# Spatial Ecology Miscellaneous Methods

## Documentation for package ‘ecospat’ version 4.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ecospat-package | Spatial Ecology Miscellaneous Methods
ecospat | Spatial Ecology Miscellaneous Methods
ecospat.adj.D2.glm | Calculate An Adjusted D2
ecospat.binary.model | Generate Binary Models
ecospat.boyce | Calculate Boyce Index
ecospat.calculate.pd | Calculate Phylogenetic Diversity Measures
ecospat.caleval | Calibration And Evaluation Dataset
ecospat.CCV.communityEvaluation.bin | Calculates a range of community evaluation metrics based on different thresholding techniques.
ecospat.CCV.communityEvaluation.prob | Evaluates community predictions directly on the probabilities (i.e., threshold independent)
ecospat.CCV.createDataSplitTable | Creates a DataSplitTable for usage in ecospat.ccv.modeling.
ecospat.CCV.modeling | Runs indivudual species distribuion models with SDMs or ESMs
ecospat.climan | A climate analogy setection tool for the modeling of species distributions
ecospat.cohen.kappa | Cohen's Kappa
ecospat.CommunityEval | Community Evaluation
ecospat.cons_Cscore | Constrained Co-Occurrence Analysis.
ecospat.cor.plot | Correlation Plot
ecospat.co_occurrences | Species Co-Occurrences
ecospat.Cscore | Pairwise co-occurrence Analysis with calculation of the C-score index.
ecospat.cv.gbm | GBM Cross Validation
ecospat.cv.glm | GLM Cross Validation
ecospat.cv.me | Maxent Cross Validation
ecospat.cv.rf | RandomForest Cross Validation
ecospat.Epred | Prediction Mean
ecospat.ESM.EnsembleEvaluation | Ensemble of Small Models: Evaluation via the Pooling procedure
ecospat.ESM.EnsembleModeling | Ensemble of Small Models: Evaluates and Averages Simple Bivariate Models To ESMs
ecospat.ESM.EnsembleProjection | Ensemble of Small Models: Projects Calibrated ESMs Into New Space Or Time.
ecospat.ESM.Modeling | Ensemble of Small Models: Calibration of Simple Bivariate Models
ecospat.ESM.Projection | Ensemble of Small Models: Projects Simple Bivariate Models Into New Space Or Time
ecospat.ESM.responsePlot | Produce response plots for ESMs
ecospat.ESM.threshold | Thresholds for Ensemble of Small Models
ecospat.ESM.VarContrib | Variable contribution in ESM
ecospat.grid.clim.dyn | Dynamic Occurrence Densities Grid
ecospat.mantel.correlogram | Mantel Correlogram
ecospat.margin | Delineation of the distribution's margin and its uncertainty
ecospat.max.kappa | Maximum Kappa
ecospat.max.tss | Maximum TSS
ecospat.maxentvarimport | Maxent Variable Importance
ecospat.mdr | Minimum Dispersal Routes)
ecospat.mess | MESS
ecospat.meva.table | Model Evaluation For A Given Threshold Value
ecospat.mpa | Minimal Predicted Area
ecospat.niche.dyn.index | Niche Expansion, Stability, and Unfilling
ecospat.niche.dynIndexProjGeo | Projection of niche dynamic indices to the Geography
ecospat.niche.equivalency.test | Niche Equivalency Test
ecospat.niche.overlap | Calculate Niche Overlap
ecospat.niche.similarity.test | Niche Similarity Test
ecospat.niche.zProjGeo | Projection of Occurrence Densities to the Geography
ecospat.nicheNBmean | Niche position and niche breadth)
ecospat.nichePOSNB | Niche position and niche breadth)
ecospat.npred | Number Of Predictors
ecospat.occ.desaggregation | Species Occurrences Desaggregation
ecospat.occupied.patch | Extract occupied patches of a species in geographic space.)
ecospat.permut.glm | GLM Permutation Function
ecospat.plot.contrib | Plot Variables Contribution
ecospat.plot.kappa | Plot Kappa
ecospat.plot.mess | Plot MESS
ecospat.plot.niche | Plot Niche
ecospat.plot.niche.dyn | Niche Categories and Species Density
ecospat.plot.overlap.test | Plot Overlap Test
ecospat.plot.tss | Plot True skill statistic (TSS)
ecospat.poolingEvaluation | Evaluation of species distribution models using the pooling procedure
ecospat.rand.pseudoabsences | Sample Pseudo-Absences
ecospat.rangesize | Quantification of the range size of a species using habitat suitability maps and IUCN criteria)
ecospat.rcls.grd | Reclassifying grids function
ecospat.recstrat_prop | Random Ecologically Stratified Sampling of propotional numbers
ecospat.recstrat_regl | Random Ecologically Stratified Sampling of equal numbers
ecospat.sample.envar | Sample Environmental Variables
ecospat.SESAM.prr | SESAM Probability Ranking Rule
ecospat.shift.centroids | Draw Centroid Arrows
ecospat.testData | Test Data For The Ecospat package
ecospat.testEnv | Test Environmental SpatRasters for The Ecospat package
ecospat.testMdr | Test Data For The ecospat.mdr function
ecospat.testNiche | Test Data For The Niche Overlap Analysis
ecospat.testNiche.inv | Test Data For The Niche Dynamics Analysis In The Invaded Range Of A Hypothetical Species
ecospat.testNiche.nat | Test Data For The Niche Dynamics Analysis In The Native Range Of A Hypothetical Species
ecospat.testNichePOSNB | Test AVS Dataset For The Ecospat package
ecospat.testTree | Test Tree For The Ecospat package
ecospat.varpart | Variation Partitioning For GLM Or GAM