POST_FATE.graphic_mapPFG: Create a map related to plant functional group results...
In MayaGueguen/RFate: Vegetation modelling with the FATE model

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

View source: R/POST_FATE.graphic_mapPFG.R

This script is designed to produce one (or several) raster map related to plant functional group results (richness, relative cover, light or soil CWM) for one (or several) specific FATE simulation year.

POST_FATE.graphic_mapPFG(
  name.simulation,
  file.simulParam = NULL,
  years,
  opt.stratum_min = 1,
  opt.stratum_max = 10,
  opt.doBinary = TRUE,
  opt.no_CPU = 1,
  opt.doPlot = TRUE
)

`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 and binary maps
`opt.stratum_min`	(optional) default `1`. An `integer` corresponding to the lowest stratum from which PFG abundances will be summed up
`opt.stratum_max`	(optional) default `10`. An `integer` corresponding to the highest stratum from which PFG abundances will be summed up
`opt.doBinary`	(optional) default `TRUE`. If `TRUE`, abundance maps (absolute or relative) are systematically multiplied by binary maps (see `Details`)
`opt.no_CPU`	(optional) default `1`. The number of resources that can be used to parallelize the `unzip/zip` of raster files
`opt.doPlot`	(optional) default `TRUE`. If `TRUE`, plot(s) will be processed, otherwise only the calculation and reorganization of outputs will occur, be saved and returned

This function allows to obtain, for a specific FATE simulation and a specific parameter file within this simulation, up to six raster maps and preanalytical graphics.

For each PFG and each selected simulation year, raster maps are retrieved from the results folders ABUND_perPFG_perStrata and BIN_perPFG_perStrata and unzipped. Informations extracted lead to the production of up to six graphics before the maps are compressed again :

map of PFG richness within each pixel, representing the sum of binary maps
Richness is calculated with the Leinster & Cobbold 2012 Ecology framework which allows to give more or less importance to the commun species through the q parameter :

q = 0
species richness

q = 1
Shannon entropy

q = 2
Simpson concentration
map of PFG relative cover, representing the sum of relative abundance maps of all PFG
(potentially above a height threshold defined by opt.stratum_min)
if light was activated (see PRE_FATE.params_globalParameters), community weighted mean of PFG light preferences (extracted from LIGHT parameter within LIGHT files, see PRE_FATE.params_PFGlight)
if soil was activated (see PRE_FATE.params_globalParameters), community weighted mean of PFG soil preferences (extracted from SOIL_CONTRIB parameter within SOIL files, see PRE_FATE.params_PFGsoil)

It requires that the POST_FATE.relativeAbund, (POST_FATE.graphic_validationStatistics) and POST_FATE.binaryMaps functions have been run and that the folders BIN_perPFG_allStrata and BIN_perPFG_perStrata exist.

If opt.doBinary = TRUE, abundance maps (absolute or relative) are systematically multiplied by binary maps extracted from BIN_perPFG_allStrata and BIN_perPFG_perStrata folders and produced by POST_FATE.binaryMaps function. This way, produced raster maps reflect the validated/refined predictions. opt.doBinary can be set to FALSE to reflect pure simulation results.

A list containing one or several (one for each simulation year) list of raster and ggplot2 objects :

tab

cover: raster of relative coverage
DIV.0: raster of species richness
DIV.1: raster of Shannon entropy
DIV.2: raster of Simpson concentration
CWM.light: raster of light community weighted mean
CWM.soil: raster of soil community weighted mean

plot

cover: ggplot2 object, representing cover raster
richness: ggplot2 object, representing DIV.0 raster
CWM.light: ggplot2 object, representing CWM.light raster
CWM.soil: ggplot2 object, representing CWM.soil raster

‘POST_FATE_GRAPHIC_C_map_PFG_[...].pdf’ file is created containing up to four graphics :

‘map_PFGcover’: to visualize the PFG cover within the studied area
‘map_PFGrichness’: to visualize the PFG richness within the studied area
‘PFGlight’: to visualize the light CWM within the studied area
‘PFGsoil’: to visualize the soil CWM within the studied area

Three ‘PFGrichness_YEAR_[...]_STRATA_all_q[...].tif’ files are created into the simulation results folder :

‘q0’: PFG richness
‘q1’: PFG Shannon entropy
‘q2’: PFG Simpson concentration

Raster files are also created for cover, and light and soil CWM if those modules were selected (see PRE_FATE.params_globalParameters).

Maya Guéguen

POST_FATE.relativeAbund, POST_FATE.graphic_validationStatistics, POST_FATE.binaryMaps

## Not run:                       
POST_FATE.graphic_mapPFG(name.simulation = "FATE_simulation"
                         , file.simulParam = "Simul_parameters_V1.txt"
                         , years = 850
                         , opt.stratum_min = 3
                         , opt.no_CPU = 1)
                                    
POST_FATE.graphic_mapPFG(name.simulation = "FATE_simulation"
                         , file.simulParam = "Simul_parameters_V1.txt"
                         , year = c(850, 950)
                         , opt.doBinary = FALSE)

## End(Not run)