Package: ecospat 4.1.0

Olivier Broennimann

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) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.

Authors:Olivier Broennimann [cre, aut, ctb], Valeria Di Cola [aut, ctb], Blaise Petitpierre [ctb], Frank Breiner [ctb], Daniel Scherrer [ctb], Manuela D`Amen [ctb], Christophe Randin [ctb], Robin Engler [ctb], Wim Hordijk [ctb], Heidi Mod [ctb], Julien Pottier [ctb], Mirko Di Febbraro [ctb], Loic Pellissier [ctb], Dorothea Pio [ctb], Ruben Garcia Mateo [ctb], Anne Dubuis [ctb], Luigi Maiorano [ctb], Achilleas Psomas [ctb], Charlotte Ndiribe [ctb], Nicolas Salamin [ctb], Niklaus Zimmermann [ctb], Flavien Collart [ctb], Valentin Verdon [ctb], Tyler Smith [ctb], Antoine Guisan [aut]

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ecospat.pdf |ecospat.html✨
ecospat/json (API)
NEWS

# Install 'ecospat' in R:
install.packages('ecospat', repos = c('https://ecospat.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ecospat/ecospat/issues

Datasets:

On CRAN:

9.16 score 32 stars 1 packages 312 scripts 1.8k downloads 62 mentions 68 exports 116 dependencies

Last updated 5 months agofrom:ded14434c3. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 09 2024
R-4.5-winNOTEOct 09 2024
R-4.5-linuxNOTEOct 09 2024
R-4.4-winOKOct 09 2024
R-4.4-macOKOct 09 2024
R-4.3-winNOTEOct 09 2024
R-4.3-macNOTEOct 09 2024

Exports:ecospat.adj.D2.glmecospat.binary.modelecospat.boyceecospat.calculate.pdecospat.calevalecospat.CCV.communityEvaluation.binecospat.CCV.communityEvaluation.probecospat.CCV.createDataSplitTableecospat.CCV.modelingecospat.climanecospat.co_occurrencesecospat.cohen.kappaecospat.CommunityEvalecospat.cons_Cscoreecospat.cor.plotecospat.Cscoreecospat.cv.gbmecospat.cv.glmecospat.cv.meecospat.cv.rfecospat.Epredecospat.ESM.EnsembleEvaluationecospat.ESM.EnsembleModelingecospat.ESM.EnsembleProjectionecospat.ESM.Modelingecospat.ESM.Projectionecospat.ESM.responsePlotecospat.ESM.thresholdecospat.ESM.VarContribecospat.grid.clim.dynecospat.mantel.correlogramecospat.marginecospat.max.kappaecospat.max.tssecospat.maxentvarimportecospat.mdrecospat.messecospat.meva.tableecospat.mpaecospat.niche.dyn.indexecospat.niche.dynIndexProjGeoecospat.niche.equivalency.testecospat.niche.overlapecospat.niche.similarity.testecospat.niche.zProjGeoecospat.nicheNBmeanecospat.nichePOSNBecospat.npredecospat.occ.desaggregationecospat.occupied.patchecospat.permut.glmecospat.plot.contribecospat.plot.kappaecospat.plot.messecospat.plot.nicheecospat.plot.niche.dynecospat.plot.overlap.testecospat.plot.tssecospat.poolingEvaluationecospat.rand.pseudoabsencesecospat.rangesizeecospat.rcls.grdecospat.recstrat_propecospat.recstrat_reglecospat.sample.envarecospat.SESAM.prrecospat.shift.centroidsecospat.varpart

Dependencies:abindade4adehabitatHRadehabitatLTadehabitatMAbackportsbase64encBHbiomod2bootbslibcachemcheckmateCircStatsclassclassIntcliclustercodetoolscolorspacecpp11data.tabledigestdismodplyre1071ecodistevaluatefansifarverfastmapFNNfontawesomeforeachforeignFormulafsgbmgenericsggplot2gluegridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrkslabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmclustmemoisemgcvmimemulticoolmunsellmvtnormnabornlmennetpermutepillarpixmappkgconfigplyrpoibinpracmaPresenceAbsencepROCproxyR6rappdirsrasterRColorBrewerRcppRcppArmadilloRcppEigenreshapereshape2rlangrmarkdownrpartrstudioapisassscalesspstringistringrsurvivalterratibbletidyselecttinytexutf8vctrsveganviridisviridisLitewithrxfunyaml

Vignette ecospat package

Rendered fromvignette_ecospat_package.Rmdusingknitr::rmarkdownon Oct 09 2024.

