POST_FATE.relativeAbund: Create relative abundance maps for each Plant Functional...

In leca-dev/RFate: FATE with R

Create relative abundance 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 simulated relative abundances for one (or several) specific FATE simulation year.

Usage

POST_FATE.relativeAbund(
  name.simulation,
  file.simulParam = NULL,
  years,
  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
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 relative abundance.

For each PFG and each selected simulation year, raster maps are retrieved from the results folder ABUND_perPFG_allStrata and unzipped. Informations extracted lead to the production of the same number of raster before the maps are compressed again :

• for each selected simulation year(s), relative abundances for all strata combined are calculated :

  \frac{abund_{\text{ PFG}_i\text{, }\text{Stratum}_{all}}} {abund_{\text{ PFG}_{all}\text{, }\text{Stratum}_{all}}}

  
  
  

These raster files can then be used by other functions :

• to produce presence/absence maps and validation statistics, and associated graphics
  (see POST_FATE.graphic_validationStatistics)

Value

One result folder is created :

‘ABUND_REL_perPFG
_allStrata’

containing relative abundance raster maps for each PFG across all strata

Author(s)

Maya Guéguen

See Also

POST_FATE.graphic_validationStatistics

Examples

## Not run:                       
POST_FATE.relativeAbund(name.simulation = "FATE_simulation"
                        , file.simulParam = "Simul_parameters_V1.txt"
                        , years = 850
                        , opt.no_CPU = 1)
                                    
POST_FATE.relativeAbund(name.simulation = "FATE_simulation"
                        , file.simulParam = "Simul_parameters_V1.txt"
                        , years = c(850, 950)
                        , opt.no_CPU = 1)

## End(Not run)
                                                        
                                    

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