Reference

Datasets

Used in the examples.

.loadData()

Load a dataset

Interface

Graphical User Interface (shiny application)

RFATE()

Shiny application to apply RFate functions and run FATE simulation

Build Plant Functional Groups

Functions to select dominant species, compute functional distance between species and build clusters.

PRE_FATE.abundBraunBlanquet()

Transform Braun-Blanquet values into relative abundances

PRE_FATE.selectDominant()

Selection of dominant species from abundance releves

PRE_FATE.speciesDistance()

Computation of distances between species based on traits and niche overlap

PRE_FATE.speciesDistanceOverlap()

Computation of niche overlap distances between species

PRE_FATE.speciesDistanceTraits()

Computation of traits distances between species

PRE_FATE.speciesDistanceCombine()

Combine several dissimilarity distance matrices

PRE_FATE.speciesClustering_step1()

Create clusters based on dissimilarity matrix

PRE_FATE.speciesClustering_step2()

Choose clusters and select determinant species

PRE_FATE.speciesClustering_step3()

Calculate PFG traits values based on determinant species traits values

Create FATE parameter files

Create user-friendly directory tree, parameter and simulation files for FATE simulation.

PRE_FATE.skeletonDirectory()

Create the skeleton folder for a FATE simulation

PRE_FATE.params_PFGsuccession()

Create SUCCESSION parameter files for a FATE simulation

PRE_FATE.params_PFGlight()

Create LIGHT parameter files for a FATE simulation

PRE_FATE.params_PFGsoil()

Create SOIL parameter files for a FATE simulation

PRE_FATE.params_PFGdispersal()

Create DISPERSAL parameter files for a FATE simulation

PRE_FATE.params_PFGdisturbance()

Create DISTURBANCE parameter files for a FATE simulation

PRE_FATE.params_PFGdrought()

Create DROUGHT parameter files for a FATE simulation

PRE_FATE.params_changingYears()

Create SCENARIO parameter files for a FATE simulation

PRE_FATE.params_savingYears()

Create SAVE parameter files for a FATE simulation

PRE_FATE.params_globalParameters()

Create Global_parameters parameter file for a FATE simulation

PRE_FATE.params_simulParameters()

Create Simul_parameters parameter file for a FATE simulation

PRE_FATE.params_multipleSet()

Create multiple set(s) of parameter files for a FATE simulation

Run FATE simulation

FATE()

FATE Wrapper

Analyze FATE outputs

Evalute predicted maps, produce summary and dynamic graphics.

POST_FATE.graphics()

Create all possible graphical representations for a FATE simulation

POST_FATE.temporalEvolution()

Create tables of pixel temporal evolution of PFG abundances (and light and soil resources if activated) for a FATE simulation

POST_FATE.graphic_evolutionCoverage()

Create a graphical representation of the evolution of PFG coverage and abundance through time for a FATE simulation

POST_FATE.graphic_evolutionPixels()

Create a graphical representation of the evolution of PFG abundance through time for 5 (or more) pixels of a FATE simulation

POST_FATE.graphic_evolutionStability()

Create a graphical representation of the evolution of habitat composition through time for a FATE simulation

POST_FATE.relativeAbund()

Create relative abundance maps for each Plant Functional Group for one (or several) specific year of a FATE simulation

POST_FATE.graphic_validationStatistics()

Create a graphical representation of several statistics for each PFG to asses the quality of the model for one (or several) specific year of a FATE simulation

POST_FATE.binaryMaps()

Create binary maps for each Plant Functional Group for one (or several) specific year of a FATE simulation

POST_FATE.graphic_mapPFGvsHS()

Create maps of both habitat suitability and simulated occurrences of each Plant Functional Group for one (or several) specific year of a FATE simulation

POST_FATE.graphic_mapPFG()

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

Save FATE simulation

SAVE_FATE.step1_PFG()

Save data to reproduce building of Plant Functional Groups

SAVE_FATE.step2_parameters()

Save data to reproduce building of parameter files

Tool box

Utility functions.

.getOS()

Find operating system of your computer

.getParam()

Extract parameter value(s) from a parameter file

.setParam()

Replace parameter value(s) from a parameter file

.setPattern()

Replace a pattern with a new within all parameter files of a FATE simulation folder

.adaptMaps()

Adapt all raster maps of a FATE simulation folder (change NA to 0, and save as .tif)

.scaleMaps() .cropMaps()

Upscale / downscale / crop all raster maps of a FATE simulation folder

.getCutoff()

Find cutoff to transform abundance values into binary values

.unzip_ALL() .unzip() .zip_ALL() .zip()

Compress (.tif, .img) or decompress (.gz) files contained in results folder