tests/testthat/test-PRE_FATE.params_PFGsoil.R
In MayaGueguen/RFate: Vegetation modelling with the FATE model
library(RFate)
context("PRE_FATE.params_PFGsoil() function")
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with missing data", {
expect_error(PRE_FATE.params_PFGsoil()
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(NA)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(NULL)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with wrong data : name.simulation", {
expect_error(PRE_FATE.params_PFGsoil(1)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil("a")
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(factor(1))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with wrong data : mat.PFG.soil", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST mat.PFG.soil : data.frame
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation")
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = NA)
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = NULL)
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = "")
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = 1)
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = factor(1))
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = matrix(1))
, "`mat.PFG.soil` must be a data.frame")
## TEST mat.PFG.soil : correct number of rows and columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame())
, "`mat.PFG.soil` does not have the appropriate number of rows (>0) or columns (PFG, type, (active_germ_low), (active_germ_medium), (active_germ_high), (strategy_ag), soil_contrib, soil_tol_min, soil_tol_max, (strategy_contrib))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1))
, "`mat.PFG.soil` does not have the appropriate number of rows (>0) or columns (PFG, type, (active_germ_low), (active_germ_medium), (active_germ_high), (strategy_ag), soil_contrib, soil_tol_min, soil_tol_max, (strategy_contrib))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1,2,3,4,5,6,7,8))
, "`mat.PFG.soil` does not have the appropriate number of rows (>0) or columns (PFG, type, (active_germ_low), (active_germ_medium), (active_germ_high), (strategy_ag), soil_contrib, soil_tol_min, soil_tol_max, (strategy_contrib))"
, fixed = TRUE)
## TEST mat.PFG.soil : correct names of columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1,2,3))
, "Column names of `mat.PFG.soil` must be `PFG`, `type`, `(active_germ_low)`, `(active_germ_medium)`, `(active_germ_high)`, `(strategy_ag)`, `soil_contrib`, `soil_tol_min`, `soil_tol_max` and `(strategy_contrib)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.soil` must be `PFG`, `type`, `(active_germ_low)`, `(active_germ_medium)`, `(active_germ_high)`, `(strategy_ag)`, `soil_contrib`, `soil_tol_min`, `soil_tol_max` and `(strategy_contrib)`"
, fixed = TRUE)
## TEST mat.PFG.soil$PFG : different values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = rep("H", 2), strategy_contrib = "indifferent"))
, "`mat.PFG.soil$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = NA, type = "H", strategy_contrib = "indifferent"))
, "`mat.PFG.soil$PFG` must contain different values", fixed = TRUE)
## TEST mat.PFG.soil$PFG : length > 0
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = "", type = "H", strategy_contrib = "indifferent"))
, "`mat.PFG.soil$PFG` must contain a character value of length > 0"
, fixed = TRUE)
## TEST mat.PFG.soil$type : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = NA, strategy_contrib = "indifferent"))
, "`mat.PFG.soil$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = 2, strategy_contrib = "indifferent"))
, "`mat.PFG.soil$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "", strategy_contrib = "indifferent"))
, "`mat.PFG.soil$type` must be either `H`, `C` or `P`", fixed = TRUE)
## TEST mat.PFG.soil$strategy_contrib : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H", strategy_contrib = 1))
, "`mat.PFG.soil$strategy_contrib` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H", strategy_contrib = NA))
, "`mat.PFG.soil$strategy_contrib` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H", strategy_contrib = ""))
, "`mat.PFG.soil$strategy_contrib` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
## TEST mat.PFG.soil$strategy_ag : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = 1, strategy_contrib = "ubiquist"))
, "`mat.PFG.soil$strategy_ag` must be either `poor_lover`, `indifferent` or `rich_lover`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = NA, strategy_contrib = "ubiquist"))
, "`mat.PFG.soil$strategy_ag` must be either `poor_lover`, `indifferent` or `rich_lover`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = "", strategy_contrib = "ubiquist"))
, "`mat.PFG.soil$strategy_ag` must be either `poor_lover`, `indifferent` or `rich_lover`"
, fixed = TRUE)
## TEST mat.PFG.soil$active_germ_low : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = c(NA, 1)
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_low` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$active_germ_low : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = -1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_low` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1.5
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_low` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.soil$active_germ_medium : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = c(NA, 1), active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_medium` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$active_germ_medium : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = -1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_medium` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1.5, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_medium` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.soil$active_germ_high : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = c(NA, 1)
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_high` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$active_germ_high : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = -1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_high` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1.5