Last update: 2024-06-11
Started: 2016-10-25

Readme and manuals

Help Manual

Help pageTopics
Spatial Ecology Miscellaneous Methodsecospat-package ecospat
Calculate An Adjusted D2ecospat.adj.D2.glm
Generate Binary Modelsecospat.binary.model
Calculate Boyce Indexecospat.boyce
Calculate Phylogenetic Diversity Measuresecospat.calculate.pd
Calibration And Evaluation Datasetecospat.caleval
Calculates a range of community evaluation metrics based on different thresholding techniques.ecospat.CCV.communityEvaluation.bin
Evaluates community predictions directly on the probabilities (i.e., threshold independent)ecospat.CCV.communityEvaluation.prob
Creates a DataSplitTable for usage in ecospat.ccv.modeling.ecospat.CCV.createDataSplitTable
Runs indivudual species distribuion models with SDMs or ESMsecospat.CCV.modeling
A climate analogy setection tool for the modeling of species distributionsecospat.climan
Species Co-Occurrencesecospat.co_occurrences
Cohen's Kappaecospat.cohen.kappa
Community Evaluationecospat.CommunityEval
Constrained Co-Occurrence Analysis.ecospat.cons_Cscore
Correlation Plotecospat.cor.plot
Pairwise co-occurrence Analysis with calculation of the C-score index.ecospat.Cscore
GBM Cross Validationecospat.cv.gbm
GLM Cross Validationecospat.cv.glm
Maxent Cross Validationecospat.cv.me
RandomForest Cross Validationecospat.cv.rf
Prediction Meanecospat.Epred
Ensemble of Small Models: Evaluation via the Pooling procedureecospat.ESM.EnsembleEvaluation
Ensemble of Small Models: Evaluates and Averages Simple Bivariate Models To ESMsecospat.ESM.EnsembleModeling
Ensemble of Small Models: Projects Calibrated ESMs Into New Space Or Time.ecospat.ESM.EnsembleProjection
Ensemble of Small Models: Calibration of Simple Bivariate Modelsecospat.ESM.Modeling
Ensemble of Small Models: Projects Simple Bivariate Models Into New Space Or Timeecospat.ESM.Projection
Produce response plots for ESMsecospat.ESM.responsePlot
Thresholds for Ensemble of Small Modelsecospat.ESM.threshold
Variable contribution in ESMecospat.ESM.VarContrib
Dynamic Occurrence Densities Gridecospat.grid.clim.dyn
Mantel Correlogramecospat.mantel.correlogram
Delineation of the distribution's margin and its uncertaintyecospat.margin
Maximum Kappaecospat.max.kappa
Maximum TSSecospat.max.tss
Maxent Variable Importanceecospat.maxentvarimport
Minimum Dispersal Routes)ecospat.mdr
MESSecospat.mess
Model Evaluation For A Given Threshold Valueecospat.meva.table
Minimal Predicted Areaecospat.mpa
Niche Pioneering, Expansion, Stability, Unfilling and Abandonmentecospat.niche.dyn.index
Projection of niche dynamic indices to the Geographyecospat.niche.dynIndexProjGeo
Niche Equivalency Testecospat.niche.equivalency.test
Calculate Niche Overlapecospat.niche.overlap
Niche Similarity Testecospat.niche.similarity.test
Projection of Occurrence Densities to the Geographyecospat.niche.zProjGeo
Niche position and niche breadth)ecospat.nicheNBmean
Niche position and niche breadth)ecospat.nichePOSNB
Number Of Predictorsecospat.npred
Species Occurrences Desaggregationecospat.occ.desaggregation
Extract occupied patches of a species in geographic space.)ecospat.occupied.patch
GLM Permutation Functionecospat.permut.glm
Plot Variables Contributionecospat.plot.contrib
Plot Kappaecospat.plot.kappa
Plot MESSecospat.plot.mess
Plot Nicheecospat.plot.niche
Plot of categories of Niche dynamics and Species Densityecospat.plot.niche.dyn
Plot Overlap Testecospat.plot.overlap.test
Plot True skill statistic (TSS)ecospat.plot.tss
Evaluation of species distribution models using the pooling procedureecospat.poolingEvaluation
Sample Pseudo-Absencesecospat.rand.pseudoabsences
Quantification of the range size of a species using habitat suitability maps and IUCN criteria)ecospat.rangesize
Reclassifying grids functionecospat.rcls.grd
Random Ecologically Stratified Sampling of propotional numbersecospat.recstrat_prop
Random Ecologically Stratified Sampling of equal numbersecospat.recstrat_regl
Sample Environmental Variablesecospat.sample.envar
SESAM Probability Ranking Ruleecospat.SESAM.prr
Draw Centroid Arrowsecospat.shift.centroids
Test Data For The Ecospat packageecospat.testData
Test Environmental SpatRasters for The Ecospat packageecospat.testEnv
Test Data For The ecospat.mdr functionecospat.testMdr
Test Data For The Niche Overlap Analysisecospat.testNiche
Test Data For The Niche Dynamics Analysis In The Invaded Range Of A Hypothetical Speciesecospat.testNiche.inv
Test Data For The Niche Dynamics Analysis In The Native Range Of A Hypothetical Speciesecospat.testNiche.nat
Test AVS Dataset For The Ecospat packageecospat.testNichePOSNB
Test Tree For The Ecospat packageecospat.testTree
Variation Partitioning For GLM Or GAMecospat.varpart