ecospat: Spatial Ecology Miscellaneous Methods
Version 2.1.1

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.

Browse man pages Browse package API and functions Browse package files

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
URL http://www.unil.ch/ecospat/home/menuguid/ecospat-resources/tools.html
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ecospat")

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

Functions

Constrperm Source code
SpeciesCooccurrenceStats Source code
boycei Source code
data2tree Source code
dsg Source code
ecospat Man page
ecospat-package Man page
ecospat.CommunityEval Man page Source code
ecospat.Cscore Man page Source code
ecospat.ESM.EnsembleModeling Man page Source code
ecospat.ESM.EnsembleProjection Man page Source code
ecospat.ESM.MergeModels Source code
ecospat.ESM.Modeling Man page Source code
ecospat.ESM.Projection Man page Source code
ecospat.Epred Man page Source code
ecospat.SESAM.prr Man page Source code
ecospat.adj.D2.glm Man page Source code
ecospat.binary.model Man page Source code
ecospat.boyce Man page Source code
ecospat.calculate.pd Man page Source code
ecospat.caleval Man page Source code
ecospat.co_occurrences Man page Source code
ecospat.cohen.kappa Man page Source code
ecospat.cons_Cscore Man page Source code
ecospat.cor.plot Man page Source code
ecospat.cv.example Man page Source code
ecospat.cv.gbm Man page Source code
ecospat.cv.glm Man page Source code
ecospat.cv.me Man page Source code
ecospat.cv.rf Man page Source code
ecospat.env Man page
ecospat.exdet Man page Source code
ecospat.grid.clim.dyn Man page Source code
ecospat.makeDataFrame Man page Source code
ecospat.mantel.correlogram Man page Source code
ecospat.max.kappa Man page Source code
ecospat.max.tss Man page Source code
ecospat.maxentvarimport Man page Source code
ecospat.mess Man page Source code
ecospat.meva.table Man page Source code
ecospat.migclim Man page Source code
ecospat.mpa Man page Source code
ecospat.niche.dyn.index Man page Source code
ecospat.niche.equivalency.test Man page Source code
ecospat.niche.overlap Man page Source code
ecospat.niche.similarity.test Man page Source code
ecospat.npred Man page Source code
ecospat.occ.desaggregation Man page Source code
ecospat.permut.glm Man page Source code
ecospat.plot.contrib Man page Source code
ecospat.plot.kappa Man page Source code
ecospat.plot.mess Man page Source code
ecospat.plot.niche Man page Source code
ecospat.plot.niche.dyn Man page Source code
ecospat.plot.overlap.test Man page Source code
ecospat.plot.tss Man page Source code
ecospat.pts2img Source code
ecospat.rand.pseudoabsences Man page Source code
ecospat.rcls.grd Man page Source code
ecospat.recstrat_prop Man page Source code
ecospat.recstrat_regl Man page Source code
ecospat.sample.envar Man page Source code
ecospat.shift.centroids Man page Source code
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 Source code
glm.gbm.me.rf.fit.model Source code
overlap.eq.gen Source code
overlap.sim.gen Source code
pairwise.pd Source code
panel.cor Source code
panel.hist Source code
panel.smooth Source code
pod Source code
root2tip Source code
sensitivity Source code
spanning.pd Source code
specificity Source code
topology.pd Source code

Files

inst
inst/extdata
inst/extdata/ecospat.testTree.tre
inst/doc
inst/doc/ecospat.pdf
inst/doc/vignette_ecospat_package.R
inst/doc/vignette_ecospat_package.Rmd
inst/doc/vignette_ecospat_package.pdf
NAMESPACE
NEWS
data
data/ecospat.testData.txt.gz
data/ecospat.testNiche.txt.gz
data/datalist
data/ecospat.testNiche.inv.txt.gz
data/ecospat.testNiche.nat.txt.gz
R
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/ecospat.cv.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
vignettes
vignettes/vignette_ecospat_package.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
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/ecospat.cv.glm.Rd
man/ecospat.cv.example.Rd
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/ecospat.cv.gbm.Rd
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/ecospat.cv.me.Rd
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/ecospat.cv.rf.Rd
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
ecospat documentation built on May 20, 2017, 1:21 a.m.