tests/testthat/test-PRE_FATE.params_PFGdisturbance.R
In MayaGueguen/RFate: Vegetation modelling with the FATE model
library(RFate)
context("PRE_FATE.params_PFGdisturbance() function")
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with missing data", {
expect_error(PRE_FATE.params_PFGdisturbance()
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(NA)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(NULL)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with wrong data : name.simulation", {
expect_error(PRE_FATE.params_PFGdisturbance(1)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance("a")
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(factor(1))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with wrong data : mat.PFG.dist", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST mat.PFG.tol : data.frame
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation")
, "`mat.PFG.tol` must be a data.frame")
## TEST mat.PFG.dist : data.frame
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = NA)
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = "")
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = 1)
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = factor(1))
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = matrix(1))
, "`mat.PFG.dist` must be a data.frame")
## TEST mat.PFG.dist : correct number of rows and columns
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame())
, "`mat.PFG.dist` does not have the appropriate number of rows (>0) or columns (PFG, type, maturity, longevity, age_above_150cm)"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(1))
, "`mat.PFG.dist` does not have the appropriate number of rows (>0) or columns (PFG, type, maturity, longevity, age_above_150cm)"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(1,2,3,4))
, "`mat.PFG.dist` does not have the appropriate number of rows (>0) or columns (PFG, type, maturity, longevity, age_above_150cm)"
, fixed = TRUE)
## TEST mat.PFG.dist : correct names of columns
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.dist` must be `PFG`, `type`, `maturity`, `longevity` and `age_above_150cm`"
, fixed = TRUE)
## TEST mat.PFG.dist$PFG : different values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = c(2,2), maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = NA, type = 2, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,NA), type = c(2,2), maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain different values", fixed = TRUE)
## TEST mat.PFG.dist$PFG : length > 0
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = "", type = 1, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.dist$type : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = NA, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = 2, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "", maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = c("H",NA), maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
## TEST mat.PFG.dist$maturity : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = NA
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = "a"
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = factor(1)
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.dist$maturity : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = c(3,NA)
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.dist$maturity : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = 2
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain values equal or inferior to `mat.PFG.dist$longevity`"
, fixed = TRUE)
## TEST mat.PFG.dist$longevity : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = NA, age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = "a", age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = factor(1), age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.dist$longevity : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = 1
, longevity = c(3,NA), age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.dist$age_above_150cm : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = 1, age_above_150cm = NA))
, "`mat.PFG.dist$age_above_150cm` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = 1, age_above_150cm = "a"))
, "`mat.PFG.dist$age_above_150cm` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = 1, age_above_150cm = factor(1)))
, "`mat.PFG.dist$age_above_150cm` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.dist$age_above_150cm : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = 1
, longevity = 1, age_above_150cm = c(3,NA)))
, "`mat.PFG.dist$age_above_150cm` must not contain NA values", fixed = TRUE)
})
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with wrong data : mat.PFG.tol", {
## TEST mat.PFG.tol : data.frame
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = NA)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = "")
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = 1)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, 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_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame())
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (nameDist, PFG, responseStage, (breakAge), (resproutAge), killedIndiv, resproutIndiv, (strategy_tol))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1))
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (nameDist, PFG, responseStage, (breakAge), (resproutAge), killedIndiv, resproutIndiv, (strategy_tol))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1,2,3,4,5,6,7,8))
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (nameDist, PFG, responseStage, (breakAge), (resproutAge), killedIndiv, resproutIndiv, (strategy_tol))"
, fixed = TRUE)
## TEST mat.PFG.tol : correct names of columns
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1,2,3))
, "Column names of `mat.PFG.tol` must be `nameDist`, `PFG`, `responseStage`, `(breakAge)`, `(resproutAge)`, `killedIndiv`, `resproutIndiv` and `(strategy_tol)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.tol` must be `nameDist`, `PFG`, `responseStage`, `(breakAge)`, `(resproutAge)`, `killedIndiv`, `resproutIndiv` and `(strategy_tol)`"
