raster(nrows = 5, ncols = 5, resolution = 50)
map_0[] = 0
map_1 = map_0
map_1[] = 1
map_hab = map_0
map_hab[] = sample(c(1, 5, 10), ncell(map_hab), replace = TRUE)
writeRaster(map_1, filename = "FATE_simulation/DATA/MASK/map_mask.tif", overwrite = TRUE)
writeRaster(map_hab, filename = "FATE_simulation/DATA/MASK/map_hab.tif", overwrite = TRUE)
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 6
, required.no_strata = 5
, required.simul_duration = 100
, required.seeding_duration = 10
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000)
PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)))
PRE_FATE.params_simulParameters(name.simulation = "FATE_simulation"
, name.MASK = "map_mask.tif")
dir.create("FATE_simulation/RESULTS/SIMUL_V1")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/LIGHT")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/SOIL")
for (i in 1:5)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
writeRaster(map_0, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG6_STRATA_all.tif"), overwrite = TRUE)
POST_FATE.relativeAbund(name.simulation = "FATE_simulation", years = 1)
## TEST output
expect_warning(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = paste0("PFG",1:6)
, X = -144
, Y = 72
, obs = 1))
, "No values for PFG PFG1.\n No validation statistics will be produced!")
expect_warning(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = paste0("PFG",1:6)
, X = -144
, Y = 72
, obs = 1))
, "No validation has been calculated for year 1!")
## TEST habitat
expect_warning(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = paste0("PFG",1:6)
, X = -144
, Y = 72
, obs = 1)
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "No validation has been calculated for year 1!")
})
## OUTPUTS
test_that("POST_FATE.graphic_validationStatistics gives correct outputs : correct", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
library(raster)
map_0 = raster(nrows = 5, ncols = 5, resolution = 50)
map_0[] = 0
map_1 = map_0
map_1[] = 1
map_hab = map_0
map_hab[] = sample(c(1, 5, 10), ncell(map_hab), replace = TRUE)
writeRaster(map_1, filename = "FATE_simulation/DATA/MASK/map_mask.tif", overwrite = TRUE)
writeRaster(map_hab, filename = "FATE_simulation/DATA/MASK/map_hab.tif", overwrite = TRUE)
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 6
, required.no_strata = 5
, required.simul_duration = 100
, required.seeding_duration = 10
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000)
PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)))
PRE_FATE.params_simulParameters(name.simulation = "FATE_simulation"
, name.MASK = "map_mask.tif")
dir.create("FATE_simulation/RESULTS/SIMUL_V1")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/LIGHT")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/SOIL")
for (i in 1:5)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
writeRaster(map_0, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG6_STRATA_all.tif"), overwrite = TRUE)
POST_FATE.relativeAbund(name.simulation = "FATE_simulation", years = 1)
mat.PFG.obs = xyFromCell(map_0, 1:ncell(map_0))
mat.PFG.obs = expand.grid(PFG = paste0("PFG",1:6)
, X = mat.PFG.obs[, 1]
, Y = mat.PFG.obs[, 2])
mat.PFG.obs$obs = sample(c(0, 1), nrow(mat.PFG.obs), prob = c(0.6, 0.4), replace = TRUE)
}
## TEST output
expect_message(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = mat.PFG.obs)
, "The output file POST_FATE_TABLE_YEAR_1_validationStatistics_SIMUL_V1.csv has been successfully created !")
validStats = POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = mat.PFG.obs)
expect_output(str(validStats), "List")
expect_equal(length(validStats), 1)
expect_output(str(validStats[[1]]), "List")
expect_equal(length(validStats[[1]]), 2)
expect_output(str(validStats[[1]]$tab), "List")
expect_equal(length(validStats[[1]]$tab), 1)
expect_output(str(validStats[[1]]$tab[[1]]), "data.frame")
expect_output(str(validStats[[1]]$tab[[1]]), "7 variables")
})
MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.
