ecospat v3.0

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Spatial Ecology Miscellaneous Methods

Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.

Functions in ecospat

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

Name
vignette_ecospat_package.Rmd
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