, fixed = TRUE)
## TEST mat.PFG.tol$nameDist : length > 0
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = "", PFG = 1, strategy_tol = 1))
, "`mat.PFG.tol$nameDist` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.tol$PFG : length > 0
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "", strategy_tol = 1))
, "`mat.PFG.tol$PFG` must contain a character value of length > 0", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = NA, strategy_tol = 1))
, "`mat.PFG.tol$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.tol$PFG : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = "B", type = "H", maturity = 1
, longevity = 1 , age_above_150cm = 1)
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", strategy_tol = 1))
, "`mat.PFG.tol$PFG` must be either `H`, `C`, `P` or `B`", fixed = TRUE)
## TEST mat.PFG.tol$breakAge : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = NA, resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = "a", resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = factor(1), resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.tol$breakAge : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = c(1,NA), resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$resproutAge : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = NA
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = "a"
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = factor(1)
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.tol$resproutAge : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = c(1,NA)
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$responseStage : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = c(1,NA)
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$responseStage` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$responseStage : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1.5
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$responseStage` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$killedIndiv : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = c(1,NA), resproutIndiv = 1))
, "`mat.PFG.tol$killedIndiv` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$killedIndiv : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = -1, resproutIndiv = 1))
, "`mat.PFG.tol$killedIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1.5, resproutIndiv = 1))
, "`mat.PFG.tol$killedIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$resproutIndiv : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1, resproutIndiv = c(1,NA)))
, "`mat.PFG.tol$resproutIndiv` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$resproutIndiv : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1, resproutIndiv = -1))
, "`mat.PFG.tol$resproutIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1, resproutIndiv = 1.5))
, "`mat.PFG.tol$resproutIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$strategy_tol : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", strategy_tol = 1))
, "`mat.PFG.tol$strategy_tol` must be either `indifferent`, `mowing_herbs`, `mowing_trees`, `grazing_herbs_1`, `grazing_herbs_2`, `grazing_herbs_3`, `grazing_trees_1`, `grazing_trees_2` or `grazing_trees_3`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", strategy_tol = NA))
, "`mat.PFG.tol$strategy_tol` must be either `indifferent`, `mowing_herbs`, `mowing_trees`, `grazing_herbs_1`, `grazing_herbs_2`, `grazing_herbs_3`, `grazing_trees_1`, `grazing_trees_2` or `grazing_trees_3`"
, fixed = TRUE)
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 0, RESPR_AGES scenario 0, FATES scenario 2"), {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_1.txt has been successfully created !")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "Missing data! The `BREAK_AGE` parameter has not been set. Please check.")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "Missing data! The `RESPR_AGE` parameter has not been set. Please check.")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent")
, opt.folder.name = "")
, "already exists. It will be replaced.")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent")
, opt.folder.name = NA)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent")
, opt.folder.name = "TEST")
, "The parameter file FATE_simulation/DATA/PFGS/DIST/TEST/DIST_1.txt has been successfully created !")
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 1, RESPR_AGES scenario 1, FATES scenario 2")
, {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1
, type = "H"
, maturity = 4
, longevity = 5
, age_above_150cm = 10000)
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_1.txt has been successfully created !")
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 2, RESPR_AGES scenario 2, FATES scenario 2")
, {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"
, responseStage = c(1, 2)
, breakAge = 2
, resproutAge = 1))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_1.txt has been successfully created !")
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 2, RESPR_AGES scenario 2, FATES scenario 1")
, {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, responseStage = c(1, 2)
, breakAge = 2
, resproutAge = 1
, killedIndiv = 5
, resproutIndiv = 4))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_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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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(RFate)
context("PRE_FATE.params_PFGdisturbance() function")
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with missing data", {
expect_error(PRE_FATE.params_PFGdisturbance()
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(NA)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(NULL)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with wrong data : name.simulation", {
expect_error(PRE_FATE.params_PFGdisturbance(1)
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance("a")
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(factor(1))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
expect_error(PRE_FATE.params_PFGdisturbance(matrix(seq(2), ncol=2))
