Man pages for adamlilith/enmSdm
Tools for Modeling Niches and Distributions of Species
| aucMultiWeighted | Calculate multivariate weighted AUC |
| aucWeighted | Weighted AUC |
| bioticVelocity | Velocity of shifts in densities across a series of rasters |
| compareNiches | Metrics of niche overlap |
| compareResponse | Compare two response curves along one or more predictors |
| contBoyce | Continuous Boyce Index (CBI) with weighting |
| contBoyce2x | Continuous Boyce Index (CBI) with weighting (2X-coverage... |
| convertTropicosCoords | Convert coordinates from TROPICOS records to decimal degrees |
| coordPrecision | Calculate the precision of a geographic coordinate |
| createPlotPoly | Create SpatialPolygon same size as a plot |
| decimalToDms | Convert geographic coordinates in decimal format to... |
| dmsToDecimal | Convert geographic coordinates in degrees-minutes-second to... |
| dot-calcTol | Automatically calculate tolerance for null model point... |
| dot-cardinalDistance | Movement of occupied cells in a given direction of a fixed... |
| dot-euclid | Euclidean distance between a pair of points |
| dot-interpCoordFromQuantile | Latitude of quantile(s) of the geographic abundance... |
| dot-makeLarsData | Add columns to a data matrix to represent polynomial and... |
| dot-randPointsReturn | Return output common to "randPointsRespecting~" functions |
| dot-sampleRastSubregion | Select random points from a portion of a raster |
| elimCellDups | Thin spatial points so that no more than one point falls... |
| enmSdm | enmSdm: Species distribution modeling and ecological niche... |
| extractLarge | Memory-wise extraction of data from a raster or spatial... |
| Fpb | Fpb measure of model accuracy with weighting |
| FpbOneThreshold | Calculate the Fpb measure of model accuracy for a single... |
| geoFold | Assign geographically-distinct k-folds |
| geoThin | Thin geographic points (mostly) deterministically |
| geoThinApprox | Thin geographic points stochastically |
| getCores | Calculate number of cores to use for multi-core functions |
| getCRS | Return a "proj4" string for a datum and projection |
| getEPSG | Return an EPSG code |
| interpolateRasters | Interpolate a stack of rasters |
| lemurs | Lemur occurrences from GBIF |
| localSpatialCorrForValues | Local characteristic distance of spatial autocorrelation for... |
| longLatRasters | Generate rasters with cell values equal to cell longitude or... |
| mad0 | Madagascar spatial object |
| mad1 | Madagascar spatial object |
| mcpFromPolys | Minimum convex polygon from a set of spatial polygons and... |
| modelSize | Number of response data in a model object |
| mop | Identify similar points in two sets using mobility-oriented... |
| nicheOverlap | Calculate niche overlap as per Broennimann et al. (2012) |
| orssWeighted | Odds ratio skill score (ORSS) |
| pointDist | Calculate distance matrix between geographic points |
| predictEnmSdm | Generic predict function for LMs, GLMs, GAMs, RFs, BRTs,... |
| predictLars | Predict using Least Angle Regression (LARS) model |
| predictMaxEnt | Predict a MaxEnt model object (with optional feature-level... |
| predictMaxNet | Predictions from a MaxNet model |
| randPointsBatch | Iterate "randPointsRespecting..." functions. |
| randPointsBatchExtract | Updates a list of random points with environmental data from... |
| randPointsBatchNicheOverlap | Niche overlap for a set of iterated "randPointsRespecting~"... |
| randPointsBatchSampled | Returns collated set of sampled sites from a set of... |
| randPointsRespectingSelf | Randomizes geographic points while observing spatial... |
| randPointsRespectingSelfOther1 | Randomizes the location of two sets of geographic points... |
| randPointsRespectingSelfOther2 | Randomizes the location of two sets of geographic points... |
| rastWithSquareCells | Create a raster with square cells |
| sampleRast | Sample random points from a raster with/out replacement |
| sampleRastStrat | Sample random points in a stratfied manner from a raster... |
| sediWeighted | Symmetric extremal dependence index (SEDI) |
| spatialCorrForPoints | Calculate spatial autocorrelation for geographic points |
| spatialCorrForPointsPlot | Plot spatial autocorrelation for geographic points |
| spatialCorrForPointsSummary | Summarize spatial autocorrelation for geographic points |
| spatialCorrForPointsWeight | Calculate weights based on pairwise distance for geographic... |
| squareRastCells | Resample a raster so cells are "square" |
| summaryByCrossValid | Summarize distribution/niche model cross-validation object |
| svToSpatial | Convert SpatVector to Spatial* |
| thresholdStats | Thresholded evaluation statistics |
| thresholdWeighted | Weighted thresholds for predictions |
| tjursR2Weighted | Weighted Tjur's R2 |
| trainBrt | Calibrate a boosted regression tree (generalized boosting... |
| trainByCrossValid | Calibrate a distribution/niche model using cross-validation |
| trainCrf | Calibrate a conditional random forest model |
| trainGam | Calibrate a generalized additive model (GAM) |
| trainGlm | Calibrate a generalized linear model (GLM) |
| trainGlmDredge | Calibrate a generalized linear model (GLM) |
| trainLars | Calibrate a least angle regression (LARS) model |
| trainMaxEnt | Calibrate a MaxEnt (ver 3.3.3+ or "maxent") model using AICc |
| trainMaxNet | Calibrate a MaxNet (MaxEnt) model using AICc |
| trainNs | Calibrate a natural splines model |
| trainRf | Calibrate a random forest model |
| tssWeighted | Weighted True Skill Statistic (TSS) |
| xToCoords | Extract geographic coordinates from an object |
