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

Install the latest version of this package by entering the following in R:
AuthorOlivier Broennimann [aut], Valeria Di Cola [cre, aut], Blaise Petitpierre [ctb], Frank Breiner [ctb], Manuela D`Amen [ctb], Christophe Randin [ctb], Robin Engler [ctb], Wim Hordijk [ctb], Julien Pottier [ctb], Mirko Di Febbraro [ctb], Loic Pellissier [ctb], Dorothea Pio [ctb], Ruben Garcia Mateo [ctb], Anne Dubuis [ctb], Daniel Scherrer [ctb], Luigi Maiorano [ctb], Achilleas Psomas [ctb], Charlotte Ndiribe [ctb], Nicolas Salamin [ctb], Niklaus Zimmermann [ctb], Antoine Guisan [aut]
Date of publication2016-11-02 17:57:16
MaintainerValeria Di Cola <>

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Man pages

ecospat.adj.D2: 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.cohen.kappa: Cohen's Kappa

ecospat.CommunityEval: Community Evaluation

ecospat.cons_Cscore: Constrained Co-Occurrence Analysis.

ecospat.co_occurrences: Species Co-Occurrences

ecospat.cor.plot: Correlation Plot

ecospat.Cscore: Pairwise co-occurrence Analysis with calculation of the... Cross Validation Example Function GBM Cross Validation GLM Cross Validation Maxent Cross Validation RandomForest Cross Validation

ecospat.env: Package Environment

ecospat.Epred: Prediction Mean

ecospat.ESM.EnsembleModeling: Ensamble of Small Models: Evaluates and Averages Simple...

ecospat.ESM.EnsembleProjection: Ensamble of Small Models: Projects Calibrated ESMs Into New...

ecospat.ESM.Modeling: Ensamble of Small Models: Calibration of Simple Bivariate...

ecospat.ESM.Projection: Ensamble of Small Models: Projects Simple Bivariate Models...

ecospat.exdet: An EXtrapolation DETection Tool For The Modeling Of Species...

ecospat.grid.clim.dyn: Dynamic Occurrence Densities Grid

ecospat.makeDataFrame: Make Data Frame

ecospat.mantel.correlogram: Mantel Correlogram

ecospat.maxentvarimport: Maxent Variable Importance

ecospat.max.kappa: Maximum Kappa

ecospat.max.tss: Maximum TSS

ecospat.mess: MESS

ecospat.meva.table: Model Evaluation For A Given Threshold Value

ecospat.migclim: Implementing Dispersal Into Species Distribution Models

ecospat.mpa: Minimal Predicted Area

ecospat.niche.dyn.index: Niche Expansion, Stability, and Unfilling

ecospat.niche.equivalency.test: Niche Equivalency Test

ecospat.niche.overlap: Calculate Niche Overlap

ecospat.niche.similarity.test: Niche Similarity Test

ecospat.npred: Number Of Predictors

ecospat.occ.desaggregation: Species Occurrences Desaggregation

ecospat-package: Spatial Ecology Miscellaneous Methods

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.rand.pseudoabsences: Sample Pseudo-Absences

ecospat.rcls.grd: Reclassifying grids function

ecospat.recstrat_prop: Random Ecologically Stratified Sampling of propotional...

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.testNiche: Test Data For The Niche Overlap Analysis

ecospat.testNiche.inv: Test Data For The Niche Dynamics Analysis In The Invaded...

ecospat.testNiche.nat: Test Data For The Niche Dynamics Analysis In The Native Range...

