tests/testthat/test-PRE_FATE.params_multipleSet.R
In leca-dev/RFate: FATE with R
library(RFate)
context("PRE_FATE.params_multipleSet() function")
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with missing data", {
expect_error(PRE_FATE.params_multipleSet()
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(NA)
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(NULL)
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : name.simulation.1", {
expect_error(PRE_FATE.params_multipleSet(1)
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet("a")
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(factor(1))
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(matrix(seq(2), ncol=2))
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
dir.create("FATE_simulation/PARAM_SIMUL")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "`name.simulation.1` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation/DATA")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "`name.simulation.1` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation/DATA/GLOBAL_PARAMETERS")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : file.simulParam.1", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = NA)
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = 1)
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = factor("a"))
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "a")
, "Wrong name file given!\n `FATE_simulation/PARAM_SIMUL/a` does not exist")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : file.simulParam.2", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = NA)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = 1)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = factor("a"))
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "a")
, "Wrong name file given!\n `FATE_simulation/PARAM_SIMUL/a` does not exist")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt")
, "You must select different simulation parameter files !")
file.create("FATE_simulation/PARAM_SIMUL/toto2.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto2.txt")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : name.simulation.2", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, name.simulation.2 = "a")
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files.")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "a")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "a")
, "`name.simulation.2` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = factor(1))
, "You must select different simulation parameter files !")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = matrix(seq(2), ncol=2))
, "You must select different simulation parameter files !")
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
dir.create("FATE_simulation2")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "`name.simulation.2` does not exist or does not contain a PARAM_SIMUL/ folder")
dir.create("FATE_simulation2/PARAM_SIMUL")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "`name.simulation.2` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation2/DATA")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "`name.simulation.2` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation2/DATA/GLOBAL_PARAMETERS")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "Wrong name file given!\n `FATE_simulation2/PARAM_SIMUL/toto.txt` does not exist")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation")
, "You must select different simulation parameter files !")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto2.txt"
, name.simulation.2 = "FATE_simulation")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
file.create("FATE_simulation2/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : no_simulations", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = NA)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = NULL)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = factor(1))
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = "")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = factor("a"))
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10.5)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_maxAbund", {
## TEST opt.percent_maxAbund : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = NA)
, "`opt.percent_maxAbund` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = NULL)
, "`opt.percent_maxAbund` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = factor(1))
, "`opt.percent_maxAbund` must contain numeric values")
## TEST opt.percent_maxAbund : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = -2)
, "`opt.percent_maxAbund` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = 1.01)
, "`opt.percent_maxAbund` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_seeding", {
## TEST opt.percent_seeding : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = NA)
, "`opt.percent_seeding` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = NULL)
, "`opt.percent_seeding` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = factor(1))
, "`opt.percent_seeding` must contain numeric values")
## TEST opt.percent_seeding : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = -2)
, "`opt.percent_seeding` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = 1.01)
, "`opt.percent_seeding` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_light", {
## TEST opt.percent_light : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = NA)
, "`opt.percent_light` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = NULL)
, "`opt.percent_light` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = factor(1))
, "`opt.percent_light` must contain numeric values")
## TEST opt.percent_light : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = -2)
, "`opt.percent_light` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = 1.01)
, "`opt.percent_light` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_soil", {
## TEST opt.percent_soil : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = NA)
, "`opt.percent_soil` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = NULL)
, "`opt.percent_soil` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = factor(1))
, "`opt.percent_soil` must contain numeric values")
## TEST opt.percent_soil : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = -2)
, "`opt.percent_soil` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = 1.01)
, "`opt.percent_soil` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : do...", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "You must select some parameters to vary !")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : within file.simulParam.1", {
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
## TEST file.simulParam.1 with no_simulations
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file FATE_simulation/PARAM_SIMUL/toto.txt is empty. Please check.")
cat("Yo\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any parameter values with the --PARAM-- flag. Please check.")
cat("--Yo--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file FATE_simulation/PARAM_SIMUL/toto.txt does not contain the --END_OF_FILE-- flag. Please check.")
cat("--Yo--\n--END_OF_FILE--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "Wrong type of data!\n `flag` (GLOBAL_PARAMS) is not found within `params.lines` (FATE_simulation/PARAM_SIMUL/toto.txt)"
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\n--END_OF_FILE--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "Wrong type of data!\n `flag` (GLOBAL_PARAMS) does not contain any value"
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--END_OF_FILE--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "Wrong name file given!\n `./FATE_simulation/glob.txt` does not exist"
, fixed = TRUE)
file.create("FATE_simulation/glob.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file ./FATE_simulation/glob.txt is empty. Please check.")
cat("Yo", file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10))
, "The flag --PFG_PARAMS_LIFE_HISTORY-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check."
