Collection of methods, utilities 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. The ecospat package was 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.
Pre-modelling:
Spatial autocorrelation:ecospat.mantel.correlogram
Variable selection: ecospat.npred
Climate Analalogy: ecospat.climan, ecospat.mess, ecospat.plot.mess
Phylogenetic diversity measures: ecospat.calculate.pd
Biotic Interactions: ecospat.cons_Cscore, ecospat.Cscore, ecospat.co_occurrences
Minimum Dispersal routes: ecospat.mdr
Niche Quantification: ecospat.grid.clim.dyn, ecospat.niche.equivalency.test, ecospat.niche.similarity.test, ecospat.plot.niche, ecospat.plot.niche.dyn, ecospat.plot.contrib, ecospat.niche.overlap, ecospat.plot.overlap.test, ecospat.niche.dyn.index, ecospat.shift.centroids, ecospat.niche.dynIndexProjGeo, ecospat.niche.zProjGeo, ecospat.margin,ecospat.nichePOSNB,ecospat.nicheNBmean
Data Preparation: ecospat.caleval, ecospat.cor.plot, ecospat.occ.desaggregation, ecospat.rand.pseudoabsences, ecospat.rcls.grd, ecospat.recstrat_prop, ecospat.recstrat_regl, ecospat.sample.envar
Core Niche Modelling:
Model evaluation: ecospat.cv.glm, ecospat.permut.glm, ecospat.cv.gbm, ecospat.cv.me, ecospat.cv.rf, ecospat.boyce, ecospat.CommunityEval, ecospat.cohen.kappa, ecospat.max.kappa, ecospat.max.tss, ecospat.meva.table, ecospat.plot.kappa, ecospat.plot.tss, ecospat.adj.D2.glm, ecospat.CCV.createDataSplitTable, ecospat.CCV.modeling, ecospat.CCV.communityEvaluation.bin, ecospat.CCV.communityEvaluation.prob,ecospat.ESM.EnsembleEvaluation,ecospat.poolingEvaluation
Spatial predictions and projections: ecospat.ESM.Modeling, ecospat.ESM.EnsembleModeling, ecospat.ESM.Projection, ecospat.ESM.EnsembleProjection, ecospat.SESAM.prr, ecospat.binary.model, ecospat.Epred, ecospat.mpa
Variable Importance: ecospat.maxentvarimport, ecospat.ESM.VarContrib
Post Modelling:
Variance Partition: ecospat.varpart
Spatial predictions of species assemblages: ecospat.cons_Cscore
Range size quantification: ecospat.rangesize, ecospat.occupied.patch