tests/testthat/test-POST_FATE.binaryMaps.R
In MayaGueguen/RFate: Vegetation modelling with the FATE model
library(RFate)
context("POST_FATE.binaryMaps() function")
## INPUTS
test_that("POST_FATE.binaryMaps gives error with missing data", {
expect_error(POST_FATE.binaryMaps()
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(NA)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(NULL)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : name.simulation", {
expect_error(POST_FATE.binaryMaps(1)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps("a")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(factor(1))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : folders", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation/")
expect_error(POST_FATE.binaryMaps(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.binaryMaps(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.binaryMaps(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.binaryMaps 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.binaryMaps(name.simulation = "FATE_simulation")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = NULL)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = NA)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(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.binaryMaps(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.binaryMaps gives error with wrong data : years", {
## TEST years : integer
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt")
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = "a")
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor("a"))
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor(1))
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NULL)
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NA)
, "`years` must be an integer > 0")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : method", {
## TEST method : correct value
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = "")
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = "a")
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = factor("a"))
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = NULL)
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = NA)
, "`method` must be either `1` or `2`")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : method1.threshold", {
## TEST method1.threshold : correct value
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = "")
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = "a")
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = factor("a"))
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = -1)
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = 1.5)
, "`method1.threshold` must contain values between `0` and `1`")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : method2.cutoff", {
## TEST method2.cutoff : NULL case
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = NULL)
, "The folder FATE_simulation/RESULTS/ does not contain adequate files")
## TEST method2.cutoff : not NULL or data.frame case
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = NA)
, "`method2.cutoff` must be either NULL or a data.frame")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = 1)
, "`method2.cutoff` must be either NULL or a data.frame")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = matrix(1))
, "`method2.cutoff` must be either NULL or a data.frame")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = "a")
, "`method2.cutoff` must be either NULL or a data.frame")
## TEST method2.cutoff : data.frame case
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = data.frame())
, "`method2.cutoff` does not have the appropriate number of rows (>0) or columns (year, PFG, cutoff)"
, fixed = TRUE)
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = data.frame(1,2))
, "`method2.cutoff` does not have the appropriate number of rows (>0) or columns (year, PFG, cutoff)"
, fixed = TRUE)
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = data.frame(1, 2, 3))
, "Column names of `method2.cutoff` must be `year`, `PFG` and `cutoff`"
, fixed = TRUE)
})
## INPUTS
test_that("POST_FATE.binaryMaps 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 RESULTS folder
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 1)
, "The folder FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/ does not contain adequate files")
file.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/Abund_YEAR_1_PFG1_STRATA_1.tif")
# expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
# , years = 1
# , method = 1)
# , "Cannot create a RasterLayer object from this file.")
})
## OUTPUTS
test_that("POST_FATE.binaryMaps 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
writeRaster(map_1, 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")
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_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_1.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)
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG6_STRATA_1.tif"), overwrite = TRUE)
POST_FATE.relativeAbund(name.simulation = "FATE_simulation", years = 1)
}
## TEST output : method 2
file.create("FATE_simulation/RESULTS/POST_FATE_TABLE_YEAR_1_validationStatistics_SIMUL_V0.csv")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2)
, "The folder FATE_simulation/RESULTS/ does not contain adequate files")
})
## OUTPUTS
test_that("POST_FATE.binaryMaps 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
writeRaster(map_1, 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")
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_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_1.tif"), overwrite = TRUE)
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_2.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)
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG6_STRATA_1.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)
validStats = POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = mat.PFG.obs)
}
## TEST output : method 1
expect_message(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 1)
, "> Binary_YEAR_1_PFG1_STRATA_1.tif")
## TEST output : method 2, NULL
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_allStrata/"
, full.names = TRUE))
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_perStrata/"
, full.names = TRUE))
expect_message(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2)
, "> Binary_YEAR_1_PFG1_STRATA_1.tif")
## TEST output : method 2, data.frame
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_allStrata/"
, full.names = TRUE))
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_perStrata/"
, full.names = TRUE))
expect_message(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2
, method2.cutoff = data.frame(year = 1, PFG = "PFG1", cutoff = 1))
, "> Binary_YEAR_1_PFG1_STRATA_1.tif")
expect_warning(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2
, method2.cutoff = data.frame(year = 1, PFG = "PFG1", cutoff = 1))
, "No cutoff for year 1, PFG PFG2.\n No binary maps will be produced!")
})
MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.