, fixed = TRUE)
## TEST file.simulParam.1 and globalParam file
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag.split` ( ) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000", file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.no_strata = FALSE
, do.DISPERSAL.mode = FALSE))
, "The file ./FATE_simulation/glob.txt does not contain any of the required parameter values (NO_PFG, SIMULATION_DURATION, ...). Please check."
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3", file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_DISPERSAL) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3\nDO_DISPERSAL 0"
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_HAB_SUITABILITY) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3\nDO_DISPERSAL 0\nDO_HAB_SUITABILITY 0"
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_LIGHT_INTERACTION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3\nDO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0"
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_SOIL_INTERACTION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nTRUC 3\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_DISTURBANCES) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nTRUC 3\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
# expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
# , file.simulParam.1 = "toto.txt"
# , no_simulations = 10
# , do.DISPERSAL.mode = FALSE
# , do.no_strata = FALSE))
# , "The flag --MASK-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check."
# , fixed = TRUE)
# cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\nFATE_simulation/glob.txt\n--END_OF_FILE--\n"
# , file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (NO_PFG) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (NO_STRATA) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SIMULATION_DURATION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SEEDING_DURATION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SEEDING_TIMESTEP) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SEEDING_INPUT) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (POTENTIAL_FECUNDITY) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (MAX_ABUND_MEDIUM) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (MAX_ABUND_HIGH) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
## TEST file.simulParam.1 and mask
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The flag --MASK-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check."
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\n--END_OF_FILE--\n"
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "`name.MASK` must contain a character value of length > 0"
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\nmask.txt\n--END_OF_FILE--\n"
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong name file given!\n `FATE_simulation_MULTIPLE_SET/DATA/MASK/mask.txt` does not exist")
dir.create("FATE_simulation/DATA/MASK")
file.create("FATE_simulation/DATA/MASK/mask.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong name file given!\n `FATE_simulation_MULTIPLE_SET/DATA/MASK/mask.txt` does not exist")
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n--END_OF_FILE--\n"
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
## TEST file.simulParam.1 and SUCC files
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "There is not the same number of files (`.txt` file starting with `SUCC`) into the FATE_simulation_MULTIPLE_SET/DATA/PFGS/SUCC/ folder as the number of PFG indicated into the file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt"
, fixed = TRUE)
dir.create("FATE_simulation/DATA/PFGS")
dir.create("FATE_simulation/DATA/PFGS/SUCC")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives correct output", {
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_warning(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE)
, "The parameter 'light_thresh_medium' is not defined in the global file"
, fixed = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/PARAM_SIMUL/Simul_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives correct output with other conditions / scenarios", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_1.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_2.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_3.txt")
file.create("FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--TEST--\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--PFG_DISP_PARAMS--\nFATE_simulation/DATA/PFGS/DISP/DISP_1.txt\n"
, "FATE_simulation/DATA/PFGS/DISP/DISP_2.txt\nFATE_simulation/DATA/PFGS/DISP/DISP_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
}
## TEST all but do.DISPERSAL.mode and do.no_strata (and light / soil / habsuit not activated)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
## TEST do.max_abund_low
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
## TEST do.DISPERSAL.mode
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = TRUE
, do.HABSUIT.mode = FALSE)
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
{
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
PRE_FATE.skeletonDirectory(name.simulation = "FATE_simulation2")
file.copy(from = list.files(path = "FATE_simulation"
, all.files = TRUE
, full.names = TRUE
, recursive = TRUE
, include.dirs = FALSE)
, to = sub("FATE_simulation/"
, "FATE_simulation2/"
, list.files(path = "FATE_simulation"
, all.files = TRUE
, full.names = TRUE
, recursive = TRUE
, include.dirs = FALSE)))
fi = readLines("FATE_simulation2/PARAM_SIMUL/toto.txt")
fi = sub("FATE_simulation/", "FATE_simulation2/", fi)
cat(fi, file = "FATE_simulation2/PARAM_SIMUL/toto.txt", sep = "\n")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation2/DATA/GLOBAL_PARAMETERS/glob.txt")
}
## TEST do.max_abund_low ==> 2 folders
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The files do not contain the same parameters to be evaluated."
