tests/testthat/test-POST_FATE.temporalEvolution.R
In MayaGueguen/RFate: Vegetation modelling with the FATE model
library(RFate)
context("POST_FATE.temporalEvolution() function")
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with missing data", {
expect_error(POST_FATE.temporalEvolution()
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(NA)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(NULL)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with wrong data : name.simulation", {
expect_error(POST_FATE.temporalEvolution(1)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution("a")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(factor(1))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with wrong data : folders", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation/")
expect_error(POST_FATE.temporalEvolution(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.temporalEvolution(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.temporalEvolution(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.temporalEvolution 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.temporalEvolution(name.simulation = "FATE_simulation")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = NULL)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = NA)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(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.temporalEvolution(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.temporalEvolution gives error with wrong data : no_years", {
## TEST no_years : integer
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt")
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = "a")
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = factor("a"))
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = factor(1))
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = NULL)
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = NA)
, "`no_years` must be an integer > 0")
})
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with wrong data : opt.ras_habitat", {
if (file.exists("toto.txt")) file.remove("toto.txt")
## TEST opt.ras_habitat : length > 0
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = 3
, opt.ras_habitat = 1)
, "`opt.ras_habitat` must contain a character value of length > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = 3
, opt.ras_habitat = factor("a"))
, "`opt.ras_habitat` must contain a character value of length > 0")
## TEST opt.ras_habitat : correct value
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = 3
, opt.ras_habitat = "toto.txt")
, "`toto.txt` does not exist")
file.create("toto.txt")
# expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
# , file.simulParam = "ParamSimul.txt"
# , no_years = 3
# , opt.ras_habitat = "toto.txt")
# , "Cannot create a RasterLayer object from this file.")
})
## INPUTS
test_that("POST_FATE.temporalEvolution 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.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "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.temporalEvolution(name.simulation = "FATE_simulation"
# , no_years = 10)
# , "Cannot create a RasterLayer object from this file.")
writeRaster(map_mask, filename = "FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/Abund_YEAR_1_PFG1_STRATA_all.tif", overwrite = TRUE)
})
## OUTPUTS
test_that("POST_FATE.temporalEvolution gives correct outputs : abundance", {
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")
## TEST .tif files
for (i in 1:6)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST .img files
for (i in 1:6)
{
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.img"), overwrite = TRUE)
}
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST .asc files
for (i in 1:6)
{
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.img"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.asc"), overwrite = TRUE)
}
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST habitat
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST parallelisation
if (.getOS() == "windows")
{
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.no_CPU = 2)
, "Parallelisation with `foreach` is not available for Windows. Sorry.")
} else
{
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.no_CPU = 2)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
}
## TEST .tif files empty
for (i in 1:6)
{
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.asc"))
writeRaster(map_0, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "No abundance values were found! Please check.")
})
## OUTPUTS
test_that("POST_FATE.temporalEvolution gives correct outputs : light", {
{
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
, doLight = TRUE
, LIGHT.thresh_medium = 4000
, LIGHT.thresh_low = 7000)
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_PFGlight(name.simulation = "FATE_simulation"
, mat.PFG.light = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P"))
, mat.PFG.tol = data.frame(PFG = paste0("PFG",1:6)
, strategy_tol = c("ubiquist", "undergrowth"
, "ubiquist", "semi_shade"
, "pioneer", "full_light")))
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 1:6)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
}
## TEST no light
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "No light values were found! Please check.")
## TEST .tif files
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.tif"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
## TEST .img files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.tif"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.img"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
## TEST .asc files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.img"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.asc"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
## TEST habitat
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
})
## OUTPUTS
test_that("POST_FATE.temporalEvolution gives correct outputs : soil", {
{
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
, doSoil = TRUE
, SOIL.init = 2.5
, SOIL.retention = 0.5)
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_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, soil_contrib = c(2, 2.5, 3.5, 3, 1.5, 3)
, soil_tol_min = c(1, 2, 2, 1.5, 1, 2)
, soil_tol_max = c(3, 3, 5, 4.5, 2, 4)))
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 1:6)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
}
## TEST no soil
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "No soil values were found! Please check.")
## TEST .tif files
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.tif"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
## TEST .img files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.tif"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.img"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
## TEST .asc files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.img"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.asc"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
## TEST habitat
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
})
MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.
