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ecospat (version 2.1.1)

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) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.

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Version

Install

install.packages('ecospat')

Monthly Downloads

1,921

Version

2.1.1

License

GPL

Maintainer

Valeria Di Cola

Last Published

November 2nd, 2016

Functions in ecospat (2.1.1)

ecospat.cohen.kappa

ecospat.caleval

Calibration And Evaluation Dataset

ecospat.cons_Cscore

Constrained Co-Occurrence Analysis.

ecospat.calculate.pd

Calculate Phylogenetic Diversity Measures

ecospat.binary.model

Generate Binary Models

ecospat.adj.D2.glm

Calculate An Adjusted D2

ecospat-package

Spatial Ecology Miscellaneous Methods

Calculate Boyce Index

ecospat.CommunityEval

Community Evaluation

ecospat.co_occurrences

Species Co-Occurrences

ecospat.cv.example

Cross Validation Example Function

RandomForest Cross Validation

Prediction Mean

Package Environment

GBM Cross Validation

ecospat.cor.plot

Correlation Plot

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

GLM Cross Validation

Maxent Cross Validation

ecospat.ESM.EnsembleModeling

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

ecospat.maxentvarimport

Maxent Variable Importance

ecospat.grid.clim.dyn

Dynamic Occurrence Densities Grid

ecospat.max.tss

ecospat.max.kappa

ecospat.ESM.Projection

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

ecospat.makeDataFrame

Make Data Frame

ecospat.ESM.EnsembleProjection

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

ecospat.ESM.Modeling

Ensamble of Small Models: Calibration of Simple Bivariate Models

ecospat.mantel.correlogram

Mantel Correlogram

An EXtrapolation DETection Tool For The Modeling Of Species Distributions

Minimal Predicted Area

ecospat.niche.dyn.index

Niche Expansion, Stability, and Unfilling

ecospat.meva.table

Model Evaluation For A Given Threshold Value

ecospat.migclim

Implementing Dispersal Into Species Distribution Models

ecospat.niche.overlap

Calculate Niche Overlap

ecospat.niche.similarity.test

Niche Similarity Test

Number Of Predictors

ecospat.occ.desaggregation

Species Occurrences Desaggregation

ecospat.niche.equivalency.test

Niche Equivalency Test

ecospat.plot.mess

ecospat.plot.kappa

ecospat.plot.niche

ecospat.plot.niche.dyn

Niche Categories and Species Density

ecospat.plot.overlap.test

Plot Overlap Test

ecospat.plot.tss

Plot True skill statistic (TSS)

ecospat.permut.glm

GLM Permutation Function

ecospat.plot.contrib

Plot Variables Contribution

ecospat.rand.pseudoabsences

Sample Pseudo-Absences

ecospat.rcls.grd

Reclassifying grids function

ecospat.testTree

Test Tree For The Ecospat package

ecospat.testNiche.nat

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

ecospat.SESAM.prr

SESAM Probability Ranking Rule

ecospat.sample.envar

Sample Environmental Variables

ecospat.shift.centroids

Draw Centroid Arrows

ecospat.testData

Test Data For The Ecospat package

ecospat.testNiche.inv

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

ecospat.testNiche

Test Data For The Niche Overlap Analysis

ecospat.varpart

Variation Partitioning For GLM Or GAM

ecospat.recstrat_prop

Random Ecologically Stratified Sampling of propotional numbers

ecospat.recstrat_regl

Random Ecologically Stratified Sampling of equal numbers