tests/testthat/test-PRE_FATE.params_PFGsuccession.R
In leca-dev/RFate: FATE with R
library(RFate)
context("PRE_FATE.params_PFGsuccession() function")
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with missing data", {
expect_error(PRE_FATE.params_PFGsuccession()
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(NA)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(NULL)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with wrong data : name.simulation", {
expect_error(PRE_FATE.params_PFGsuccession(1)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession("a")
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(factor(1))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with wrong data : mat.PFG.succ", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST mat.PFG.succ : data.frame
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation")
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = NA)
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = NULL)
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = "")
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = 1)
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = factor(1))
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = matrix(1))
, "`mat.PFG.succ` must be a data.frame")
## TEST mat.PFG.succ : correct number of rows and columns
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame())
, "`mat.PFG.succ` does not have the appropriate number of rows (>0) or columns (PFG, type, height, maturity, longevity, (max_abundance), (potential_fecundity), (immature_size), (is_alien), (flammability))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1))
, "`mat.PFG.succ` does not have the appropriate number of rows (>0) or columns (PFG, type, height, maturity, longevity, (max_abundance), (potential_fecundity), (immature_size), (is_alien), (flammability))"
, fixed = TRUE)
## TEST mat.PFG.succ : correct names of columns
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6,7))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6,7,8))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6,7,8,9))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, hop = 1))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
## TEST mat.PFG.succ$PFG : different values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = c(2,2)
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = NA, type = 2
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,NA), type = c(2,2)
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain different values", fixed = TRUE)
## TEST mat.PFG.succ$PFG : length > 0
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = "", type = NA
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.succ$type : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = NA
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = 2
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = ""
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = c(2,NA)
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
## TEST mat.PFG.succ$height : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = NA, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = "a", maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = factor(1), maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$height : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = c(3,NA), maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$maturity : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = NA
, longevity = 10))
, "`mat.PFG.succ$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = "a"
, longevity = 10))
, "`mat.PFG.succ$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = factor(1)
, longevity = 10))
, "`mat.PFG.succ$maturity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$maturity : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = c(4,NA)
, longevity = 10))
, "`mat.PFG.succ$maturity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$longevity : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = NA))
, "`mat.PFG.succ$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = "a"))
, "`mat.PFG.succ$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = factor(1)))
, "`mat.PFG.succ$longevity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$longevity : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = c(10,NA)))
, "`mat.PFG.succ$longevity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$maturity : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 2))
, "`mat.PFG.succ$maturity` must contain values equal or inferior to `mat.PFG.succ$longevity`"
, fixed = TRUE)
## TEST mat.PFG.succ$max_abundance : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, max_abundance = c(10,NA)))
, "`mat.PFG.succ$max_abundance` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$potential_fecundity : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = NA))
, "`mat.PFG.succ$potential_fecundity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = "a"))
, "`mat.PFG.succ$potential_fecundity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = factor(1)))
, "`mat.PFG.succ$potential_fecundity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$potential_fecundity : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = c(10,NA)))
, "`mat.PFG.succ$potential_fecundity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$immature_size : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = c(10,NA)))
, "`mat.PFG.succ$immature_size` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$immature_size : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = "a"))
, "`mat.PFG.succ$immature_size` must be an integer > 0"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = 1.5))
, "`mat.PFG.succ$immature_size` must be an integer > 0"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = 101))
, "`mat.PFG.succ$immature_size` must contain values between `0` and `100`"
, fixed = TRUE)
## TEST mat.PFG.succ$is_alien : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = c(10,NA)))
, "`mat.PFG.succ$is_alien` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$is_alien : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = "a"))
, "`mat.PFG.succ$is_alien` must be either `0` or `1`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = 1.5))
, "`mat.PFG.succ$is_alien` must be either `0` or `1`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = 11))
, "`mat.PFG.succ$is_alien` must be either `0` or `1`", fixed = TRUE)
## TEST mat.PFG.succ$flammability : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = NA))
, "`mat.PFG.succ$flammability` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = "a"))
, "`mat.PFG.succ$flammability` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = factor(1)))
, "`mat.PFG.succ$flammability` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$flammability : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = c(10,NA)))
, "`mat.PFG.succ$flammability` must not contain NA values", fixed = TRUE)
})
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with wrong data : strata.limits", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST strata.limits : integer
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = NA)
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = "a")
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = factor(1))
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = -1)
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
## TEST classic input
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ)
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/SUCC_PFG1.txt has been successfully created !")
expect_warning(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = "")
, "already exists. It will be replaced.")
