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ecospat (version 2.0)

Spatial Ecology Miscellaneous Methods

Description

Colection 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

1,848

Version

2.0

License

GPL

Maintainer

Valeria Di Cola

Last Published

May 26th, 2016

Functions in ecospat (2.0)

ecospat.binary.model

Generate Binary Models
ecospat.boyce

Calculate Boyce Index
ecospat.cv.gbm

GBM Cross Validation
ecospat.cor.plot

Correlation Plot
ecospat.ESM.EnsembleModeling

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

Package Environment
ecospat.cv.me

Maxent Cross Validation
ecospat.cv.glm

GLM Cross Validation
ecospat.cv.example

Cross Validation Example Function
ecospat.cv.rf

RandomForest Cross Validation
ecospat.Epred

Prediction Mean
ecospat.ESM.EnsembleProjection

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

Make Data Frame
ecospat.max.tss

Maximum TSS
ecospat.mantel.correlogram

Mantel Correlogram
ecospat.maxentvarimport

Maxent Variable Importance
ecospat.ESM.Projection

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

MESS
ecospat.ESM.Modeling

Ensamble of Small Models: Calibration of Simple Bivariate Models
ecospat.exdet

An EXtrapolation DETection Tool For The Modeling Of Species Distributions
ecospat.grid.clim.dyn

Dynamic Occurrence Densities Grid
ecospat.max.kappa

Maximum Kappa
ecospat.mpa

Minimal Predicted Area
ecospat.niche.similarity.test

Niche Similarity Test
ecospat.niche.dyn.index

Niche Expansion, Stability, and Unfilling
ecospat.npred

Number Of Predictors
ecospat.occ.desaggregation

Species Occurrences Desaggregation
ecospat.permut.glm

GLM Permutation Function
ecospat.niche.equivalency.test

Niche Equivalency Test
ecospat.niche.overlap

Calculate Niche Overlap
ecospat.meva.table

Model Evaluation For A Given Threshold Value
ecospat.migclim

Implementing Dispersal Into Species Distribution Models
ecospat.plot.tss

Plot True skill statistic (TSS)
ecospat.rand.pseudoabsences

Sample Pseudo-Absences
ecospat.plot.contrib

Plot Variables Contribution
ecospat.plot.kappa

Plot Kappa
ecospat.plot.niche.dyn

Niche Categories and Species Density
ecospat.plot.mess

Plot MESS
ecospat.plot.overlap.test

Plot Overlap Test
ecospat.plot.niche

Plot Niche
ecospat.sample.envar

Sample Environmental Variables
ecospat.SESAM.prr

SESAM Probability Ranking Rule
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.shift.centroids

Draw Centroid Arrows
ecospat.testData

Test Data For The Ecospat package
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.cons_Cscore

Constrained Co-Occurrence Analysis.
ecospat.caleval

Calibration And Evaluation Dataset
ecospat.varpart

Variation Partitioning For GLM Or GAM
ecospat-package

Spatial Ecology Miscellaneous Methods
ecospat.adj.D2.glm

Calculate An Adjusted D2
ecospat.co_occurrences

Species Co-Occurrences
ecospat.cohen.kappa

Cohen's Kappa
ecospat.calculate.pd

Calculate Phylogenetic Diversity Measures
ecospat.CommunityEval

Community Evaluation