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 4\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 10\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation2/DATA/GLOBAL_PARAMETERS/glob.txt")
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The global files have different fixed parameter values."
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation2/DATA/GLOBAL_PARAMETERS/glob.txt")
fi = readLines("FATE_simulation2/PARAM_SIMUL/toto.txt")
fi = sub("FATE_simulation2/DATA/MASK/mask.txt", "FATE_simulation2/DATA/MASK/maski.txt", fi)
cat(fi, file = "FATE_simulation2/PARAM_SIMUL/toto.txt", sep = "\n")
file.create("FATE_simulation2/DATA/MASK/maski.txt")
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The simulation files have different fixed parameter values."
, fixed = TRUE)
fi = readLines("FATE_simulation2/PARAM_SIMUL/toto.txt")
fi = sub("FATE_simulation2/DATA/MASK/maski.txt", "FATE_simulation2/DATA/MASK/mask.txt", fi)
cat(fi, file = "FATE_simulation2/PARAM_SIMUL/toto.txt", sep = "\n")
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 5
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = TRUE
, do.HABSUIT.mode = FALSE)
, "The number of data sets requested (`no_simulations`) is too small compared to the number of parameters that must vary."
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives error for other conditions / scenarios", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_1.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_2.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_3.txt")
file.create("FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
cat(paste0("## Test file\n"
, "TEST 10000\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
}
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The global parameter file indicated in FATE_simulation/PARAM_SIMUL/toto.txt does not contain any of the required parameter values (MAX_ABUND_LOW). Please check."
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives error for scenario NO_STRATA", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_1.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_2.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_3.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
file.create("FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
cat(paste0("## Test file\n"
, "NO_STRATA 3\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
}
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The flag --PFG_PARAMS_LIFE_HISTORY-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check.")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "Wrong type of data!\n `flag.split` ( ) is not found within `params.lines` (./FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt)"
, fixed = TRUE)
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "Wrong type of data!\n `flag.split` ( ) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/PFGS/SUCC/REP-1/SUCC_FG1.txt has been successfully created !")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 1\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The flag --PFG_PARAMS_LIGHT-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check.")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--PFG_PARAMS_LIGHT--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "`flag` (LIGHT) is not found within `params.lines` (./FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt)"
, fixed = TRUE)
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\nLIGHT 1\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\nLIGHT 3\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\nLIGHT 5\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "`flag` (LIGHT_THRESH_MEDIUM) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 1\n"
, "LIGHT_THRESH_MEDIUM 5\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "`flag` (LIGHT_THRESH_LOW) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 1\n"
, "LIGHT_THRESH_MEDIUM 5\nLIGHT_THRESH_LOW 10\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/PFGS/LIGHT/REP-1/LIGHT_FG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives error for scenario SOIL", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\n")
, file = "FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\n")
, file = "FATE_simulation/DATA/PFGS/SOIL/SOIL_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\n")
, file = "FATE_simulation/DATA/PFGS/SOIL/SOIL_3.txt")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 1\nSOIL_INIT 0.1\nSOIL_RETENTION 0.1\n"
, "DO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--PFG_PARAMS_SOIL--\nFATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt\n"
, "FATE_simulation/DATA/PFGS/SOIL/SOIL_2.txt\nFATE_simulation/DATA/PFGS/SOIL/SOIL_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
}
expect_message(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = 0.9
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = TRUE
, do.SOIL.retention = TRUE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/PFGS/SUCC/REP-1/SUCC_FG1.txt has been successfully created !")
})
leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.
