POST_FATE.binaryMaps: Create binary maps for each Plant Functional Group for one...

In leca-dev/RFate: FATE with R

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

Description

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

Usage

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

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 :

• to produce graphics of PFG modelled presence vs PFG Habitat Suitability maps
  (see POST_FATE.graphic_mapPFGvsHS)

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))

Author(s)

Maya Guéguen

See Also

POST_FATE.relativeAbund, POST_FATE.graphic_validationStatistics .getCutoff, POST_FATE.graphic_mapPFGvsHS

leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.