POST_FATE.graphic_mapPFGvsHS: Create maps of both habitat suitability and simulated...

In MayaGueguen/RFate: Vegetation modelling with the FATE model

Description

This script is designed to produce raster maps of PFG habitat suitability and simulated occurrences for one (or several) specific FATE simulation year.

Usage

POST_FATE.graphic_mapPFGvsHS(
  name.simulation,
  file.simulParam = NULL,
  years,
  opt.stratum = "all"
)

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 binary maps
opt.stratum	(optional) default all. The stratum number from which to extract PFG binary maps

Details

This function allows to obtain, for a specific FATE simulation and a specific parameter file within this simulation, one preanalytical graphic.

For each PFG and each selected simulation year, raster maps are retrieved from the results folder BIN_perPFG_allStrata (unless the opt.stratum is used, then it will be from the folder BIN_perPFG_perStrata) and unzipped. Informations extracted lead to the production of one graphic before the maps are compressed again :

• the comparison between each PFG habitat suitability map and its simulated map of presence
  
  

It requires that the POST_FATE.relativeAbund and the POST_FATE.binaryMaps function have been run and that the folders BIN_perPFG_allStrata and BIN_perPFG_perStrata exist.

Value

A list containing one or several (one for each simulation year) list of ggplot2 objects, representing for each plant functional group its map of modelled presence / absence vs its habitat suitability map.

One POST_FATE_[...].pdf file is created :

‘GRAPHIC_B
map_PFGvsHS’

to visualize the PFG presence within the studied area (probability and simulated occurrence)

Author(s)

Maya Guéguen

See Also

POST_FATE.relativeAbund, POST_FATE.binaryMaps

Examples

## Not run:                       
POST_FATE.graphic_mapPFGvsHS(name.simulation = "FATE_simulation"
                             , file.simulParam = "Simul_parameters_V1.txt"
                             , years = 850)
                                    
POST_FATE.graphic_mapPFGvsHS(name.simulation = "FATE_simulation"
                             , file.simulParam = "Simul_parameters_V1.txt"
                             , years = c(850, 950))
                                    
POST_FATE.graphic_mapPFGvsHS(name.simulation = "FATE_simulation"
                             , file.simulParam = "Simul_parameters_V1.txt"
                             , years = 850
                             , opt.stratum = 2)

## End(Not run)
                                    
                                    

MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.