Man pages for leca-dev/RFate
FATE with R
| beta.pair | From betapart package 1.5.4 : beta.pair and betapart.core... |
| cluster.stats | From fpc package 2.2-9 : cluster.stats function |
| designLHD | From SPOT package 2.5.0 : designLHD and designLHDNorm... |
| divLeinster | Find cutoff to transform abundance values into binary values |
| dot-adaptMaps | Adapt all raster maps of a 'FATE' simulation folder (change... |
| dot-createParams | Create a parameters file |
| dot-getCutoff | Find cutoff to transform abundance values into binary values |
| dot-getELLIPSE | Obtain ellipse coordinates from (PCO) X,Y and a factor value |
| dot-getOS | Find operating system of your computer |
| dot-getParam | Extract parameter value(s) from a parameter file |
| dot-loadData | Load a dataset |
| dot-loadPackage | Load a 'R' package and install it if necessary |
| dot-scaleMaps | Upscale / downscale / crop all raster maps of a 'FATE'... |
| dot-setParam | Replace parameter value(s) from a parameter file |
| dot-setPattern | Replace a pattern with a new within all parameter files of a... |
| dot-unzip_ALL | Compress ('.tif', '.img') or decompress ('.gz') files... |
| dunn | From clValid package O.7 : dunn function |
| ecospat.niche.overlap | From ecospat package 3.2 : ecospat.kd, ecospat.grid.clim.dyn... |
| FATE | FATE Wrapper |
| POST_FATE.binaryMaps | Create binary maps for each Plant Functional Group for one... |
| POST_FATE.graphic_evolutionCoverage | Create a graphical representation of the evolution of PFG... |
| POST_FATE.graphic_evolutionPixels | Create a graphical representation of the evolution of PFG... |
| POST_FATE.graphic_evolutionStability | Create a graphical representation of the evolution of habitat... |
| POST_FATE.graphic_mapPFG | Create a map related to plant functional group results... |
| POST_FATE.graphic_mapPFGvsHS | Create maps of both habitat suitability and simulated... |
| POST_FATE.graphics | Create all possible graphical representations for a 'FATE'... |
| POST_FATE.graphic_validationStatistics | Create a graphical representation of several statistics for... |
| POST_FATE.relativeAbund | Create relative abundance maps for each Plant Functional... |
| POST_FATE.temporalEvolution | Create tables of pixel temporal evolution of PFG abundances... |
| PRE_FATE.abundBraunBlanquet | Transform Braun-Blanquet values into relative abundances |
| PRE_FATE.params_changingYears | Create _SCENARIO_ parameter files for a 'FATE' simulation |
| PRE_FATE.params_globalParameters | Create _Global_parameters_ parameter file for a 'FATE'... |
| PRE_FATE.params_multipleSet | Create multiple set(s) of parameter files for a 'FATE'... |
| 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_PFGlight | Create _LIGHT_ parameter files for a 'FATE' simulation |
| PRE_FATE.params_PFGsoil | Create _SOIL_ parameter files for a 'FATE' simulation |
| PRE_FATE.params_PFGsuccession | Create _SUCCESSION_ parameter files for a 'FATE' simulation |
| PRE_FATE.params_savingYears | Create _SAVE_ parameter files for a 'FATE' simulation |
| PRE_FATE.params_simulParameters | Create _Simul_parameters_ parameter file for a 'FATE'... |
| PRE_FATE.selectDominant | Selection of dominant species from abundance releves |
| PRE_FATE.skeletonDirectory | Create the skeleton folder for a 'FATE' simulation |
| 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... |
| PRE_FATE.speciesDistance | Computation of distances between species based on traits and... |
| PRE_FATE.speciesDistanceCombine | Combine several dissimilarity distance matrices |
| PRE_FATE.speciesDistanceOverlap | Computation of niche overlap distances between species |
| PRE_FATE.speciesDistanceTraits | Computation of traits distances between species |
| RFATE | Shiny application to apply 'RFate' functions and run 'FATE'... |
| 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 |