, "`name.simulation` does not exist or does not contain a DATA/PFGS/DIST/ folder")
})
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with wrong data : mat.PFG.dist", {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
## TEST mat.PFG.tol : data.frame
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation")
, "`mat.PFG.tol` must be a data.frame")
## TEST mat.PFG.dist : data.frame
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = NA)
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = "")
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = 1)
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = factor(1))
, "`mat.PFG.dist` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation", mat.PFG.dist = matrix(1))
, "`mat.PFG.dist` must be a data.frame")
## TEST mat.PFG.dist : correct number of rows and columns
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame())
, "`mat.PFG.dist` does not have the appropriate number of rows (>0) or columns (PFG, type, maturity, longevity, age_above_150cm)"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(1))
, "`mat.PFG.dist` does not have the appropriate number of rows (>0) or columns (PFG, type, maturity, longevity, age_above_150cm)"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(1,2,3,4))
, "`mat.PFG.dist` does not have the appropriate number of rows (>0) or columns (PFG, type, maturity, longevity, age_above_150cm)"
, fixed = TRUE)
## TEST mat.PFG.dist : correct names of columns
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.dist` must be `PFG`, `type`, `maturity`, `longevity` and `age_above_150cm`"
, fixed = TRUE)
## TEST mat.PFG.dist$PFG : different values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = c(2,2), maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = NA, type = 2, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain different values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,NA), type = c(2,2), maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain different values", fixed = TRUE)
## TEST mat.PFG.dist$PFG : length > 0
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = "", type = 1, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.dist$type : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = NA, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = 2, maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "", maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = c("H",NA), maturity = 1
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$type` must be either `H`, `C` or `P`", fixed = TRUE)
## TEST mat.PFG.dist$maturity : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = NA
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = "a"
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = factor(1)
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.dist$maturity : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = c(3,NA)
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.dist$maturity : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = 2
, longevity = 1, age_above_150cm = 1))
, "`mat.PFG.dist$maturity` must contain values equal or inferior to `mat.PFG.dist$longevity`"
, fixed = TRUE)
## TEST mat.PFG.dist$longevity : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = NA, age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = "a", age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = factor(1), age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.dist$longevity : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = 1
, longevity = c(3,NA), age_above_150cm = 1))
, "`mat.PFG.dist$longevity` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.dist$age_above_150cm : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = 1, age_above_150cm = NA))
, "`mat.PFG.dist$age_above_150cm` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = 1, age_above_150cm = "a"))
, "`mat.PFG.dist$age_above_150cm` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1, type = "H", maturity = 1
, longevity = 1, age_above_150cm = factor(1)))
, "`mat.PFG.dist$age_above_150cm` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.dist$age_above_150cm : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = c(1,2), type = "H", maturity = 1
, longevity = 1, age_above_150cm = c(3,NA)))
, "`mat.PFG.dist$age_above_150cm` must not contain NA values", fixed = TRUE)
})
## INPUTS
test_that("PRE_FATE.params_PFGdisturbance gives error with wrong data : mat.PFG.tol", {
## TEST mat.PFG.tol : data.frame
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = NA)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = "")
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = 1)
, "`mat.PFG.tol` must be a data.frame")
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, 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_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame())
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (nameDist, PFG, responseStage, (breakAge), (resproutAge), killedIndiv, resproutIndiv, (strategy_tol))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1))
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (nameDist, PFG, responseStage, (breakAge), (resproutAge), killedIndiv, resproutIndiv, (strategy_tol))"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1,2,3,4,5,6,7,8))
, "`mat.PFG.tol` does not have the appropriate number of rows (>0) or columns (nameDist, PFG, responseStage, (breakAge), (resproutAge), killedIndiv, resproutIndiv, (strategy_tol))"
, fixed = TRUE)
## TEST mat.PFG.tol : correct names of columns
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1,2,3))
, "Column names of `mat.PFG.tol` must be `nameDist`, `PFG`, `responseStage`, `(breakAge)`, `(resproutAge)`, `killedIndiv`, `resproutIndiv` and `(strategy_tol)`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(1,2,3,4,5))
, "Column names of `mat.PFG.tol` must be `nameDist`, `PFG`, `responseStage`, `(breakAge)`, `(resproutAge)`, `killedIndiv`, `resproutIndiv` and `(strategy_tol)`"
, fixed = TRUE)
## TEST mat.PFG.tol$nameDist : length > 0
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = "", PFG = 1, strategy_tol = 1))