## TEST opt.folder.name
expect_warning(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = NA)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_warning(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = 1)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = "scen1")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/scen1/SUCC_PFG1.txt has been successfully created !")
## TEST selection of strata limits
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = "PFG1"
, type = "C"
, height = 10
, maturity = 5
, longevity = 12)
, opt.folder.name = "scen2")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/scen2/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario max_abundance", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, max_abundance = c(2, 2, 1, 1, 2, 3))
, opt.folder.name = "max_abund")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/max_abund/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario potential_fecundity", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, potential_fecundity = rep(150, 6))
, opt.folder.name = "pot_fecund")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/pot_fecund/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario immature_size", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, immature_size = c(80, 80, 100, 100, 50, 60))
, opt.folder.name = "imm_size")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/imm_size/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario is_alien", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, is_alien = c(0, 0, 1, 0, 0, 0))
, opt.folder.name = "is_alien")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/is_alien/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario flammability", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, flammability = c(0, 0, 1, 0, 0, 0))
, opt.folder.name = "flammability")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/flammability/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario no strata.limits reduction", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits_reduce = FALSE
, opt.folder.name = "strat")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/strat/SUCC_PFG1.txt has been successfully created !")
})
leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.
R Package Documentation
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library(RFate)
context("PRE_FATE.params_PFGsuccession() function")
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with missing data", {
expect_error(PRE_FATE.params_PFGsuccession()
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(NA)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(NULL)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with wrong data : name.simulation", {
expect_error(PRE_FATE.params_PFGsuccession(1)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession("a")
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(factor(1))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
expect_error(PRE_FATE.params_PFGsuccession(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SUCC/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with wrong data : mat.PFG.succ", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST mat.PFG.succ : data.frame
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation")
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = NA)
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = NULL)
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = "")
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = 1)
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = factor(1))
, "`mat.PFG.succ` must be a data.frame")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation", mat.PFG.succ = matrix(1))
, "`mat.PFG.succ` must be a data.frame")
## TEST mat.PFG.succ : correct number of rows and columns
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame())
, "`mat.PFG.succ` does not have the appropriate number of rows (>0) or columns (PFG, type, height, maturity, longevity, (max_abundance), (potential_fecundity), (immature_size), (is_alien), (flammability))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1))
, "`mat.PFG.succ` does not have the appropriate number of rows (>0) or columns (PFG, type, height, maturity, longevity, (max_abundance), (potential_fecundity), (immature_size), (is_alien), (flammability))"
, fixed = TRUE)
## TEST mat.PFG.succ : correct names of columns
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6,7))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6,7,8))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(1,2,3,4,5,6,7,8,9))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, hop = 1))
, "Column names of `mat.PFG.succ` must be `PFG`, `type`, `height`, `maturity`, `longevity`, `(max_abundance)`, `(potential_fecundity)`, `(immature_size)`, `(is_alien)` and `(flammability)`"
, fixed = TRUE)
## TEST mat.PFG.succ$PFG : different values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = c(2,2)
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = NA, type = 2
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,NA), type = c(2,2)
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain different values", fixed = TRUE)
## TEST mat.PFG.succ$PFG : length > 0
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = "", type = NA
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.succ$type : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = NA
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = 2
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = ""
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = c(2,NA)
, height = 3, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$type` must be either `H`, `C` or `P`", fixed = TRUE)
## TEST mat.PFG.succ$height : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = NA, maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = "a", maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = factor(1), maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$height : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = c(3,NA), maturity = 4
, longevity = 10))
, "`mat.PFG.succ$height` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$maturity : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = NA
, longevity = 10))
, "`mat.PFG.succ$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = "a"
, longevity = 10))
, "`mat.PFG.succ$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = factor(1)
, longevity = 10))
, "`mat.PFG.succ$maturity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$maturity : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = c(4,NA)
, longevity = 10))
, "`mat.PFG.succ$maturity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$longevity : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = NA))
