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.

Author
Olivier 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 publication
2016-11-02 17:57:16
Maintainer
Valeria Di Cola <valeria.dicola@unil.ch>
License
GPL
Version
2.1.1
URLs

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