, "`mat.PFG.tol$nameDist` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.tol$PFG : length > 0
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "", strategy_tol = 1))
, "`mat.PFG.tol$PFG` must contain a character value of length > 0", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = NA, strategy_tol = 1))
, "`mat.PFG.tol$PFG` must contain a character value of length > 0", fixed = TRUE)
## TEST mat.PFG.tol$PFG : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = "B", type = "H", maturity = 1
, longevity = 1 , age_above_150cm = 1)
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", strategy_tol = 1))
, "`mat.PFG.tol$PFG` must be either `H`, `C`, `P` or `B`", fixed = TRUE)
## TEST mat.PFG.tol$breakAge : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = NA, resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = "a", resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = factor(1), resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.tol$breakAge : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = c(1,NA), resproutAge = 1
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$breakAge` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$resproutAge : numeric values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = NA
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = "a"
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must contain numeric values", fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = factor(1)
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must contain numeric values", fixed = TRUE)
## TEST mat.PFG.tol$resproutAge : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, breakAge = 1, resproutAge = c(1,NA)
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$resproutAge` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$responseStage : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = c(1,NA)
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$responseStage` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$responseStage : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1.5
, killedIndiv = 1, resproutIndiv = 1))
, "`mat.PFG.tol$responseStage` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$killedIndiv : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = c(1,NA), resproutIndiv = 1))
, "`mat.PFG.tol$killedIndiv` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$killedIndiv : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = -1, resproutIndiv = 1))
, "`mat.PFG.tol$killedIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1.5, resproutIndiv = 1))
, "`mat.PFG.tol$killedIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$resproutIndiv : no NA values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1, resproutIndiv = c(1,NA)))
, "`mat.PFG.tol$resproutIndiv` must not contain NA values", fixed = TRUE)
## TEST mat.PFG.tol$resproutIndiv : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1, resproutIndiv = -1))
, "`mat.PFG.tol$resproutIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", responseStage = 1
, killedIndiv = 1, resproutIndiv = 1.5))
, "`mat.PFG.tol$resproutIndiv` must be either `0`, `1`, `2`, `3`, `4`, `5`, `6`, `7`, `8`, `9` or `10`"
, fixed = TRUE)
## TEST mat.PFG.tol$strategy_tol : correct values
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", strategy_tol = 1))
, "`mat.PFG.tol$strategy_tol` must be either `indifferent`, `mowing_herbs`, `mowing_trees`, `grazing_herbs_1`, `grazing_herbs_2`, `grazing_herbs_3`, `grazing_trees_1`, `grazing_trees_2` or `grazing_trees_3`"
, fixed = TRUE)
expect_error(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.tol = data.frame(nameDist = 1, PFG = "A", strategy_tol = NA))
, "`mat.PFG.tol$strategy_tol` must be either `indifferent`, `mowing_herbs`, `mowing_trees`, `grazing_herbs_1`, `grazing_herbs_2`, `grazing_herbs_3`, `grazing_trees_1`, `grazing_trees_2` or `grazing_trees_3`"
, fixed = TRUE)
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 0, RESPR_AGES scenario 0, FATES scenario 2"), {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_1.txt has been successfully created !")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "Missing data! The `BREAK_AGE` parameter has not been set. Please check.")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "Missing data! The `RESPR_AGE` parameter has not been set. Please check.")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent")
, opt.folder.name = "")
, "already exists. It will be replaced.")
expect_warning(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent")
, opt.folder.name = NA)
, "As `opt.folder.name` does not contain character value, it will be ignored")
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent")
, opt.folder.name = "TEST")
, "The parameter file FATE_simulation/DATA/PFGS/DIST/TEST/DIST_1.txt has been successfully created !")
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 1, RESPR_AGES scenario 1, FATES scenario 2")
, {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = data.frame(PFG = 1
, type = "H"
, maturity = 4
, longevity = 5
, age_above_150cm = 10000)
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_1.txt has been successfully created !")
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 2, RESPR_AGES scenario 2, FATES scenario 2")
, {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, strategy_tol = "indifferent"
, responseStage = c(1, 2)
, breakAge = 2
, resproutAge = 1))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_1.txt has been successfully created !")
})
## OUTPUTS
test_that(paste0("PRE_FATE.params_PFGdisturbance gives correct output : "
, "BREAK_AGES scenario 2, RESPR_AGES scenario 2, FATES scenario 1")
, {
if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
PRE_FATE.skeletonDirectory()
expect_message(PRE_FATE.params_PFGdisturbance(name.simulation = "FATE_simulation"
, mat.PFG.dist = NULL
, mat.PFG.tol = data.frame(nameDist = "MOW"
, PFG = 1
, responseStage = c(1, 2)
, breakAge = 2
, resproutAge = 1
, killedIndiv = 5
, resproutIndiv = 4))
, "The parameter file FATE_simulation/DATA/PFGS/DIST/DIST_1.txt has been successfully created !")
})
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