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library(RFate)
context("POST_FATE.graphic_validationStatistics() function")
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with missing data", {
expect_error(POST_FATE.graphic_validationStatistics()
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(NA)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(NULL)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : name.simulation", {
expect_error(POST_FATE.graphic_validationStatistics(1)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics("a")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(factor(1))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.graphic_validationStatistics(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : folders", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation/")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
dir.create("FATE_simulation/PARAM_SIMUL/")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "`name.simulation` does not exist or does not contain a RESULTS/ folder")
dir.create("FATE_simulation/RESULTS/")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "`name.simulation` does not exist or does not contain a DATA/ folder")
dir.create("FATE_simulation/DATA/")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : file.simulParam", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST file.simulParam : correct content
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = NULL)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = NA)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
## TEST file.simulParam : correct value
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "toto")
, "`FATE_simulation/PARAM_SIMUL/toto` does not exist")
file.create("FATE_simulation/PARAM_SIMUL/ParamSimul.txt")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : years", {
## TEST years : integer
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt")
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = "a")
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor("a"))
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor(1))
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NULL)
, "`years` must be an integer > 0")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NA)
, "`years` must be an integer > 0")
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : mat.PFG.obs", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/PARAM_SIMUL/ParamSimul.txt")
## TEST mat.PFG.obs : data.frame
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = NA)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = NULL)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = "")
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = 1)
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = factor(1))
, "`mat.PFG.obs` must be a data.frame")
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = matrix(1))
, "`mat.PFG.obs` must be a data.frame")
## TEST mat.PFG.obs : correct number of rows and columns
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame())
, "`mat.PFG.obs` does not have the appropriate number of rows (>0) or columns (PFG, X, Y, obs)"
, fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(1))
, "`mat.PFG.obs` does not have the appropriate number of rows (>0) or columns (PFG, X, Y, obs)"
, fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(1,2,3,4,5))
, "`mat.PFG.obs` does not have the appropriate number of rows (>0) or columns (PFG, X, Y, obs)"
, fixed = TRUE)
## TEST mat.PFG.obs : correct names of columns
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(1,2,3,4))
, "Column names of `mat.PFG.obs` must be `PFG`, `X`, `Y` and `obs`"
, fixed = TRUE)
## TEST mat.PFG.obs$PFG : length > 0
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = "", X = 1, Y = 1, obs =0))
, "`mat.PFG.obs$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.obs$X : numeric values
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = NA, Y = 1, obs = 0))
, "Missing data!\n Too many NA values. Please check.", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = "a", Y = 1, obs = 0))
, "`mat.PFG.obs$X` must contain numeric values", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = factor(1), Y = 1, obs = 0))
, "`mat.PFG.obs$X` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.obs$Y : numeric values
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = NA, obs = 0))
, "Missing data!\n Too many NA values. Please check.", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = "a", obs = 0))
, "`mat.PFG.obs$Y` must contain numeric values", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = factor(1), obs = 0))
, "`mat.PFG.obs$Y` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.obs$obs : correct values
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = 1, obs = -1))
, "`mat.PFG.obs$obs` must be either `0` or `1`", fixed = TRUE)
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 10
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = 1, obs = 1.5))
, "`mat.PFG.obs$obs` must be either `0` or `1`", fixed = TRUE)
})
## INPUTS
test_that("POST_FATE.graphic_validationStatistics gives error with wrong data : rasters", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
library(raster)
map_mask = raster(nrows = 5, ncols = 5)
map_mask[] = 1
writeRaster(map_mask, filename = "FATE_simulation/DATA/MASK/map_mask.tif", overwrite = TRUE)
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 6
, required.no_strata = 5
, required.simul_duration = 100
, required.seeding_duration = 10
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000)
PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG", 1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)))
PRE_FATE.params_simulParameters(name.simulation = "FATE_simulation"
, name.MASK = "map_mask.tif")
dir.create("FATE_simulation/RESULTS/SIMUL_V1")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/LIGHT")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/SOIL")
## TEST PFG names
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = 1, X = 1, Y = 1, obs = 1))
, "The names of PFG within `mat.PFG.obs` is different from the names of PFG contained from FATE_simulation/DATA/PFGS/SUCC/")
## TEST RESULTS folder
expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = "PFG1", X = 1, Y = 1, obs = 1))
, "The folder FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/ does not contain adequate files")
file.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/Abund_YEAR_1_PFG1_STRATA_all.tif")
