Function reference • RFate

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

Reference

Datasets

Interface

Build Plant Functional Groups

Create FATE parameter files

Run FATE simulation

Analyze FATE outputs

Save FATE simulation

Tool box