POST_FATE.relativeAbund: Create relative abundance maps for each Plant Functional...
In MayaGueguen/RFate: Vegetation modelling with the FATE model

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/POST_FATE.relativeAbund.R

This script is designed to produce raster maps of PFG simulated relative abundances for one (or several) specific FATE simulation year.

POST_FATE.relativeAbund(
  name.simulation,
  file.simulParam = NULL,
  years,
  opt.no_CPU = 1
)

`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

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)

One result folder is created :

‘ABUND_REL_perPFG _allStrata’: containing relative abundance raster maps for each PFG across all strata

Maya Guéguen

POST_FATE.graphic_validationStatistics

## 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)
                                                        
                                                        
                                                        
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## Load example data