ecospat-package {ecospat}

Spatial Ecology Miscellaneous Methods

Description

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