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library(RFate)
context("PRE_FATE.params_multipleSet() function")
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with missing data", {
expect_error(PRE_FATE.params_multipleSet()
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(NA)
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(NULL)
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : name.simulation.1", {
expect_error(PRE_FATE.params_multipleSet(1)
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet("a")
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(factor(1))
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(matrix(seq(2), ncol=2))
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
dir.create("FATE_simulation")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "`name.simulation.1` does not exist or does not contain a PARAM_SIMUL/ folder")
dir.create("FATE_simulation/PARAM_SIMUL")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "`name.simulation.1` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation/DATA")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "`name.simulation.1` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation/DATA/GLOBAL_PARAMETERS")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ does not contain adequate files")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation")
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : file.simulParam.1", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = NA)
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = 1)
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = factor("a"))
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "a")
, "Wrong name file given!\n `FATE_simulation/PARAM_SIMUL/a` does not exist")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : file.simulParam.2", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = NA)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = 1)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = factor("a"))
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "a")
, "Wrong name file given!\n `FATE_simulation/PARAM_SIMUL/a` does not exist")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt")
, "You must select different simulation parameter files !")
file.create("FATE_simulation/PARAM_SIMUL/toto2.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto2.txt")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : name.simulation.2", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, name.simulation.2 = "a")
, "Missing data!\n The folder FATE_simulation/PARAM_SIMUL/ contain one or more files.")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "a")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "a")
, "`name.simulation.2` does not exist or does not contain a PARAM_SIMUL/ folder")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = factor(1))
, "You must select different simulation parameter files !")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = matrix(seq(2), ncol=2))
, "You must select different simulation parameter files !")
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
dir.create("FATE_simulation2")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "`name.simulation.2` does not exist or does not contain a PARAM_SIMUL/ folder")
dir.create("FATE_simulation2/PARAM_SIMUL")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "`name.simulation.2` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation2/DATA")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "`name.simulation.2` does not exist or does not contain a DATA/GLOBAL_PARAMETERS/ folder")
dir.create("FATE_simulation2/DATA/GLOBAL_PARAMETERS")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "Wrong name file given!\n `FATE_simulation2/PARAM_SIMUL/toto.txt` does not exist")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation")
, "You must select different simulation parameter files !")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto2.txt"
, name.simulation.2 = "FATE_simulation")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
file.create("FATE_simulation2/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, file.simulParam.2 = "toto.txt"
, name.simulation.2 = "FATE_simulation2")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : no_simulations", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = NA)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = NULL)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = factor(1))
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = "")
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = factor("a"))
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10.5)
, "Wrong type of data!\n `no_simulations` must be an integer > 0")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_maxAbund", {
## TEST opt.percent_maxAbund : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = NA)
, "`opt.percent_maxAbund` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = NULL)
, "`opt.percent_maxAbund` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = factor(1))
, "`opt.percent_maxAbund` must contain numeric values")
## TEST opt.percent_maxAbund : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = -2)
, "`opt.percent_maxAbund` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_maxAbund = 1.01)
, "`opt.percent_maxAbund` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_seeding", {
## TEST opt.percent_seeding : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = NA)
, "`opt.percent_seeding` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = NULL)
, "`opt.percent_seeding` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = factor(1))
, "`opt.percent_seeding` must contain numeric values")
## TEST opt.percent_seeding : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = -2)
, "`opt.percent_seeding` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_seeding = 1.01)
, "`opt.percent_seeding` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_light", {
## TEST opt.percent_light : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = NA)
, "`opt.percent_light` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = NULL)
, "`opt.percent_light` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = factor(1))
, "`opt.percent_light` must contain numeric values")
## TEST opt.percent_light : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = -2)
, "`opt.percent_light` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_light = 1.01)
, "`opt.percent_light` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : opt.percent_soil", {
## TEST opt.percent_soil : numeric values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = NA)
, "`opt.percent_soil` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = NULL)
, "`opt.percent_soil` must contain numeric values")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = factor(1))
, "`opt.percent_soil` must contain numeric values")
## TEST opt.percent_soil : correct values
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = -2)
, "`opt.percent_soil` must contain values between `0` and `1`")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = 1.01)
, "`opt.percent_soil` must contain values between `0` and `1`")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : do...", {
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "You must select some parameters to vary !")