, "`mat.PFG.succ$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = "a"))
, "`mat.PFG.succ$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = factor(1)))
, "`mat.PFG.succ$longevity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$longevity : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = c(10,NA)))
, "`mat.PFG.succ$longevity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$maturity : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 2))
, "`mat.PFG.succ$maturity` must contain values equal or inferior to `mat.PFG.succ$longevity`"
, fixed = TRUE)
## TEST mat.PFG.succ$max_abundance : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, max_abundance = c(10,NA)))
, "`mat.PFG.succ$max_abundance` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$potential_fecundity : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = NA))
, "`mat.PFG.succ$potential_fecundity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = "a"))
, "`mat.PFG.succ$potential_fecundity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = factor(1)))
, "`mat.PFG.succ$potential_fecundity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$potential_fecundity : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, potential_fecundity = c(10,NA)))
, "`mat.PFG.succ$potential_fecundity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$immature_size : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = c(10,NA)))
, "`mat.PFG.succ$immature_size` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$immature_size : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = "a"))
, "`mat.PFG.succ$immature_size` must be an integer > 0"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = 1.5))
, "`mat.PFG.succ$immature_size` must be an integer > 0"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, immature_size = 101))
, "`mat.PFG.succ$immature_size` must contain values between `0` and `100`"
, fixed = TRUE)
## TEST mat.PFG.succ$is_alien : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = c(10,NA)))
, "`mat.PFG.succ$is_alien` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.succ$is_alien : correct values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = "a"))
, "`mat.PFG.succ$is_alien` must be either `0` or `1`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = 1.5))
, "`mat.PFG.succ$is_alien` must be either `0` or `1`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, is_alien = 11))
, "`mat.PFG.succ$is_alien` must be either `0` or `1`", fixed = TRUE)
## TEST mat.PFG.succ$flammability : numeric values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = NA))
, "`mat.PFG.succ$flammability` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = "a"))
, "`mat.PFG.succ$flammability` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = 1, type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = factor(1)))
, "`mat.PFG.succ$flammability` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.succ$flammability : no NA values
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = c(1,2), type = "H"
, height = 3, maturity = 4
, longevity = 10, flammability = c(10,NA)))
, "`mat.PFG.succ$flammability` must not contain NA values", fixed = TRUE)
})
## INPUTS
test_that("PRE_FATE.params_PFGsuccession gives error with wrong data : strata.limits", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST strata.limits : integer
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = NA)
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = "a")
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = factor(1))
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
expect_error(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits = -1)
, "Wrong type of data!\n `strata.limits` must be an integer > 0")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
## TEST classic input
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ)
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/SUCC_PFG1.txt has been successfully created !")
expect_warning(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = "")
, "already exists. It will be replaced.")
## TEST opt.folder.name
expect_warning(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = NA)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_warning(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = 1)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = mat.PFG.succ
, opt.folder.name = "scen1")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/scen1/SUCC_PFG1.txt has been successfully created !")
## TEST selection of strata limits
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = "PFG1"
, type = "C"
, height = 10
, maturity = 5
, longevity = 12)
, opt.folder.name = "scen2")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/scen2/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario max_abundance", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, max_abundance = c(2, 2, 1, 1, 2, 3))
, opt.folder.name = "max_abund")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/max_abund/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario potential_fecundity", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, potential_fecundity = rep(150, 6))
, opt.folder.name = "pot_fecund")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/pot_fecund/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario immature_size", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, immature_size = c(80, 80, 100, 100, 50, 60))
, opt.folder.name = "imm_size")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/imm_size/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario is_alien", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, is_alien = c(0, 0, 1, 0, 0, 0))
, opt.folder.name = "is_alien")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/is_alien/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario flammability", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70)
, flammability = c(0, 0, 1, 0, 0, 0))
, opt.folder.name = "flammability")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/flammability/SUCC_PFG1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsuccession gives correct output : scenario no strata.limits reduction", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsuccession(name.simulation = "FATE_simulation"
, mat.PFG.succ = data.frame(PFG = paste0("PFG",1:6)
, type = c("C", "C", "H", "H", "P", "P")
, height = c(10, 250, 36, 68, 1250, 550)
, maturity = c(5, 5, 3, 3, 8, 9)
, longevity = c(12, 200, 25, 4, 110, 70))
, strata.limits_reduce = FALSE
, opt.folder.name = "strat")
, "The parameter file FATE_simulation/DATA/PFGS/SUCC/strat/SUCC_PFG1.txt has been successfully created !")
})
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