ecospat.testTree: Test Tree For The Ecospat package

ecospat.varpart: Variation Partitioning For GLM Or GAM


ecospat Man page
ecospat.adj.D2.glm Man page
ecospat.binary.model Man page
ecospat.boyce Man page
ecospat.calculate.pd Man page
ecospat.caleval Man page
ecospat.cohen.kappa Man page
ecospat.CommunityEval Man page
ecospat.cons_Cscore Man page
ecospat.co_occurrences Man page
ecospat.cor.plot Man page
ecospat.Cscore Man page Man page Man page Man page Man page Man page
ecospat.env Man page
ecospat.Epred Man page
ecospat.ESM.EnsembleModeling Man page
ecospat.ESM.EnsembleProjection Man page
ecospat.ESM.Modeling Man page
ecospat.ESM.Projection Man page
ecospat.exdet Man page
ecospat.grid.clim.dyn Man page
ecospat.makeDataFrame Man page
ecospat.mantel.correlogram Man page
ecospat.maxentvarimport Man page
ecospat.max.kappa Man page
ecospat.max.tss Man page
ecospat.mess Man page
ecospat.meva.table Man page
ecospat.migclim Man page
ecospat.mpa Man page
ecospat.niche.dyn.index Man page
ecospat.niche.equivalency.test Man page
ecospat.niche.overlap Man page
ecospat.niche.similarity.test Man page
ecospat.npred Man page
ecospat.occ.desaggregation Man page
ecospat-package Man page
ecospat.permut.glm Man page
ecospat.plot.contrib Man page
ecospat.plot.kappa Man page
ecospat.plot.mess Man page
ecospat.plot.niche Man page
ecospat.plot.niche.dyn Man page
ecospat.plot.overlap.test Man page
ecospat.plot.tss Man page
ecospat.rand.pseudoabsences Man page
ecospat.rcls.grd Man page
ecospat.recstrat_prop Man page
ecospat.recstrat_regl Man page
ecospat.sample.envar Man page
ecospat.SESAM.prr Man page
ecospat.shift.centroids Man page
ecospat.testData Man page
ecospat.testNiche Man page
ecospat.testNiche.inv Man page
ecospat.testNiche.nat Man page
ecospat.testTree Man page
ecospat.varpart Man page


R/ecospat.pd_measure.R R/ecospat.boyce.R R/ecospat.sampling.R R/ecospat.ESM.R R/ecospat.cor.panel.R R/ecospat.co_occ.R R/ecospat.mess.R R/ecospat.nicheoverlap.R R/ecospat.exdet.R R/ecospat.makeDataFrame.R R/ecospat.adj.D2.R R/ecospat.occprep.R R/ R/ecospat.binary_models.R R/ecospat.CommunityEval.R R/ecospat.nichedynamic.R R/ecospat.eval.R R/ecospat.modelingtools.R R/ecospat.SESAM.prr.R R/ecospat.migclim.R
man/ecospat.cor.plot.Rd man/ecospat.meva.table.Rd man/ecospat.calculate.pd.Rd man/ecospat.max.tss.Rd man/ecospat.recstrat_prop.Rd man/ecospat.boyce.Rd man/ecospat.ESM.EnsembleProjection.Rd man/ man/ man/ecospat.plot.tss.Rd man/ecospat.recstrat_regl.Rd man/ecospat.sample.envar.Rd man/ecospat.grid.clim.dyn.Rd man/ecospat.permut.glm.Rd man/ecospat.mess.Rd man/ecospat.shift.centroids.Rd man/ man/ecospat.plot.kappa.Rd man/ecospat.co_occurrences.Rd man/ecospat-package.Rd man/ecospat.plot.mess.Rd man/ecospat.niche.overlap.Rd man/ecospat.npred.Rd man/ecospat.plot.niche.Rd man/ecospat.niche.similarity.test.Rd man/ecospat.cons_Cscore.Rd man/ecospat.ESM.Projection.Rd man/ecospat.cohen.kappa.Rd man/ man/ecospat.caleval.Rd man/ecospat.env.Rd man/ecospat.binary.model.Rd man/ecospat.adj.D2.Rd man/ecospat.testNiche.Rd man/ecospat.makeDataFrame.Rd man/ecospat.testNiche.nat.Rd man/ecospat.plot.niche.dyn.Rd man/ecospat.testTree.Rd man/ecospat.exdet.Rd man/ecospat.CommunityEval.Rd man/ecospat.niche.dyn.index.Rd man/ecospat.migclim.Rd man/ecospat.SESAM.prr.Rd man/ecospat.max.kappa.Rd man/ecospat.rand.pseudoabsences.Rd man/ecospat.Epred.Rd man/ecospat.ESM.EnsembleModeling.Rd man/ man/ecospat.rcls.grd.Rd man/ecospat.varpart.Rd man/ecospat.ESM.Modeling.Rd man/ecospat.Cscore.Rd man/ecospat.plot.contrib.Rd man/ecospat.plot.overlap.test.Rd man/ecospat.niche.equivalency.test.Rd man/ecospat.maxentvarimport.Rd man/ecospat.testData.Rd man/ecospat.occ.desaggregation.Rd man/ecospat.mantel.correlogram.Rd man/ecospat.mpa.Rd man/ecospat.testNiche.inv.Rd

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