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.

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 <valeria.dicola@unil.ch>
LicenseGPL
Version2.1.1
http://www.unil.ch/ecospat/home/menuguid/ecospat-resources/tools.html

View on CRAN

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...

ecospat.cv.example: Cross Validation Example Function

ecospat.cv.gbm: GBM Cross Validation

ecospat.cv.glm: GLM Cross Validation

ecospat.cv.me: Maxent Cross Validation

ecospat.cv.rf: 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

Files in this package

ecospat
ecospat/inst
ecospat/inst/extdata
ecospat/inst/extdata/ecospat.testTree.tre
ecospat/inst/doc
ecospat/inst/doc/ecospat.pdf
ecospat/inst/doc/vignette_ecospat_package.R
ecospat/inst/doc/vignette_ecospat_package.Rmd
ecospat/inst/doc/vignette_ecospat_package.pdf
ecospat/NAMESPACE
ecospat/NEWS
ecospat/data
ecospat/data/ecospat.testData.txt.gz
ecospat/data/ecospat.testNiche.txt.gz
ecospat/data/datalist
ecospat/data/ecospat.testNiche.inv.txt.gz
ecospat/data/ecospat.testNiche.nat.txt.gz
ecospat/R
ecospat/R/ecospat.pd_measure.R ecospat/R/ecospat.boyce.R ecospat/R/ecospat.sampling.R ecospat/R/ecospat.ESM.R ecospat/R/ecospat.cor.panel.R ecospat/R/ecospat.co_occ.R ecospat/R/ecospat.mess.R ecospat/R/ecospat.nicheoverlap.R ecospat/R/ecospat.exdet.R ecospat/R/ecospat.makeDataFrame.R ecospat/R/ecospat.adj.D2.R ecospat/R/ecospat.occprep.R ecospat/R/ecospat.cv.R ecospat/R/ecospat.binary_models.R ecospat/R/ecospat.CommunityEval.R ecospat/R/ecospat.nichedynamic.R ecospat/R/ecospat.eval.R ecospat/R/ecospat.modelingtools.R ecospat/R/ecospat.SESAM.prr.R ecospat/R/ecospat.migclim.R
ecospat/vignettes
ecospat/vignettes/vignette_ecospat_package.Rmd
ecospat/MD5
ecospat/build
ecospat/build/vignette.rds
ecospat/DESCRIPTION
ecospat/man
ecospat/man/ecospat.cor.plot.Rd ecospat/man/ecospat.meva.table.Rd ecospat/man/ecospat.calculate.pd.Rd ecospat/man/ecospat.max.tss.Rd ecospat/man/ecospat.recstrat_prop.Rd ecospat/man/ecospat.boyce.Rd ecospat/man/ecospat.ESM.EnsembleProjection.Rd ecospat/man/ecospat.cv.glm.Rd ecospat/man/ecospat.cv.example.Rd ecospat/man/ecospat.plot.tss.Rd ecospat/man/ecospat.recstrat_regl.Rd ecospat/man/ecospat.sample.envar.Rd ecospat/man/ecospat.grid.clim.dyn.Rd ecospat/man/ecospat.permut.glm.Rd ecospat/man/ecospat.mess.Rd ecospat/man/ecospat.shift.centroids.Rd ecospat/man/ecospat.cv.gbm.Rd ecospat/man/ecospat.plot.kappa.Rd ecospat/man/ecospat.co_occurrences.Rd ecospat/man/ecospat-package.Rd ecospat/man/ecospat.plot.mess.Rd ecospat/man/ecospat.niche.overlap.Rd ecospat/man/ecospat.npred.Rd ecospat/man/ecospat.plot.niche.Rd ecospat/man/ecospat.niche.similarity.test.Rd ecospat/man/ecospat.cons_Cscore.Rd ecospat/man/ecospat.ESM.Projection.Rd ecospat/man/ecospat.cohen.kappa.Rd ecospat/man/ecospat.cv.me.Rd ecospat/man/ecospat.caleval.Rd ecospat/man/ecospat.env.Rd ecospat/man/ecospat.binary.model.Rd ecospat/man/ecospat.adj.D2.Rd ecospat/man/ecospat.testNiche.Rd ecospat/man/ecospat.makeDataFrame.Rd ecospat/man/ecospat.testNiche.nat.Rd ecospat/man/ecospat.plot.niche.dyn.Rd ecospat/man/ecospat.testTree.Rd ecospat/man/ecospat.exdet.Rd ecospat/man/ecospat.CommunityEval.Rd ecospat/man/ecospat.niche.dyn.index.Rd ecospat/man/ecospat.migclim.Rd ecospat/man/ecospat.SESAM.prr.Rd ecospat/man/ecospat.max.kappa.Rd ecospat/man/ecospat.rand.pseudoabsences.Rd ecospat/man/ecospat.Epred.Rd ecospat/man/ecospat.ESM.EnsembleModeling.Rd ecospat/man/ecospat.cv.rf.Rd ecospat/man/ecospat.rcls.grd.Rd ecospat/man/ecospat.varpart.Rd ecospat/man/ecospat.ESM.Modeling.Rd ecospat/man/ecospat.Cscore.Rd ecospat/man/ecospat.plot.contrib.Rd ecospat/man/ecospat.plot.overlap.test.Rd ecospat/man/ecospat.niche.equivalency.test.Rd ecospat/man/ecospat.maxentvarimport.Rd ecospat/man/ecospat.testData.Rd ecospat/man/ecospat.occ.desaggregation.Rd ecospat/man/ecospat.mantel.correlogram.Rd ecospat/man/ecospat.mpa.Rd ecospat/man/ecospat.testNiche.inv.Rd

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