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ecospat (version 3.5)

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

2,614

Version

3.5

License

GPL

Maintainer

Olivier Broennimann

Last Published

January 31st, 2023

Functions in ecospat (3.5)

ecospat.CCV.communityEvaluation.prob

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

Creates a DataSplitTable for usage in ecospat.ccv.modeling.
ecospat.CommunityEval

Community Evaluation
ecospat.CCV.modeling

Runs indivudual species distribuion models with SDMs or ESMs
ecospat.ESM.threshold

Thresholds for Ensemble of Small Models
ecospat.adj.D2.glm

Calculate An Adjusted D2
ecospat.Epred

Prediction Mean
ecospat.SESAM.prr

SESAM Probability Ranking Rule
ecospat-package

Spatial Ecology Miscellaneous Methods
ecospat.CCV.communityEvaluation.bin

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

Species Co-Occurrences
ecospat.climan

A climate analogy setection tool for the modeling of species distributions
ecospat.calculate.pd

Calculate Phylogenetic Diversity Measures
ecospat.caleval

Calibration And Evaluation Dataset
ecospat.Cscore

Pairwise co-occurrence Analysis with calculation of the C-score index.
ecospat.cohen.kappa

Cohen's Kappa
ecospat.cons_Cscore

Constrained Co-Occurrence Analysis.
ecospat.cv.rf

RandomForest Cross Validation
ecospat.grid.clim.dyn

Dynamic Occurrence Densities Grid
ecospat.ESM.VarContrib

Variable contribution in ESM
ecospat.ESM.responsePlot

Produce response plots for ESMs
ecospat.niche.similarity.test

Niche Similarity Test
ecospat.cv.gbm

GBM Cross Validation
ecospat.niche.zProjGeo

Projection of Occurrence Densities to the Geography
ecospat.cor.plot

Correlation Plot
ecospat.margin

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

Make Data Frame
ecospat.mantel.correlogram

Mantel Correlogram
ecospat.ESM.EnsembleEvaluation

Ensemble of Small Models: Evaluation via the Pooling procedure
ecospat.max.kappa

Maximum Kappa
ecospat.nichePOSNB

Niche position and niche breadth)
ecospat.nicheNBmean

Niche position and niche breadth)
ecospat.npred

Number Of Predictors
ecospat.occ.desaggregation

Species Occurrences Desaggregation
ecospat.binary.model

Generate Binary Models
ecospat.niche.dyn.index

Niche Expansion, Stability, and Unfilling
ecospat.niche.dynIndexProjGeo

Projection of niche dynamic indices to the Geography
ecospat.boyce

Calculate Boyce Index
ecospat.testData

Test Data For The Ecospat package
ecospat.shift.centroids

Draw Centroid Arrows
ecospat.niche.equivalency.test

Niche Equivalency Test
ecospat.niche.overlap

Calculate Niche Overlap
ecospat.plot.tss

Plot True skill statistic (TSS)
ecospat.plot.mess

Plot MESS
ecospat.plot.niche

Plot Niche
ecospat.ESM.EnsembleProjection

Ensemble of Small Models: Projects Calibrated ESMs Into New Space Or Time.
ecospat.ESM.Modeling

Ensemble of Small Models: Calibration of Simple Bivariate Models
ecospat.ESM.EnsembleModeling

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

Test Data For The Niche Overlap Analysis
ecospat.testNiche.inv

Test Data For The Niche Dynamics Analysis In The Invaded Range Of A Hypothetical Species
ecospat.rcls.grd

Reclassifying grids function
ecospat.testEnvRaster

Test Environmental Rasters for The Ecospat package
ecospat.testMdr

Test Data For The ecospat.mdr function
ecospat.poolingEvaluation

Evaluation of species distribution models using the pooling procedure
ecospat.plot.overlap.test

Plot Overlap Test
ecospat.plot.niche.dyn

Niche Categories and Species Density
ecospat.max.tss

Maximum TSS
ecospat.cv.me

Maxent Cross Validation
ecospat.cv.glm

GLM Cross Validation
ecospat.ESM.Projection

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

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

Random Ecologically Stratified Sampling of propotional numbers
ecospat.maxentvarimport

Maxent Variable Importance
ecospat.meva.table

Model Evaluation For A Given Threshold Value
ecospat.testNichePOSNB

Test AVS Dataset For The Ecospat package
ecospat.mdr

Minimum Dispersal Routes)
ecospat.rand.pseudoabsences

Sample Pseudo-Absences
ecospat.permut.glm

GLM Permutation Function
ecospat.mess

MESS
ecospat.occupied.patch

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

Plot Variables Contribution
ecospat.mpa

Minimal Predicted Area
ecospat.plot.kappa

Plot Kappa
ecospat.recstrat_regl

Random Ecologically Stratified Sampling of equal numbers
ecospat.sample.envar

Sample Environmental Variables
ecospat.rangesize

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

Test Tree For The Ecospat package
ecospat.varpart

Variation Partitioning For GLM Or GAM