Man pages for CeresBarros/ToolsCB
Ceres's Useful R Functions
| abgDecompQ | alpha-, beta- and gamma-diversity multiplicative... |
| addDietCat | ADD MISSING DIET CATEGORIES (BASL NODES) TO A NETWORK |
| BetaDisQ | Pairwise beta-diversity calculation |
| beta.nes | Nested beta-diversity |
| beta.sim | Simpsons's beta-diversity |
| beta.sor | Sorensen's beta-diversity |
| BL_localweb | Function to calculate local webs - Baseline |
| calcCrossValidMetrics | CALCULATE VALIDATION METRICS AND CONFUSION MATRIX |
| calc.extThresh | CALCULATE MIN PREY EXTINCTION THRESHOLDS |
| calcMeanBEINF | CALCULATION OF THE MEAN FROM A ZERO- AND ONE-INFLATED... |
| calcNetMeanDistances | CALCULATE MEAN BETA DIVERSITY (PAIRWISE DISTANCE) Summarizes... |
| calcNetworkBLMetricsPCA | NETWORK METRICS PCA FUNCTION |
| calcNetworkMetricsSummStats | AVERAGING NETWORK METRICS FUNCTION |
| calcP0BEINF | CALCULATION OF THE PROBABILITY OF ZERO FROM A ZERO- AND... |
| calcP1BEINF | CALCULATION OF THE PROBABILITY OF ONE FROM A ZERO- AND... |
| calcSpaceBetaDiv | SPATIAL BETA-DIVERSITY WRAPPER FUNCTION |
| calcSppTL | Calculate species trophic levels |
| calcTempBetaDivBAMR | TEMPORAL BETA-DIVERSITY PER TETRAPOD FAMILY WRAPPER FUNCTION |
| calcTempBetaDiv.master | TEMPORAL BETA-DIVERSITY WRAPPER FUNCTION FOR PIXEL BY SPP... |
| CalculatePredatorOverlap | Network average predator overlap |
| calcVarBEINF | CALCULATION OF THE VARIANCE OF A ZERO- AND ONE-INFLATED... |
| chaoObjects | Data prep for diversity metrics |
| checkProjections | CHECK PROJECTIONS |
| col_convert | CONVERT COLUMN NAMES IN MATRIX |
| compileResultsMasterBL | LOAD BASELINE MASTER MATRICES (SPP X PIXEL MATRICES) FUNCTION |
| compileResultsMasterScen | LOAD SCENARIO MASTER MATRICES (SPP X PIXEL MATRICES) FUNCTION... |
| compileSDMsppRichness | COMPILE SDM PROJECTIONS PRESENCE/ABSENCES |
| cropToStudyArea | CROP & MASK TO STUDY AREA |
| crossValidFunction | CROSS-VALIDATION FUNCTION |
| Degree | Node degree |
| densityDegreeDistribution | Density of degree distribution calculation |
| divLeinster | Site diversity according to Leinster & Cobbold 2012. |
| do.PAmaster | EXTRACT PRESENCE ABSENCE MATRICES FROM SPECIES DISTRIBUTIONS |
| dot-calcCentrality | CALCULATE SPECIES CENTRALITY |
| dot-compileMasterBL | internal function |
| dot-compileMasterScen | internal function |
| dot-convert2igraph | CONVERT LIST OF ADJENCY MATRICES TO IGRAPH |
| dot-HVcalc | HYPERVOLUME COMPUTATION WRAPPER |
| dot-networkTempBetaDiversityFamilies | NETWORK BETA DIVERSITY PER FAMILY USING WEBS AS INPUTS |
| dot-ordinationPlots | ORDINATION PLOT SAVING FUNCTION |
| dot-plot.HypervolumeListEdited | Edited version of 'hypervolume::plot.HypervolumeList' |
| dot-scaleVars | SCALE VARIABLES |
| findIUCNAcceptedName | FIND SPECIES ACCEPTED NAMES (IUCN) |
| findIUCNStatus | FIND SPECIES IUCN STATUS |
| fitting2 | Modified version of 'fitting' from the 'brainwaver' R... |
| FractionOfBasal | Proportion of basal nodes |
| FractionOfCannibalism | Proportion of cannibalistic links |
| FractionOfIntermediate | Proportion of intermediate consumers |
| FractionOfTop | Proportion of top consumers |
| fun.dbf2raster | CONVERT SPECIES DATABASE FILES TO RASTERS |
| fun.load.many.rdata | READ SEVERAL RDATA FILES TO A LIST |
| fun.PRESENCE.ABSENCE | DETECT SPECIES PRESENCES IN PIXEL BY A THRESHOLD NUMBER OF... |
| getPEF.own | Modified 'gamlss::getPEF' |
| HabLoss_localweb | Function to build local networks according to habitat loss/LC... |
| HabLoss_SppDist_localweb | Local networks after land-cover and species distribution... |
| HVordination | CALCULATE ORDINATION FOR HYPERVOLUME COMPUTATION |
| hypervolumes | CALCULATE AND COMPARE TWO HYPERVOLUMES |
| InDegree | In-degree per node |
