ecospat v3.1

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by Olivier Broennimann View Source

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.

Functions in ecospat

Name	Description
ecospat.CCV.communityEvaluation.prob	Evaluates community predictions directly on the probabilities (i.e., threshold independent)
ecospat-package	Spatial Ecology Miscellaneous Methods
ecospat.CCV.createDataSplitTable	Creates a DataSplitTable for usage in ecospat.ccv.modeling.
ecospat.ESM.EnsembleProjection	Ensamble of Small Models: Projects Calibrated ESMs Into New Space Or Time.
ecospat.CCV.communityEvaluation.bin	Calculates a range of community evaluation metrics based on different thresholding techniques.
ecospat.ESM.Modeling	Ensamble of Small Models: Calibration of Simple Bivariate Models
ecospat.CommunityEval	Community Evaluation
ecospat.ESM.EnsembleModeling	Ensamble of Small Models: Evaluates and Averages Simple Bivariate Models To ESMs
ecospat.Cscore	Pairwise co-occurrence Analysis with calculation of the C-score index.
ecospat.CCV.modeling	Runs indivudual species distribuion models with SDMs or ESMs
ecospat.ESM.responsePlot	Produce response plots for ESMs
ecospat.ESM.threshold	Thresholds for Ensamble of Small Models
ecospat.Epred	Prediction Mean
ecospat.SESAM.prr	SESAM Probability Ranking Rule
ecospat.binary.model	Generate Binary Models
ecospat.adj.D2.glm	Calculate An Adjusted D2
ecospat.ESM.VarContrib	Variable contribution in ESM
ecospat.ESM.Projection	Ensamble of Small Models: Projects Simple Bivariate Models Into New Space Or Time
ecospat.co_occurrences	Species Co-Occurrences
ecospat.cv.me	Maxent Cross Validation
ecospat.cohen.kappa	Cohen's Kappa
ecospat.cons_Cscore	Constrained Co-Occurrence Analysis.
ecospat.calculate.pd	Calculate Phylogenetic Diversity Measures
ecospat.boyce	Calculate Boyce Index
ecospat.caleval	Calibration And Evaluation Dataset
ecospat.mdr	Minimum Dispersal Routes)
ecospat.climan	A climate analogy setection tool for the modeling of species distributions
ecospat.max.tss	Maximum TSS
ecospat.maxentvarimport	Maxent Variable Importance
ecospat.cor.plot	Correlation Plot
ecospat.mpa	Minimal Predicted Area
ecospat.niche.overlap	Calculate Niche Overlap
ecospat.meva.table	Model Evaluation For A Given Threshold Value
ecospat.mess	MESS
ecospat.niche.equivalency.test	Niche Equivalency Test
ecospat.cv.gbm	GBM Cross Validation
ecospat.niche.similarity.test	Niche Similarity Test
ecospat.mantel.correlogram	Mantel Correlogram
ecospat.cv.glm	GLM Cross Validation
ecospat.max.kappa	Maximum Kappa
ecospat.niche.zProjGeo	Projection of Occurrence Densities to the Geography
ecospat.grid.clim.dyn	Dynamic Occurrence Densities Grid
ecospat.plot.tss	Plot True skill statistic (TSS)
ecospat.cv.rf	RandomForest Cross Validation
ecospat.testNiche.nat	Test Data For The Niche Dynamics Analysis In The Native Range Of A Hypothetical Species
ecospat.rand.pseudoabsences	Sample Pseudo-Absences
ecospat.testNiche.inv	Test Data For The Niche Dynamics Analysis In The Invaded Range Of A Hypothetical Species
ecospat.occupied.patch	Extract occupied patches of a species in geographic space.)
ecospat.makeDataFrame	Make Data Frame
ecospat.niche.dyn.index	Niche Expansion, Stability, and Unfilling
ecospat.permut.glm	GLM Permutation Function
ecospat.niche.dynIndexProjGeo	Projection of niche dynamic indices to the Geography
ecospat.plot.niche.dyn	Niche Categories and Species Density
ecospat.rangesize	Quantification of the range size of a species using habitat suitability maps and IUCN criteria)
ecospat.occ.desaggregation	Species Occurrences Desaggregation
ecospat.npred	Number Of Predictors
ecospat.plot.mess	Plot MESS
ecospat.rcls.grd	Reclassifying grids function
ecospat.testTree	Test Tree For The Ecospat package
ecospat.testEnvRaster	Test Environmental Rasters for The Ecospat package
ecospat.plot.overlap.test	Plot Overlap Test
ecospat.testData	Test Data For The Ecospat package
ecospat.testMdr	Test Data For The ecospat.mdr function
ecospat.testNiche	Test Data For The Niche Overlap Analysis
ecospat.plot.contrib	Plot Variables Contribution
ecospat.plot.niche	Plot Niche
ecospat.shift.centroids	Draw Centroid Arrows
ecospat.sample.envar	Sample Environmental Variables
ecospat.varpart	Variation Partitioning For GLM Or GAM
ecospat.plot.kappa	Plot Kappa
ecospat.recstrat_prop	Random Ecologically Stratified Sampling of propotional numbers
ecospat.recstrat_regl	Random Ecologically Stratified Sampling of equal numbers
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Vignettes of ecospat

Name
vignette_ecospat_package.Rmd
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Last month downloads

Details

Date	2020-03-23
VignetteBuilder	knitr
LazyData	true
URL	http://www.unil.ch/ecospat/home/menuguid/ecospat-resources/tools.html
License	GPL
BugReports	https://github.com/ecospat/ecospat
RoxygenNote	7.1.0
NeedsCompilation	no
Packaged	2020-03-23 07:55:03 UTC; obroenni
Repository	CRAN
Date/Publication	2020-03-25 15:20:03 UTC

depends	ade4 (>= 1.6-2) , ape (>= 3.2) , gbm (>= 2.1.1) , sp (>= 1.0-15)
imports	adehabitatHR (>= 0.4.11) , adehabitatMA (>= 0.3.8) , biomod2 (>= 3.1-64) , classInt (>= 0.1-23) , dismo (>= 0.9-3) , doParallel (>= 1.0.10) , ecodist (>= 1.2.9) , foreach (>= 1.4.3) , gtools (>= 3.4.1) , iterators (>= 1.0.8) , maps (>= 3.0.0) , maptools (>= 0.8-39) , matrixStats (>= 0.53.1) , methods (>= 3.1.1) , parallel , poibin (>= 1.3) , PresenceAbsence (>= 1.1.9) , randomForest (>= 4.6-7) , raster (>= 2.5-8) , rms (>= 4.5-0) , snowfall (>= 1.61) , spatstat (>= 1.37-0) , vegan (>= 2.4-1)
suggests	alphahull (>= 2.1) , igraph (>= 1.2.1) , knitr (>= 1.14) , markdown (>= 1.1) , rgdal (>= 1.2-15) , rgeos (>= 0.3-28) , rJava (>= 0.9-6) , XML (>= 3.98-1.1)
Contributors	Antoine Guisan, Robin Engler, Frank Breiner, Blaise Petitpierre, Manuela D`Amen, Christophe Randin, Wim Hordijk, Julien Pottier, Mirko Di Febbraro, Loic Pellissier, Dorothea Pio, Ruben Garcia Mateo, Anne Dubuis, Daniel Scherrer, Luigi Maiorano, Achilleas Psomas, Charlotte Ndiribe, Nicolas Salamin, Niklaus Zimmermann, Valeria Di Cola, Heidi Mod