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_high` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.soil$soil_contrib : numeric values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = NA, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = "a", soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = factor(1), soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = factor("a"), soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.soil$soil_contrib : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = c(NA, 1), soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_min : numeric values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = NA, soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = "a", soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = factor(1), soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = factor("a"), soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_min : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = c(NA, 1), soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_max : numeric values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = NA))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = "a"))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = factor(1)))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = factor("a")))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_max : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = c(NA, 1)))
, "`mat.PFG.soil$soil_tol_max` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_min : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 2, soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain values equal or inferior to `mat.PFG.soil$soil_contrib`"
, fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_max : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 0))
, "`mat.PFG.soil$soil_tol_max` must contain values equal or superior to `mat.PFG.soil$soil_contrib`"
, fixed = TRUE)
})
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with wrong data : mat.PFG.tol", {
## TEST mat.PFG.tol : data.frame
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = NA)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = "")
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = 1)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = matrix(1))
, "`mat.PFG.tol` must be a data.frame")
## TEST mat.PFG.tol : correct number of rows and columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame())
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (PFG, lifeStage, resources, tolerance, (strategy_tol)"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(1))
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (PFG, lifeStage, resources, tolerance, (strategy_tol)"
, fixed = TRUE)
## TEST mat.PFG.tol : correct names of columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(1,2))
, "Column names of `mat.PFG.tol` must be `PFG`, `lifeStage`, `resources`, `tolerance` and `(strategy_tol)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(1,2,3,4))
, "Column names of `mat.PFG.tol` must be `PFG`, `lifeStage`, `resources`, `tolerance` and `(strategy_tol)`"
, fixed = TRUE)
## TEST mat.PFG.tol$PFG : length > 0
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = NA, lifeStage = 1
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$PFG` must contain a character value of length > 0"
, fixed = TRUE)
## TEST mat.PFG.tol$lifeStage : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = 1
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$lifeStage` must be either `Germinant`, `Immature` or `Mature`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = NA
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$lifeStage` must be either `Germinant`, `Immature` or `Mature`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = ""
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$lifeStage` must be either `Germinant`, `Immature` or `Mature`"
, fixed = TRUE)
## TEST mat.PFG.tol$resources : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$resources` must be either `Low`, `Medium` or `High`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = NA, tolerance = 1))
, "`mat.PFG.tol$resources` must be either `Low`, `Medium` or `High`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "", tolerance = 1))
, "`mat.PFG.tol$resources` must be either `Low`, `Medium` or `High`"
, fixed = TRUE)
## TEST mat.PFG.tol$tolerance : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = c(NA, 1)))
, "`mat.PFG.tol$tolerance` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$tolerance : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = -1))
, "`mat.PFG.tol$tolerance` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = 1.5))
, "`mat.PFG.tol$tolerance` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$strategy_tol : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = 1))
, "`mat.PFG.tol$strategy_tol` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = NA))
, "`mat.PFG.tol$strategy_tol` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = factor("a")))
, "`mat.PFG.tol$strategy_tol` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 1, CONTRIB scenario 1, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
expect_warning(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL
, opt.folder.name = "")
, "already exists. It will be replaced.")
expect_warning(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL
, opt.folder.name = NA)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL
, opt.folder.name = "TEST")
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/TEST/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 2, CONTRIB scenario 1, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, active_germ_low = 1
, active_germ_medium = 5
, active_germ_high = 9
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 1, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "poor_lover"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 2, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "poor_lover"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 2, SOIL_TOL scenario 2", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "poor_lover"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = 3))
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 2, SOIL_TOL scenario 3", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = "poor_lover"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = "ubiquist"))
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.
