Create a map related to plant functional group results (richness, relative cover, light or soil CWM) for one (or several) specific year of a FATE simulation

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,
  doRichness = TRUE,
  doCover = FALSE,
  doLeinster = FALSE,
  doCWM = FALSE,
  opt.stratum_min = 0,
  opt.stratum_max = 10,
  opt.doBinary = TRUE,
  opt.no_CPU = 1,
  opt.doPlot = TRUE
)

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 and binary maps
doRichness: default TRUE.
If TRUE, PFG richness will be computed from binary maps
doCover: default FALSE.
If TRUE, PFG cover will be computed from abundance maps (PFG total abundance / max(PFG total abundance) per pixel)
doLeinster: default FALSE.
If TRUE, PFG diversity will be computed from abundance maps based on Leinster's formul
doCWM: default FALSE.
If TRUE, FATE light and/or soil resources maps will be computed, and weighted by PFG light and/or soil preferences/contribution to obtain a kind a community weighted mean value per pixel
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

Value

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

tab

richness: raster of PFG richness
cover: raster of relative coverage
DIV.0: raster of PFG 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

richness: ggplot2 object, representing richness raster
cover: ggplot2 object, representing cover raster
leinster: 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 five graphics :

map_PFGrichness: to visualize the PFG richness within the studied area
map_PFGcover: to visualize the PFG cover within the studied area
map_PFGleinster: to visualize the PFG diversity 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 PFGleinster_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).

Details

This function allows to obtain, for a specific FATE simulation and a specific parameter file within this simulation, up to seven 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 seven graphics before the maps are compressed again :

map of PFG richness within each pixel, representing the sum of binary maps
maps of PFG diversity within each pixel, calculated from PFG abundances with the Leinster & Cobbold 2012 Ecology framework which allows to give more or less importance to the common 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.

Author

Maya Guéguen

Examples


if (FALSE) { # \dontrun{                      
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)
} # }

Create a map related to plant functional group results (richness, relative cover, light or soil CWM) for one (or several) specific year of a `FATE` simulation

Arguments

Value

Details

See also

Author

Examples