})
## INPUTS
test_that("PRE_FATE.params_multipleSet gives error with wrong data : within file.simulParam.1", {
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
## TEST file.simulParam.1 with no_simulations
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file FATE_simulation/PARAM_SIMUL/toto.txt is empty. Please check.")
cat("Yo\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any parameter values with the --PARAM-- flag. Please check.")
cat("--Yo--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file FATE_simulation/PARAM_SIMUL/toto.txt does not contain the --END_OF_FILE-- flag. Please check.")
cat("--Yo--\n--END_OF_FILE--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "Wrong type of data!\n `flag` (GLOBAL_PARAMS) is not found within `params.lines` (FATE_simulation/PARAM_SIMUL/toto.txt)"
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\n--END_OF_FILE--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "Wrong type of data!\n `flag` (GLOBAL_PARAMS) does not contain any value"
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--END_OF_FILE--\n", file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "Wrong name file given!\n `./FATE_simulation/glob.txt` does not exist"
, fixed = TRUE)
file.create("FATE_simulation/glob.txt")
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10)
, "The file ./FATE_simulation/glob.txt is empty. Please check.")
cat("Yo", file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10))
, "The flag --PFG_PARAMS_LIFE_HISTORY-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check."
, fixed = TRUE)
## TEST file.simulParam.1 and globalParam file
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag.split` ( ) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000", file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.no_strata = FALSE
, do.DISPERSAL.mode = FALSE))
, "The file ./FATE_simulation/glob.txt does not contain any of the required parameter values (NO_PFG, SIMULATION_DURATION, ...). Please check."
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3", file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_DISPERSAL) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3\nDO_DISPERSAL 0"
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_HAB_SUITABILITY) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3\nDO_DISPERSAL 0\nDO_HAB_SUITABILITY 0"
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_LIGHT_INTERACTION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat("MAX_ABUND_LOW 10000\nTRUC 3\nDO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0"
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_SOIL_INTERACTION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nTRUC 3\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (DO_DISTURBANCES) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nTRUC 3\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
# expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
# , file.simulParam.1 = "toto.txt"
# , no_simulations = 10
# , do.DISPERSAL.mode = FALSE
# , do.no_strata = FALSE))
# , "The flag --MASK-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check."
# , fixed = TRUE)
# cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\nFATE_simulation/glob.txt\n--END_OF_FILE--\n"
# , file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (NO_PFG) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (NO_STRATA) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SIMULATION_DURATION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SEEDING_DURATION) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SEEDING_TIMESTEP) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (SEEDING_INPUT) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (POTENTIAL_FECUNDITY) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("MAX_ABUND_LOW 10000\nNO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (MAX_ABUND_MEDIUM) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong type of data!\n `flag` (MAX_ABUND_HIGH) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 2\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\nDO_HAB_SUITABILITY 0\n"
, "DO_LIGHT_INTERACTION 0\nDO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0")
, file = "FATE_simulation/glob.txt")
## TEST file.simulParam.1 and mask
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The flag --MASK-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check."
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\n--END_OF_FILE--\n"
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "`name.MASK` must contain a character value of length > 0"
, fixed = TRUE)
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\nmask.txt\n--END_OF_FILE--\n"
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong name file given!\n `FATE_simulation_MULTIPLE_SET/DATA/MASK/mask.txt` does not exist")
dir.create("FATE_simulation/DATA/MASK")
file.create("FATE_simulation/DATA/MASK/mask.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "Wrong name file given!\n `FATE_simulation_MULTIPLE_SET/DATA/MASK/mask.txt` does not exist")
cat("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n--END_OF_FILE--\n"
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
## TEST file.simulParam.1 and SUCC files
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "There is not the same number of files (`.txt` file starting with `SUCC`) into the FATE_simulation_MULTIPLE_SET/DATA/PFGS/SUCC/ folder as the number of PFG indicated into the file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt"
, fixed = TRUE)
dir.create("FATE_simulation/DATA/PFGS")
dir.create("FATE_simulation/DATA/PFGS/SUCC")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives correct output", {
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_warning(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE)
, "The parameter 'light_thresh_medium' is not defined in the global file"
, fixed = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/PARAM_SIMUL/Simul_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives correct output with other conditions / scenarios", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_1.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_2.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_3.txt")
file.create("FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--TEST--\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--PFG_DISP_PARAMS--\nFATE_simulation/DATA/PFGS/DISP/DISP_1.txt\n"
, "FATE_simulation/DATA/PFGS/DISP/DISP_2.txt\nFATE_simulation/DATA/PFGS/DISP/DISP_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
}
## TEST all but do.DISPERSAL.mode and do.no_strata (and light / soil / habsuit not activated)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.DISPERSAL.mode = FALSE
, do.no_strata = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
## TEST do.max_abund_low
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
## TEST do.DISPERSAL.mode
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = TRUE
, do.HABSUIT.mode = FALSE)
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
{
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
PRE_FATE.skeletonDirectory(name.simulation = "FATE_simulation2")
file.copy(from = list.files(path = "FATE_simulation"
, all.files = TRUE
, full.names = TRUE
, recursive = TRUE
, include.dirs = FALSE)
, to = sub("FATE_simulation/"
, "FATE_simulation2/"
, list.files(path = "FATE_simulation"
, all.files = TRUE
, full.names = TRUE
, recursive = TRUE
, include.dirs = FALSE)))
fi = readLines("FATE_simulation2/PARAM_SIMUL/toto.txt")
fi = sub("FATE_simulation/", "FATE_simulation2/", fi)
cat(fi, file = "FATE_simulation2/PARAM_SIMUL/toto.txt", sep = "\n")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation2/DATA/GLOBAL_PARAMETERS/glob.txt")
}
## TEST do.max_abund_low ==> 2 folders
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The files do not contain the same parameters to be evaluated."