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library(RFate)
context("POST_FATE.binaryMaps() function")
## INPUTS
test_that("POST_FATE.binaryMaps gives error with missing data", {
expect_error(POST_FATE.binaryMaps()
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(NA)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(NULL)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : name.simulation", {
expect_error(POST_FATE.binaryMaps(1)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps("a")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(factor(1))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.binaryMaps(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : folders", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation/")
expect_error(POST_FATE.binaryMaps(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.binaryMaps(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.binaryMaps(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.binaryMaps 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.binaryMaps(name.simulation = "FATE_simulation")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = NULL)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = NA)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.binaryMaps(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.binaryMaps(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.binaryMaps gives error with wrong data : years", {
## TEST years : integer
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt")
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = "a")
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor("a"))
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = factor(1))
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NULL)
, "`years` must be an integer > 0")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = NA)
, "`years` must be an integer > 0")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : method", {
## TEST method : correct value
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = "")
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = "a")
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = factor("a"))
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = NULL)
, "`method` must be either `1` or `2`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = NA)
, "`method` must be either `1` or `2`")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : method1.threshold", {
## TEST method1.threshold : correct value
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = "")
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = "a")
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = factor("a"))
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = -1)
, "`method1.threshold` must contain values between `0` and `1`")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 1
, method1.threshold = 1.5)
, "`method1.threshold` must contain values between `0` and `1`")
})
## INPUTS
test_that("POST_FATE.binaryMaps gives error with wrong data : method2.cutoff", {
## TEST method2.cutoff : NULL case
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = NULL)
, "The folder FATE_simulation/RESULTS/ does not contain adequate files")
## TEST method2.cutoff : not NULL or data.frame case
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = NA)
, "`method2.cutoff` must be either NULL or a data.frame")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = 1)
, "`method2.cutoff` must be either NULL or a data.frame")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = matrix(1))
, "`method2.cutoff` must be either NULL or a data.frame")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = "a")
, "`method2.cutoff` must be either NULL or a data.frame")
## TEST method2.cutoff : data.frame case
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = data.frame())
, "`method2.cutoff` does not have the appropriate number of rows (>0) or columns (year, PFG, cutoff)"
, fixed = TRUE)
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = data.frame(1,2))
, "`method2.cutoff` does not have the appropriate number of rows (>0) or columns (year, PFG, cutoff)"
, fixed = TRUE)
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, years = 1
, method = 2
, method2.cutoff = data.frame(1, 2, 3))
, "Column names of `method2.cutoff` must be `year`, `PFG` and `cutoff`"
, fixed = TRUE)
})
## INPUTS
test_that("POST_FATE.binaryMaps 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 RESULTS folder
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 1)
, "The folder FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/ does not contain adequate files")
file.create("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/Abund_YEAR_1_PFG1_STRATA_1.tif")
# expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
# , years = 1
# , method = 1)
# , "Cannot create a RasterLayer object from this file.")
})
## OUTPUTS
test_that("POST_FATE.binaryMaps 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
writeRaster(map_1, 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")
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_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_1.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)
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG6_STRATA_1.tif"), overwrite = TRUE)
POST_FATE.relativeAbund(name.simulation = "FATE_simulation", years = 1)
}
## TEST output : method 2
file.create("FATE_simulation/RESULTS/POST_FATE_TABLE_YEAR_1_validationStatistics_SIMUL_V0.csv")
expect_error(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2)
, "The folder FATE_simulation/RESULTS/ does not contain adequate files")
})
## OUTPUTS
test_that("POST_FATE.binaryMaps 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
writeRaster(map_1, 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")
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_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_1.tif"), overwrite = TRUE)
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_2.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)
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_perStrata/"
, "Abund_YEAR_1_PFG6_STRATA_1.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)
validStats = POST_FATE.graphic_validationStatistics(name.simulation = "FATE_simulation"
, years = 1
, mat.PFG.obs = mat.PFG.obs)
}
## TEST output : method 1
expect_message(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 1)
, "> Binary_YEAR_1_PFG1_STRATA_1.tif")
## TEST output : method 2, NULL
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_allStrata/"
, full.names = TRUE))
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_perStrata/"
, full.names = TRUE))
expect_message(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2)
, "> Binary_YEAR_1_PFG1_STRATA_1.tif")
## TEST output : method 2, data.frame
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_allStrata/"
, full.names = TRUE))
file.remove(list.files("FATE_simulation/RESULTS/SIMUL_V1/BIN_perPFG_perStrata/"
, full.names = TRUE))
expect_message(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2
, method2.cutoff = data.frame(year = 1, PFG = "PFG1", cutoff = 1))
, "> Binary_YEAR_1_PFG1_STRATA_1.tif")
expect_warning(POST_FATE.binaryMaps(name.simulation = "FATE_simulation"
, years = 1
, method = 2
, method2.cutoff = data.frame(year = 1, PFG = "PFG1", cutoff = 1))
, "No cutoff for year 1, PFG PFG2.\n No binary maps will be produced!")
})
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