Create binary maps for each Plant Functional Group for one (or several) specific year of a FATE simulation

Source: R/POST_FATE.binaryMaps.R

This script is designed to produce raster maps of PFG presence / absence for one (or several) specific FATE simulation year.

POST_FATE.binaryMaps(
  name.simulation,
  file.simulParam = NULL,
  years,
  method,
  method1.threshold = 0.05,
  method2.cutoff = NULL,
  opt.no_CPU = 1
)

Arguments

name.simulation

a string corresponding to the main directory or simulation name of the FATE simulation

file.simulParam

default NULL.
A string corresponding to the name of a parameter file that will be contained into the PARAM_SIMUL folder of the FATE simulation

years

an integer, or a vector of integer, corresponding to the simulation year(s) that will be used to extract PFG abundance maps

method

an integer to choose the transformation method :
1 (relative abundance) or 2 (optimizing TSS) (see Details)

method1.threshold

default 0.05.
If method = 1, minimum relative abundance required for each PFG to be considered as present in the concerned pixel

method2.cutoff

default NULL.
If method = 2, a data.frame with 3 columns : year, PFG, cutoff
(see Details)

opt.no_CPU

(optional) default 1.
The number of resources that can be used to parallelize the unzip/zip of raster files

Value

Two folders are created :

BIN_perPFG
_allStrata

containing presence / absence raster maps for each PFG across all strata

BIN_perPFG
_perStrata

containing presence / absence raster maps for each PFG for each stratum
(if pixel abundances per PFG per stratum were saved (see PRE_FATE.params_globalParameters))

Details

This function allows to obtain, for a specific FATE simulation and a specific parameter file within this simulation, raster maps of PFG presence / absence.

For each PFG and each selected simulation year, raster maps are retrieved from the results folder ABUND_REL_perPFG_allStrata and lead to the production of as many maps as those found :

1 fixed threshold

relative abundance maps are transformed into binary maps according to the threshold given by method1.threshold : $$abund\_rel_{\text{ PFG}_i} > \text{method1.threshold} \;\; \Leftrightarrow \;\; 1$$

2 optimizing TSS

relative abundance maps are transformed into binary maps according to the cutoff found with the POST_FATE.graphic_validationStatistics function : $$abund\_rel_{\text{ PFG}_i} > \text{method2.cutoff}_{\text{ PFG}_i} \;\; \Leftrightarrow \;\; 1$$

It requires that the POST_FATE.relativeAbund function has been run and that the folder ABUND_REL_perPFG_allStrata exists.
If method = 2, it requires that the POST_FATE.graphic_validationStatistics function has been run.

If pixel abundances per PFG per stratum were saved (see PRE_FATE.params_globalParameters), binary maps per stratum are obtained by multiplying raster maps from ABUND_perPFG_perStrata folder by corresponding raster maps from BIN_perPFG_allStrata folder.

These binary raster files can then be used by other functions :

Author

Maya Guéguen