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 4\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 10\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation2/DATA/GLOBAL_PARAMETERS/glob.txt")
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The global files have different fixed parameter values."
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 1\nDISPERSAL_MODE 1\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation2/DATA/GLOBAL_PARAMETERS/glob.txt")
fi = readLines("FATE_simulation2/PARAM_SIMUL/toto.txt")
fi = sub("FATE_simulation2/DATA/MASK/mask.txt", "FATE_simulation2/DATA/MASK/maski.txt", fi)
cat(fi, file = "FATE_simulation2/PARAM_SIMUL/toto.txt", sep = "\n")
file.create("FATE_simulation2/DATA/MASK/maski.txt")
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The simulation files have different fixed parameter values."
, fixed = TRUE)
fi = readLines("FATE_simulation2/PARAM_SIMUL/toto.txt")
fi = sub("FATE_simulation2/DATA/MASK/maski.txt", "FATE_simulation2/DATA/MASK/mask.txt", fi)
cat(fi, file = "FATE_simulation2/PARAM_SIMUL/toto.txt", sep = "\n")
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_message(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt has been successfully created !"
, fixed = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, name.simulation.2 = "FATE_simulation2"
, file.simulParam.2 = "toto.txt"
, no_simulations = 5
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = TRUE
, do.HABSUIT.mode = FALSE)
, "The number of data sets requested (`no_simulations`) is too small compared to the number of parameters that must vary."
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives error for other conditions / scenarios", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_1.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_2.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_3.txt")
file.create("FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
cat(paste0("## Test file\n"
, "TEST 10000\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
}
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = TRUE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = FALSE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The global parameter file indicated in FATE_simulation/PARAM_SIMUL/toto.txt does not contain any of the required parameter values (MAX_ABUND_LOW). Please check."
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives error for scenario NO_STRATA", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_1.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_2.txt")
file.create("FATE_simulation/DATA/PFGS/DISP/DISP_3.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
file.create("FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
cat(paste0("## Test file\n"
, "NO_STRATA 3\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
}
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
expect_error(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The flag --PFG_PARAMS_LIFE_HISTORY-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check.")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "Wrong type of data!\n `flag.split` ( ) is not found within `params.lines` (./FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt)"
, fixed = TRUE)
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "Wrong type of data!\n `flag.split` ( ) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/PFGS/SUCC/REP-1/SUCC_FG1.txt has been successfully created !")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 1\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The flag --PFG_PARAMS_LIGHT-- in the file FATE_simulation/PARAM_SIMUL/toto.txt does not contain any value. Please check.")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--PFG_PARAMS_LIGHT--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "`flag` (LIGHT) is not found within `params.lines` (./FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt)"