| IsOmnivore2 | Calculate if a spp is an omnivore based on the number of... |
| length2 | New version of length which can handle NA's |
| loadAndSummarizeResults | LOAD AND SUMMARISE METRICS RESULTS FUNCTION |
| loadBindSpatialObjs | JOIN SPATIAL OBJECTS FUNCTION |
| loadResultsMetrics | LOAD METRICS RESULTS FUNCTION compiles simulation resuls and... |
| loadResultsSpaceBetaDiv | LOAD SPATIAL BETA DIVERSITY RESULTS FUNCTION |
| loadResultsTempBetaDiv | LOAD TEMPORAL BETA DIVERSITY RESULTS FUNCTION |
| makeAndSaveMasterBL | MAKE AND SAVE BASELINE MASTER MATRICES (SPP X PIXEL MATRICES)... |
| makeAndSaveMasterScen | MAKE AND SAVE SCENARIO MASTER MATRICES (SPP X PIXEL MATRICES)... |
| makeBioregDT | MAKE TABLE OF BIOGEOGRAPHIC REGION BY PIXEL ID |
| makeTransparent | Function to make transparent versions of R colors. |
| MaximumSimilarity | Network similarity this is more like mean similarity than... |
| MeanFoodChainLength | Network mean food chain length |
| MeanGenerality | Network mean Generality |
| MeanGenerality_norm | Network normalised mean Generality |
| MeanGenerality_norm2 | Network normalised mean Generality - following Williams and... |
| MeanVulnerability | Network mean Vulnerability |
| MeanVulnerability_norm | Network normalised mean Vulnerability |
| MeanVulnerability_norm2 | Network normalised mean Vulnerability - following Williams... |
| neighboursMatrix | FIND NEIGHBOURS IN MATRIX |
| netw.metrics | CALCULATE NETWORK METRICS Function to calculate several... |
| networkTempBetaDiv | TAXONOMIC BETA-DIVERSITY FUNCTION calculates beta diversity... |
| networkTempBetaDiv.master | TAXONOMIC BETA-DIVERSITY FUNCTION FOR PIXEL BY SPP MATRICES |
| NormalisedGenerality | Node normalised Generality |
| NormalisedVulnerability | Node normalised Vulnerability |
| NumberOfBasal | Number of basal nodes |
| NumberOfIntermediate | Number of intermediate consumers |
| NumberOfTop | Number of top consumers |
| Omnivory2 | Network omnivory |
| OutDegree | Out-degree per node |
| outerBuffer | DRAW CONVEX HULL AROUND POLYGON |
| pixXspp_function | CONVERT LIST OF WEBS/SPP IN PIXELS INTO A PIXELS x SSP MATRIX |
| plotHypervolumes3D | PLOT 3D HYPERVOLUMES WITH ORDINATION LOADINGS AND POST-HOC... |
| potential.inter | DETECT INTERACTIONS FUNCTION |
| prepCorrTable | LATEX/RMARKDOWN CORRELATION TABLES |
| prepKMZ2shapefile | DOWNLOAD KMZ AND CONVERT TO SHAPEFILE |
| ras2matrix | CONVERT RASTER TO MATRIX OF PRESENCE/ABSENCES |
| rasterizeCover | FAST RASTERIZE ALL POLYGONS COVERED BY POLYGON |
| renameCleanSfFields | RENAME AND SUBSET FIELDS IN SF OBJECT ACCORDING TO TABLE |
| replaceNAs | REPLACE NAs BY ANOTHER VALUE IN A DATA.TABLE |
| replaceNAs.data.table | REPLACE NAs IN DATA.TABLE ——– replaces NAs in a... |
| robustnessMaps | MAKE MAPS OF ROBUSTNESS METRICS |
| SDGenerality | Network SD Generality |
| SDGenerality_norm | Network normalised SD Generality |
| SDGenerality_norm2 | Network normalised SD Generality - following Williams and... |
| SDVulnerability | Network SD Vulnerability |
| SDVulnerability_norm | Network normalised SD Vulnerability |
| SDVulnerability_norm2 | Network normalised SD Vulnerability - following Williams and... |
| sfRmDupNACols | CLEAN SF OBJECT FROM DUPLICATED COLUMNS |
| spp.centrality | SPECIES CENTRALITY FUNCTION |
| SppDist_localweb | Function to build local networks according to changes in spp... |
| SppRm_localweb | Function to build local networks according to spp removal... |
| summarySE | Summarize data |
| tlstats | CALCULATE TROPHIC LEVEL STATISTICS Function to calculate... |
| updateModelCached | CACHE-COMPATIBLE MODEL UPDATE |
| validateGeomsSf | VALIDATE GEOMETRIES |
| vector2binmatrix | VECTOR TO BINARY MATRIX |
| whois | IDENTIFY SPP BY CODE |