# expect_error(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
# , years = 1
# , mat.PFG.obs = data.frame(PFG = "PFG1", X = 1, Y = 1, obs = 1))
# , "Cannot create a RasterLayer object from this file.")
})
## OUTPUTS
test_that("POST_FATE.graphic_validationStatistics gives correct outputs : warnings", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
library(raster)
map_0 = raster(nrows = 5, ncols = 5, resolution = 50)
map_0[] = 0
map_1 = map_0
map_1[] = 1
map_hab = map_0
map_hab[] = sample(c(1, 5, 10), ncell(map_hab), replace = TRUE)
writeRaster(map_1, filename = "FATE_simulation/DATA/MASK/map_mask.tif", overwrite = TRUE)
writeRaster(map_hab, filename = "FATE_simulation/DATA/MASK/map_hab.tif", overwrite = TRUE)
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 6
, required.no_strata = 5
, required.simul_duration = 100
, required.seeding_duration = 10
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000)
PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)))
PRE_FATE.params_simulParameters(name.simulation = "FATE_simulation"
, name.MASK = "map_mask.tif")
dir.create("FATE_simulation/RESULTS/SIMUL_V1")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/LIGHT")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/SOIL")
for (i in 1:5)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
writeRaster(map_0, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG6_STRATA_all.tif"), overwrite = TRUE)
POST_FATE.relativeAbund(name.simulation = "FATE_simulation", years = 1)
## TEST output
expect_warning(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = paste0("PFG",1:6)
, X = -144
, Y = 72
, obs = 1))
, "No values for PFG PFG1.\n No validation statistics will be produced!")
expect_warning(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = paste0("PFG",1:6)
, X = -144
, Y = 72
, obs = 1))
, "No validation has been calculated for year 1!")
## TEST habitat
expect_warning(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = data.frame(PFG = paste0("PFG",1:6)
, X = -144
, Y = 72
, obs = 1)
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "No validation has been calculated for year 1!")
})
## OUTPUTS
test_that("POST_FATE.graphic_validationStatistics gives correct outputs : correct", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
library(raster)
map_0 = raster(nrows = 5, ncols = 5, resolution = 50)
map_0[] = 0
map_1 = map_0
map_1[] = 1
map_hab = map_0
map_hab[] = sample(c(1, 5, 10), ncell(map_hab), replace = TRUE)
writeRaster(map_1, filename = "FATE_simulation/DATA/MASK/map_mask.tif", overwrite = TRUE)
writeRaster(map_hab, filename = "FATE_simulation/DATA/MASK/map_hab.tif", overwrite = TRUE)
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 6
, required.no_strata = 5
, required.simul_duration = 100
, required.seeding_duration = 10
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000)
PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)))
PRE_FATE.params_simulParameters(name.simulation = "FATE_simulation"
, name.MASK = "map_mask.tif")
dir.create("FATE_simulation/RESULTS/SIMUL_V1")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/LIGHT")
dir.create("FATE_simulation/RESULTS/SIMUL_V1/SOIL")
for (i in 1:5)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
writeRaster(map_0, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG6_STRATA_all.tif"), overwrite = TRUE)
POST_FATE.relativeAbund(name.simulation = "FATE_simulation", years = 1)
mat.PFG.obs = xyFromCell(map_0, 1:ncell(map_0))
mat.PFG.obs = expand.grid(PFG = paste0("PFG",1:6)
, X = mat.PFG.obs[, 1]
, Y = mat.PFG.obs[, 2])
mat.PFG.obs$obs = sample(c(0, 1), nrow(mat.PFG.obs), prob = c(0.6, 0.4), replace = TRUE)
}
## TEST output
expect_message(POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = mat.PFG.obs)
, "The output file POST_FATE_TABLE_YEAR_1_validationStatistics_SIMUL_V1.csv has been successfully created !")
validStats = POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = mat.PFG.obs)
expect_output(str(validStats), "List")
expect_equal(length(validStats), 1)
expect_output(str(validStats[[1]]), "List")
expect_equal(length(validStats[[1]]), 2)
expect_output(str(validStats[[1]]$tab), "List")
expect_equal(length(validStats[[1]]$tab), 1)
expect_output(str(validStats[[1]]$tab[[1]]), "data.frame")
expect_output(str(validStats[[1]]$tab[[1]]), "7 variables")
})
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