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ecospat (version 3.0)

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

2,588

Version

3.0

License

GPL

Maintainer

Olivier Broennimann

Last Published

June 27th, 2018

Functions in ecospat (3.0)

A climate analogy setection tool for the modeling of species distributions

ecospat.ESM.Modeling

Ensamble of Small Models: Calibration of Simple Bivariate Models

ecospat.niche.similarity.test

Niche Similarity Test

ecospat.migclim

Implementing Dispersal Into Species Distribution Models

ecospat.recstrat_regl

Random Ecologically Stratified Sampling of equal numbers

ecospat.niche.overlap

Calculate Niche Overlap

ecospat.max.kappa

GLM Cross Validation

GBM Cross Validation

ecospat.niche.equivalency.test

Niche Equivalency Test

ecospat.niche.dynIndexProjGeo

Projection of niche dynamic indices to the Geography

ecospat.cv.example

Cross Validation Example Function

ecospat.plot.mess

ecospat.plot.kappa

ecospat.mantel.correlogram

Mantel Correlogram

ecospat.SESAM.prr

SESAM Probability Ranking Rule

ecospat.testNiche.nat

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

ecospat.testTree

Test Tree For The Ecospat package

ecospat.sample.envar

Sample Environmental Variables

ecospat.rcls.grd

Reclassifying grids function

ecospat.cons_Cscore

Constrained Co-Occurrence Analysis.

Package Environment

Maxent Cross Validation

ecospat.niche.zProjGeo

Projection of Occurrence Densities to the Geography

ecospat.recstrat_prop

Random Ecologically Stratified Sampling of propotional numbers

Number Of Predictors

ecospat.grid.clim.dyn

Dynamic Occurrence Densities Grid

ecospat.cor.plot

Correlation Plot

ecospat.makeDataFrame

Make Data Frame

ecospat.cohen.kappa

Minimum Dispersal Routes)

Minimal Predicted Area

ecospat.rand.pseudoabsences

Sample Pseudo-Absences

ecospat.co_occurrences

Species Co-Occurrences

ecospat.niche.dyn.index

Niche Expansion, Stability, and Unfilling

ecospat.rangesize

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

ecospat.occ.desaggregation

Species Occurrences Desaggregation

ecospat.max.tss

ecospat.maxentvarimport

Maxent Variable Importance

ecospat.testEnvRaster

Test Environmental Rasters for The Ecospat package

ecospat.plot.niche

ecospat.permut.glm

GLM Permutation Function

ecospat.occupied.patch

Extract occupied patches of a species in geographic space.)

ecospat.plot.contrib

Plot Variables Contribution

ecospat.testMdr

Test Data For The ecospat.mdr function

ecospat.plot.niche.dyn

Niche Categories and Species Density

ecospat.shift.centroids

Draw Centroid Arrows

ecospat.plot.overlap.test

Plot Overlap Test

ecospat.plot.tss

Plot True skill statistic (TSS)

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.testData

Test Data For The Ecospat package

ecospat.varpart

Variation Partitioning For GLM Or GAM

ecospat-package

Spatial Ecology Miscellaneous Methods

ecospat.CommunityEval

Community Evaluation

ecospat.CCV.modeling

Runs indivudual species distribuion models with SDMs or ESMs

ecospat.CCV.communityEvaluation.bin

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

ecospat.ESM.EnsembleProjection

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

ecospat.adj.D2.glm

Calculate An Adjusted D2

ecospat.binary.model

Generate Binary Models

ecospat.CCV.communityEvaluation.prob

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

ecospat.caleval

Calibration And Evaluation Dataset

Prediction Mean

ecospat.CCV.createDataSplitTable

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

RandomForest Cross Validation

ecospat.meva.table

Model Evaluation For A Given Threshold Value

ecospat.ESM.Projection

Ensamble of Small Models: Projects Simple Bivariate Models Into New Space Or Time

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

ecospat.ESM.VarContrib

Variable contribution in ESM

ecospat.ESM.EnsembleModeling

Ensamble of Small Models: Evaluates and Averages Simple Bivariate Models To ESMs

Calculate Boyce Index

ecospat.calculate.pd

Calculate Phylogenetic Diversity Measures