R Package Documentation
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library(RFate)
context("PRE_FATE.params_PFGsoil() function")
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with missing data", {
expect_error(PRE_FATE.params_PFGsoil()
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(NA)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(NULL)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with wrong data : name.simulation", {
expect_error(PRE_FATE.params_PFGsoil(1)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil("a")
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(factor(1))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
expect_error(PRE_FATE.params_PFGsoil(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/SOIL/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with wrong data : mat.PFG.soil", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST mat.PFG.soil : data.frame
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation")
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = NA)
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = NULL)
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = "")
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = 1)
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = factor(1))
, "`mat.PFG.soil` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = matrix(1))
, "`mat.PFG.soil` must be a data.frame")
## TEST mat.PFG.soil : correct number of rows and columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame())
, "`mat.PFG.soil` does not have the appropriate number of rows (>0) or columns (PFG, type, (active_germ_low), (active_germ_medium), (active_germ_high), (strategy_ag), soil_contrib, soil_tol_min, soil_tol_max, (strategy_contrib))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1))
, "`mat.PFG.soil` does not have the appropriate number of rows (>0) or columns (PFG, type, (active_germ_low), (active_germ_medium), (active_germ_high), (strategy_ag), soil_contrib, soil_tol_min, soil_tol_max, (strategy_contrib))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1,2,3,4,5,6,7,8))
, "`mat.PFG.soil` does not have the appropriate number of rows (>0) or columns (PFG, type, (active_germ_low), (active_germ_medium), (active_germ_high), (strategy_ag), soil_contrib, soil_tol_min, soil_tol_max, (strategy_contrib))"
, fixed = TRUE)
## TEST mat.PFG.soil : correct names of columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1,2,3))
, "Column names of `mat.PFG.soil` must be `PFG`, `type`, `(active_germ_low)`, `(active_germ_medium)`, `(active_germ_high)`, `(strategy_ag)`, `soil_contrib`, `soil_tol_min`, `soil_tol_max` and `(strategy_contrib)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation", mat.PFG.soil = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.soil` must be `PFG`, `type`, `(active_germ_low)`, `(active_germ_medium)`, `(active_germ_high)`, `(strategy_ag)`, `soil_contrib`, `soil_tol_min`, `soil_tol_max` and `(strategy_contrib)`"
, fixed = TRUE)
## TEST mat.PFG.soil$PFG : different values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = rep("H", 2), strategy_contrib = "indifferent"))
, "`mat.PFG.soil$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = NA, type = "H", strategy_contrib = "indifferent"))
, "`mat.PFG.soil$PFG` must contain different values", fixed = TRUE)
## TEST mat.PFG.soil$PFG : length > 0
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = "", type = "H", strategy_contrib = "indifferent"))
, "`mat.PFG.soil$PFG` must contain a character value of length > 0"
, fixed = TRUE)
## TEST mat.PFG.soil$type : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = NA, strategy_contrib = "indifferent"))
, "`mat.PFG.soil$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = 2, strategy_contrib = "indifferent"))
, "`mat.PFG.soil$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "", strategy_contrib = "indifferent"))
, "`mat.PFG.soil$type` must be either `H`, `C` or `P`", fixed = TRUE)
## TEST mat.PFG.soil$strategy_contrib : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H", strategy_contrib = 1))
, "`mat.PFG.soil$strategy_contrib` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H", strategy_contrib = NA))
, "`mat.PFG.soil$strategy_contrib` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H", strategy_contrib = ""))
, "`mat.PFG.soil$strategy_contrib` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
## TEST mat.PFG.soil$strategy_ag : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = 1, strategy_contrib = "ubiquist"))
, "`mat.PFG.soil$strategy_ag` must be either `poor_lover`, `indifferent` or `rich_lover`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = NA, strategy_contrib = "ubiquist"))
, "`mat.PFG.soil$strategy_ag` must be either `poor_lover`, `indifferent` or `rich_lover`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = "", strategy_contrib = "ubiquist"))
, "`mat.PFG.soil$strategy_ag` must be either `poor_lover`, `indifferent` or `rich_lover`"
, fixed = TRUE)
## TEST mat.PFG.soil$active_germ_low : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = c(NA, 1)
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_low` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$active_germ_low : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = -1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_low` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1.5
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_low` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.soil$active_germ_medium : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = c(NA, 1), active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_medium` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$active_germ_medium : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = -1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_medium` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1.5, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_medium` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.soil$active_germ_high : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = c(NA, 1)
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_high` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$active_germ_high : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = -1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_high` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1.5
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$active_germ_high` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.soil$soil_contrib : numeric values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = NA, soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = "a", soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = factor(1), soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = factor("a"), soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.soil$soil_contrib : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = c(NA, 1), soil_tol_min = 1, soil_tol_max = 1))
