tests/testthat/test_fordyn.R

In medfate: Mediterranean Forest Simulation

library(medfate)

data(exampleforest)
data(SpParamsMED)


forest_herbs <- exampleforest
forest_herbs$herbData <- forest_herbs$shrubData

data(examplemeteo)
#Prepare a two-year meteorological data with half precipitation during 
#the second year
meteo2001 <- examplemeteo
meteo2002 <- examplemeteo
meteo2002$Precipitation <- meteo2002$Precipitation/2
meteo2002$dates <- seq(as.Date("2002-01-01"), 
                       as.Date("2002-12-31"), by="day")
meteo_01_02 <- rbind(meteo2001, meteo2002)
meteo_01_02_B <- meteo_01_02
meteo_01_02_B$dates <- as.Date(meteo_01_02_B$dates)
row.names(meteo_01_02_B) <- NULL

#Load example plot plant data
data(exampleforest)

#Default species parameterization
data(SpParamsMED)

#Initialize control parameters
control <- defaultControl("Granier")
control$verbose <- FALSE

#Initialize soil with default soil params (4 layers)
examplesoil <- defaultSoilParams(4)

test_that("fordyn can be run and continued in example, herbs and empty forests",{
  fd <- fordyn(exampleforest, examplesoil, 
               SpParamsMED, meteo_01_02, control,
               latitude = 41.82592, elevation = 100)
  expect_s3_class(fd, "fordyn")
  expect_s3_class(fordyn(fd, examplesoil, 
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100), "fordyn")
  expect_s3_class(fordyn(forest_herbs, examplesoil,
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100), "fordyn")
  expect_s3_class(fordyn(emptyforest(), examplesoil,
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100), "fordyn")
})

test_that("fordyn can be run using species codes",{
  f <- exampleforest
  f$treeData$Species <- c(SpParamsMED$SpIndex[SpParamsMED$Name=="Pinus halepensis"], SpParamsMED$SpIndex[SpParamsMED$Name=="Quercus ilex"])
  f$shrubData$Species <- SpParamsMED$SpIndex[SpParamsMED$Name=="Quercus coccifera"]
  expect_s3_class(fordyn(f, examplesoil,
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100), "fordyn")
})
test_that("fordyn can be run using single soilDomains",{
  control_single <- control
  control_single$soilDomains <- "single"
  expect_s3_class(fordyn(exampleforest, examplesoil,
                         SpParamsMED, meteo_01_02, control_single,
                         latitude = 41.82592, elevation = 100), "fordyn")
})

test_that("fordyn can be run using dual soilDomains",{
  control_dual <- control
  control_dual$soilDomains <- "dual"
  expect_s3_class(fordyn(exampleforest, examplesoil,
                         SpParamsMED, meteo_01_02, control_dual,
                         latitude = 41.82592, elevation = 100), "fordyn")
})

test_that("fordyn can be run using partial rhizosphere overlap",{
  control_partial_overlap <- control
  control_partial_overlap$rhizosphereOverlap <- "partial"
  expect_s3_class(fordyn(exampleforest, examplesoil,
                         SpParamsMED, meteo_01_02, control_partial_overlap,
                         latitude = 41.82592, elevation = 100), "fordyn")
})

test_that("fordyn can be run using different recruitment modes",{
  control_recr <- control
  for(mode in c("annual/stochastic", "annual/deterministic", "daily/stochastic", "daily/deterministic")) {
    control_recr$recruitmentMode <- mode
    expect_s3_class(fordyn(exampleforest, examplesoil,
                           SpParamsMED, meteo_01_02, control_recr,
                           latitude = 41.82592, elevation = 100), "fordyn")
  }
})

test_that("fordyn can be run in example, herbs and empty forests using management",{
  expect_s3_class(fordyn(exampleforest, examplesoil,
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100,
                         management_function = defaultManagementFunction,
                         management_args = defaultManagementArguments()), "fordyn")
  expect_s3_class(fordyn(forest_herbs, examplesoil,
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100,
                         management_function = defaultManagementFunction,
                         management_args = defaultManagementArguments()), "fordyn")
  expect_s3_class(fordyn(emptyforest(), examplesoil,
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100,
                         management_function = defaultManagementFunction,
                         management_args = defaultManagementArguments()), "fordyn")
})
test_that("fordyn can be run with fire hazard results",{
  expect_s3_class(fordyn(exampleforest, examplesoil,
                         SpParamsMED, meteo_01_02, control,
                         latitude = 41.82592, elevation = 100), "fordyn")
})
test_that("fordyn can be run using dates as columns",{
  control_fh <- control
  control_fh$fireHazardResults <- TRUE
  expect_s3_class(fordyn(exampleforest, examplesoil,
                         SpParamsMED, meteo_01_02_B, control_fh,
                         latitude = 41.82592, elevation = 100), "fordyn")
})