ecospat v2.0


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by Valeria Di Cola

Spatial Ecology Miscellaneous Methods

Colection 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) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.

Functions in ecospat

Name Description
ecospat.binary.model Generate Binary Models
ecospat.boyce Calculate Boyce Index GBM Cross Validation
ecospat.cor.plot Correlation Plot
ecospat.ESM.EnsembleModeling Ensamble of Small Models: Evaluates and Averages Simple Bivariate Models To ESMs
ecospat.env Package Environment Maxent Cross Validation GLM Cross Validation Cross Validation Example Function RandomForest Cross Validation
ecospat.Epred Prediction Mean
ecospat.ESM.EnsembleProjection Ensamble of Small Models: Projects Calibrated ESMs Into New Space Or Time.
ecospat.makeDataFrame Make Data Frame
ecospat.max.tss Maximum TSS
ecospat.mantel.correlogram Mantel Correlogram
ecospat.maxentvarimport Maxent Variable Importance
ecospat.ESM.Projection Ensamble of Small Models: Projects Simple Bivariate Models Into New Space Or Time
ecospat.mess MESS
ecospat.ESM.Modeling Ensamble of Small Models: Calibration of Simple Bivariate Models
ecospat.exdet An EXtrapolation DETection Tool For The Modeling Of Species Distributions
ecospat.grid.clim.dyn Dynamic Occurrence Densities Grid
ecospat.max.kappa Maximum Kappa
ecospat.mpa Minimal Predicted Area
ecospat.niche.similarity.test Niche Similarity Test
ecospat.niche.dyn.index Niche Expansion, Stability, and Unfilling
ecospat.npred Number Of Predictors
ecospat.occ.desaggregation Species Occurrences Desaggregation
ecospat.permut.glm GLM Permutation Function
ecospat.niche.equivalency.test Niche Equivalency Test
ecospat.niche.overlap Calculate Niche Overlap
ecospat.meva.table Model Evaluation For A Given Threshold Value
ecospat.migclim Implementing Dispersal Into Species Distribution Models
ecospat.plot.tss Plot True skill statistic (TSS)
ecospat.rand.pseudoabsences Sample Pseudo-Absences
ecospat.plot.contrib Plot Variables Contribution
ecospat.plot.kappa Plot Kappa
ecospat.plot.niche.dyn Niche Categories and Species Density
ecospat.plot.mess Plot MESS
ecospat.plot.overlap.test Plot Overlap Test
ecospat.plot.niche Plot Niche
ecospat.sample.envar Sample Environmental Variables
ecospat.SESAM.prr SESAM Probability Ranking Rule
ecospat.testNiche.inv Test Data For The Niche Dynamics Analysis In The Invaded Range Of A Hypothetical Species
ecospat.testNiche Test Data For The Niche Overlap Analysis
ecospat.shift.centroids Draw Centroid Arrows
ecospat.testData Test Data For The Ecospat package
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.cons_Cscore Constrained Co-Occurrence Analysis.
ecospat.caleval Calibration And Evaluation Dataset
ecospat.varpart Variation Partitioning For GLM Or GAM
ecospat-package Spatial Ecology Miscellaneous Methods
ecospat.adj.D2.glm Calculate An Adjusted D2
ecospat.co_occurrences Species Co-Occurrences
ecospat.cohen.kappa Cohen's Kappa
ecospat.calculate.pd Calculate Phylogenetic Diversity Measures
ecospat.CommunityEval Community Evaluation
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