, "`mat.PFG.soil$soil_contrib` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_min : numeric values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = NA, soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = "a", soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = factor(1), soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = factor("a"), soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_min : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = c(NA, 1), soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_max : numeric values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = NA))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = "a"))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = factor(1)))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = factor("a")))
, "`mat.PFG.soil$soil_tol_max` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_max : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = c(1,2), active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = c(NA, 1)))
, "`mat.PFG.soil$soil_tol_max` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_min : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 2, soil_tol_max = 1))
, "`mat.PFG.soil$soil_tol_min` must contain values equal or inferior to `mat.PFG.soil$soil_contrib`"
, fixed = TRUE)
## TEST mat.PFG.soil$soil_tol_max : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, active_germ_low = 1
, active_germ_medium = 1, active_germ_high = 1
, soil_contrib = 1, soil_tol_min = 1, soil_tol_max = 0))
, "`mat.PFG.soil$soil_tol_max` must contain values equal or superior to `mat.PFG.soil$soil_contrib`"
, fixed = TRUE)
})
## INPUTS
test_that("PRE_FATE.params_PFGsoil gives error with wrong data : mat.PFG.tol", {
## TEST mat.PFG.tol : data.frame
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = NA)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = "")
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = 1)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = matrix(1))
, "`mat.PFG.tol` must be a data.frame")
## TEST mat.PFG.tol : correct number of rows and columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame())
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (PFG, lifeStage, resources, tolerance, (strategy_tol)"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(1))
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (PFG, lifeStage, resources, tolerance, (strategy_tol)"
, fixed = TRUE)
## TEST mat.PFG.tol : correct names of columns
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(1,2))
, "Column names of `mat.PFG.tol` must be `PFG`, `lifeStage`, `resources`, `tolerance` and `(strategy_tol)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(1,2,3,4))
, "Column names of `mat.PFG.tol` must be `PFG`, `lifeStage`, `resources`, `tolerance` and `(strategy_tol)`"
, fixed = TRUE)
## TEST mat.PFG.tol$PFG : length > 0
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = NA, lifeStage = 1
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$PFG` must contain a character value of length > 0"
, fixed = TRUE)
## TEST mat.PFG.tol$lifeStage : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = 1
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$lifeStage` must be either `Germinant`, `Immature` or `Mature`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = NA
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$lifeStage` must be either `Germinant`, `Immature` or `Mature`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = ""
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$lifeStage` must be either `Germinant`, `Immature` or `Mature`"
, fixed = TRUE)
## TEST mat.PFG.tol$resources : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = 1, tolerance = 1))
, "`mat.PFG.tol$resources` must be either `Low`, `Medium` or `High`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = NA, tolerance = 1))
, "`mat.PFG.tol$resources` must be either `Low`, `Medium` or `High`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "", tolerance = 1))
, "`mat.PFG.tol$resources` must be either `Low`, `Medium` or `High`"
, fixed = TRUE)
## TEST mat.PFG.tol$tolerance : no NA values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = c(NA, 1)))
, "`mat.PFG.tol$tolerance` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$tolerance : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = -1))
, "`mat.PFG.tol$tolerance` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = 1.5))
, "`mat.PFG.tol$tolerance` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$strategy_tol : correct values
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = 1))
, "`mat.PFG.tol$strategy_tol` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = NA))
, "`mat.PFG.tol$strategy_tol` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "indifferent"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = factor("a")))
, "`mat.PFG.tol$strategy_tol` must be either `full_light`, `pioneer`, `ubiquist`, `semi_shade` or `undergrowth`"
, fixed = TRUE)
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 1, CONTRIB scenario 1, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
expect_warning(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL
, opt.folder.name = "")
, "already exists. It will be replaced.")
expect_warning(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL
, opt.folder.name = NA)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, type = "H"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL
, opt.folder.name = "TEST")
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/TEST/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 2, CONTRIB scenario 1, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, active_germ_low = 1
, active_germ_medium = 5
, active_germ_high = 9
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 1, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "poor_lover"
, soil_contrib = 2
, soil_tol_min = 1
, soil_tol_max = 3)
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 2, SOIL_TOL scenario 1", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "poor_lover"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = NULL)
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 2, SOIL_TOL scenario 2", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1
, strategy_ag = "poor_lover"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, lifeStage = "Germinant"
, resources = "Low", tolerance = 3))
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
## OUTPUTS
test_that("PRE_FATE.params_PFGsoil gives correct output : ACTIVE_GERM scenario 3, CONTRIB scenario 2, SOIL_TOL scenario 3", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
, mat.PFG.soil = data.frame(PFG = 1, strategy_ag = "poor_lover"
, strategy_contrib = "ubiquist")
, mat.PFG.tol = data.frame(PFG = 1, strategy_tol = "ubiquist"))
, "The parameter file FATE_simulation/DATA/PFGS/SOIL/SOIL_1.txt has been successfully created !")
})
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