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ecospat (version 3.3)

Spatial Ecology Miscellaneous Methods

Description

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) for details.

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Version

Install

install.packages('ecospat')

Monthly Downloads

2,162

Version

3.3

License

GPL

Maintainer

Olivier Broennimann

Last Published

June 3rd, 2022

Functions in ecospat (3.3)

ecospat.ESM.EnsembleEvaluation

Ensemble of Small Models: Evaluation via the Pooling procedure
ecospat-package

Spatial Ecology Miscellaneous Methods
ecospat.ESM.EnsembleModeling

Ensemble of Small Models: Evaluates and Averages Simple Bivariate Models To ESMs
ecospat.CCV.createDataSplitTable

Creates a DataSplitTable for usage in ecospat.ccv.modeling.
ecospat.CCV.communityEvaluation.prob

Evaluates community predictions directly on the probabilities (i.e., threshold independent)
ecospat.CCV.communityEvaluation.bin

Calculates a range of community evaluation metrics based on different thresholding techniques.
ecospat.ESM.EnsembleProjection

Ensemble of Small Models: Projects Calibrated ESMs Into New Space Or Time.
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.CommunityEval

Community Evaluation
ecospat.ESM.Modeling

Ensemble of Small Models: Calibration of Simple Bivariate Models
ecospat.Epred

Prediction Mean
ecospat.cv.gbm

GBM Cross Validation
ecospat.cor.plot

Correlation Plot
ecospat.ESM.threshold

Thresholds for Ensemble of Small Models
ecospat.ESM.Projection

Ensemble of Small Models: Projects Simple Bivariate Models Into New Space Or Time
ecospat.co_occurrences

Species Co-Occurrences
ecospat.maxentvarimport

Maxent Variable Importance
ecospat.max.tss

Maximum TSS
ecospat.climan

A climate analogy setection tool for the modeling of species distributions
ecospat.cv.glm

GLM Cross Validation
ecospat.SESAM.prr

SESAM Probability Ranking Rule
ecospat.cv.me

Maxent Cross Validation
ecospat.niche.overlap

Calculate Niche Overlap
ecospat.niche.equivalency.test

Niche Equivalency Test
ecospat.ESM.VarContrib

Variable contribution in ESM
ecospat.cv.rf

RandomForest Cross Validation
ecospat.niche.similarity.test

Niche Similarity Test
ecospat.ESM.responsePlot

Produce response plots for ESMs
ecospat.grid.clim.dyn

Dynamic Occurrence Densities Grid
ecospat.niche.zProjGeo

Projection of Occurrence Densities to the Geography
ecospat.boyce

Calculate Boyce Index
ecospat.binary.model

Generate Binary Models
ecospat.occupied.patch

Extract occupied patches of a species in geographic space.)
ecospat.margin

Delineation of the distribution's margin and its uncertainty
ecospat.permut.glm

GLM Permutation Function
ecospat.max.kappa

Maximum Kappa
ecospat.mpa

Minimal Predicted Area
ecospat.plot.overlap.test

Plot Overlap Test
ecospat.plot.niche.dyn

Niche Categories and Species Density
ecospat.meva.table

Model Evaluation For A Given Threshold Value
ecospat.cohen.kappa

Cohen's Kappa
ecospat.plot.contrib

Plot Variables Contribution
ecospat.adj.D2.glm

Calculate An Adjusted D2
ecospat.recstrat_prop

Random Ecologically Stratified Sampling of propotional numbers
ecospat.rcls.grd

Reclassifying grids function
ecospat.testNichePOSNB

Test AVS Dataset For The Ecospat package
ecospat.rangesize

Quantification of the range size of a species using habitat suitability maps and IUCN criteria)
ecospat.caleval

Calibration And Evaluation Dataset
ecospat.calculate.pd

Calculate Phylogenetic Diversity Measures
ecospat.plot.kappa

Plot Kappa
ecospat.recstrat_regl

Random Ecologically Stratified Sampling of equal numbers
ecospat.plot.tss

Plot True skill statistic (TSS)
ecospat.testTree

Test Tree For The Ecospat package
ecospat.varpart

Variation Partitioning For GLM Or GAM
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.mantel.correlogram

Mantel Correlogram
ecospat.makeDataFrame

Make Data Frame
ecospat.cons_Cscore

Constrained Co-Occurrence Analysis.
ecospat.mess

MESS
ecospat.niche.dyn.index

Niche Expansion, Stability, and Unfilling
ecospat.mdr

Minimum Dispersal Routes)
ecospat.testNiche.nat

Test Data For The Niche Dynamics Analysis In The Native Range Of A Hypothetical Species
ecospat.shift.centroids

Draw Centroid Arrows
ecospat.sample.envar

Sample Environmental Variables
ecospat.nicheNBmean

Niche position and niche breadth)
ecospat.niche.dynIndexProjGeo

Projection of niche dynamic indices to the Geography
ecospat.nichePOSNB

Niche position and niche breadth)
ecospat.testNiche

Test Data For The Niche Overlap Analysis
ecospat.testMdr

Test Data For The ecospat.mdr function
ecospat.npred

Number Of Predictors
ecospat.occ.desaggregation

Species Occurrences Desaggregation
ecospat.plot.niche

Plot Niche
ecospat.plot.mess

Plot MESS
ecospat.testData

Test Data For The Ecospat package
ecospat.testEnvRaster

Test Environmental Rasters for The Ecospat package