, fixed = TRUE)
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\nLIGHT 1\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\nLIGHT 3\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\nLIGHT 5\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "`flag` (LIGHT_THRESH_MEDIUM) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 1\n"
, "LIGHT_THRESH_MEDIUM 5\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_error(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "`flag` (LIGHT_THRESH_LOW) is not found within `params.lines` (FATE_simulation_MULTIPLE_SET/tmp_global_param.txt)"
, fixed = TRUE)
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 1\n"
, "LIGHT_THRESH_MEDIUM 5\nLIGHT_THRESH_LOW 10\n"
, "DO_SOIL_INTERACTION 0\nDO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
expect_message(suppressWarnings(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = FALSE
, do.SOIL.retention = FALSE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE))
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/PFGS/LIGHT/REP-1/LIGHT_FG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_multipleSet gives error for scenario SOIL", {
{
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
if (dir.exists("FATE_simulation2")) unlink("FATE_simulation2", recursive = TRUE)
if (dir.exists("FATE_simulation_MULTIPLE_SET")) unlink("FATE_simulation_MULTIPLE_SET", recursive = TRUE)
PRE_FATE.skeletonDirectory()
file.create("FATE_simulation/DATA/MASK/mask.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
file.create("FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\n")
, file = "FATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt")
cat(paste0("NAME FG1\nTYPE H\nHEIGHT 15\nMATURITY 2\nLONGEVITY 5\n")
, file = "FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt")
cat(paste0("NAME FG2\nTYPE C\nHEIGHT 150\nMATURITY 5\nLONGEVITY 10\n")
, file = "FATE_simulation/DATA/PFGS/SOIL/SOIL_2.txt")
cat(paste0("NAME FG3\nTYPE P\nHEIGHT 1100\nMATURITY 20\nLONGEVITY 80\n")
, file = "FATE_simulation/DATA/PFGS/SOIL/SOIL_3.txt")
cat(paste0("## Test file\n"
, "NO_PFG 3\nNO_STRATA 4\nSIMULATION_DURATION 50\n"
, "SEEDING_DURATION 10\nSEEDING_TIMESTEP 1\nSEEDING_INPUT 100\nPOTENTIAL_FECUNDITY 10\n"
, "MAX_ABUND_LOW 5000\nMAX_ABUND_MEDIUM 6000\nMAX_ABUND_HIGH 7000\n"
, "DO_DISPERSAL 0\n"
, "DO_HAB_SUITABILITY 0\nDO_LIGHT_INTERACTION 0\n"
, "DO_SOIL_INTERACTION 1\nSOIL_INIT 0.1\nSOIL_RETENTION 0.1\n"
, "DO_DISTURBANCES 0\n")
, file = "FATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt")
file.create("FATE_simulation/PARAM_SIMUL/toto.txt")
cat(paste0("--GLOBAL_PARAMS--\nFATE_simulation/DATA/GLOBAL_PARAMETERS/glob.txt\n"
, "--MASK--\nFATE_simulation/DATA/MASK/mask.txt\n"
, "--PFG_PARAMS_LIFE_HISTORY--\nFATE_simulation/DATA/PFGS/SUCC/SUCC_1.txt\n"
, "FATE_simulation/DATA/PFGS/SUCC/SUCC_2.txt\nFATE_simulation/DATA/PFGS/SUCC/SUCC_3.txt\n"
, "--PFG_PARAMS_SOIL--\nFATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt\n"
, "FATE_simulation/DATA/PFGS/SOIL/SOIL_2.txt\nFATE_simulation/DATA/PFGS/SOIL/SOIL_3.txt\n"
, "--END_OF_FILE--\n")
, file = "FATE_simulation/PARAM_SIMUL/toto.txt")
}
expect_message(PRE_FATE.params_multipleSet(name.simulation.1 = "FATE_simulation"
, file.simulParam.1 = "toto.txt"
, no_simulations = 10
, opt.percent_soil = 0.9
, do.max_abund_low = FALSE
, do.max_abund_medium = FALSE
, do.max_abund_high = FALSE
, do.seeding_duration = FALSE
, do.seeding_timestep = FALSE
, do.seeding_input = FALSE
, do.potential_fecundity = FALSE
, do.no_strata = TRUE
, do.LIGHT.thresh_medium = FALSE
, do.LIGHT.thresh_low = FALSE
, do.SOIL.init = TRUE
, do.SOIL.retention = TRUE
, do.DISPERSAL.mode = FALSE
, do.HABSUIT.mode = FALSE)
, "The parameter file FATE_simulation_MULTIPLE_SET/DATA/PFGS/SUCC/REP-1/SUCC_FG1.txt has been successfully created !")
})
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