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library(RFate)
context("POST_FATE.temporalEvolution() function")
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with missing data", {
expect_error(POST_FATE.temporalEvolution()
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(NA)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(NULL)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with wrong data : name.simulation", {
expect_error(POST_FATE.temporalEvolution(1)
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution("a")
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(factor(1))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(POST_FATE.temporalEvolution(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with wrong data : folders", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation/")
expect_error(POST_FATE.temporalEvolution(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.temporalEvolution(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.temporalEvolution(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.temporalEvolution 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.temporalEvolution(name.simulation = "FATE_simulation")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = NULL)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = NA)
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "")
, "The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
expect_error(POST_FATE.temporalEvolution(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.temporalEvolution(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.temporalEvolution gives error with wrong data : no_years", {
## TEST no_years : integer
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt")
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = "a")
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = factor("a"))
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = factor(1))
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = NULL)
, "`no_years` must be an integer > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = NA)
, "`no_years` must be an integer > 0")
})
## INPUTS
test_that("POST_FATE.temporalEvolution gives error with wrong data : opt.ras_habitat", {
if (file.exists("toto.txt")) file.remove("toto.txt")
## TEST opt.ras_habitat : length > 0
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = 3
, opt.ras_habitat = 1)
, "`opt.ras_habitat` must contain a character value of length > 0")
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = 3
, opt.ras_habitat = factor("a"))
, "`opt.ras_habitat` must contain a character value of length > 0")
## TEST opt.ras_habitat : correct value
expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, file.simulParam = "ParamSimul.txt"
, no_years = 3
, opt.ras_habitat = "toto.txt")
, "`toto.txt` does not exist")
file.create("toto.txt")
# expect_error(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
# , file.simulParam = "ParamSimul.txt"
# , no_years = 3
# , opt.ras_habitat = "toto.txt")
# , "Cannot create a RasterLayer object from this file.")
})
## INPUTS
test_that("POST_FATE.temporalEvolution 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.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "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.temporalEvolution(name.simulation = "FATE_simulation"
# , no_years = 10)
# , "Cannot create a RasterLayer object from this file.")
writeRaster(map_mask, filename = "FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/Abund_YEAR_1_PFG1_STRATA_all.tif", overwrite = TRUE)
})
## OUTPUTS
test_that("POST_FATE.temporalEvolution gives correct outputs : abundance", {
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")
## TEST .tif files
for (i in 1:6)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST .img files
for (i in 1:6)
{
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.img"), overwrite = TRUE)
}
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST .asc files
for (i in 1:6)
{
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.img"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.asc"), overwrite = TRUE)
}
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST habitat
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
## TEST parallelisation
if (.getOS() == "windows")
{
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.no_CPU = 2)
, "Parallelisation with `foreach` is not available for Windows. Sorry.")
} else
{
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.no_CPU = 2)
, "> POST_FATE_TABLE_PIXEL_evolution_abundance_SIMUL_V1.csv")
}
## TEST .tif files empty
for (i in 1:6)
{
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.asc"))
writeRaster(map_0, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "No abundance values were found! Please check.")
})
## OUTPUTS
test_that("POST_FATE.temporalEvolution gives correct outputs : light", {
{
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
, doLight = TRUE
, LIGHT.thresh_medium = 4000
, LIGHT.thresh_low = 7000)
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_PFGlight(name.simulation = "FATE_simulation"
, mat.PFG.light = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P"))
, mat.PFG.tol = data.frame(PFG = paste0("PFG",1:6)
, strategy_tol = c("ubiquist", "undergrowth"
, "ubiquist", "semi_shade"
, "pioneer", "full_light")))
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 1:6)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
}
## TEST no light
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "No light values were found! Please check.")
## TEST .tif files
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.tif"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
## TEST .img files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.tif"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.img"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
## TEST .asc files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.img"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/LIGHT/"
, "Light_Resources_YEAR_1_STRATA_1.asc"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
## TEST habitat
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "> POST_FATE_TABLE_PIXEL_evolution_light_SIMUL_V1.csv")
})
## OUTPUTS
test_that("POST_FATE.temporalEvolution gives correct outputs : soil", {
{
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
, doSoil = TRUE
, SOIL.init = 2.5
, SOIL.retention = 0.5)
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_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, soil_contrib = c(2, 2.5, 3.5, 3, 1.5, 3)
, soil_tol_min = c(1, 2, 2, 1.5, 1, 2)
, soil_tol_max = c(3, 3, 5, 4.5, 2, 4)))
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 1:6)
{
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/ABUND_perPFG_allStrata/"
, "Abund_YEAR_1_PFG", i, "_STRATA_all.tif"), overwrite = TRUE)
}
}
## TEST no soil
expect_warning(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "No soil values were found! Please check.")
## TEST .tif files
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.tif"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
## TEST .img files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.tif"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.img"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
## TEST .asc files
file.remove(paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.img"))
writeRaster(map_1, filename = paste0("FATE_simulation/RESULTS/SIMUL_V1/SOIL/"
, "Soil_Resources_YEAR_1.asc"), overwrite = TRUE)
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10)
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
## TEST habitat
expect_message(POST_FATE.temporalEvolution(name.simulation = "FATE_simulation"
, no_years = 10
, opt.ras_habitat = "FATE_simulation/DATA/MASK/map_hab.tif")
, "> POST_FATE_TABLE_PIXEL_evolution_soil_SIMUL_V1.csv")
})
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