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EcoSimR (version 0.1.0)

Null Model Analysis for Ecological Data

Description

Given a site by species interaction matrix, users can make inferences about species interactions by performance hypothesis comparing test statistics against a null distribution. The current package provides algorithms and metrics for niche-overlap, body size ratios and species co-occurrence. Users can also integrate their own algorithms and metrics within these frameworks or completely novel null models. Detailed explanations about the underlying assumptions of null model analysis in ecology can be found at http://ecosimr.org.

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Version

Install

install.packages('EcoSimR')

Monthly Downloads

17

Version

0.1.0

License

MIT + file LICENSE

Maintainer

Last Published

April 3rd, 2015

Functions in EcoSimR (0.1.0)

czekanowski_var

CzekanowskiVariance Niche Overlap Metric

RA4 Niche Overlap Randomization Algorithm

RA3 Niche Overlap Randomization Algorithm

SchlutersVRatio Co-occurrence Metric

Sim2 Co-occurrence Randomization Algorithm

summary.coocnullmod

Generic function for calculating null model summary statistics.

cooc_null_model

Co-Occurrence Null model

RA1 Niche Overlap Randomization Algorithm

Czekanowski Niche Overlap Metric

RA2 Niche Overlap Randomization Algorithm

plot a histogram null model

VarRatio Size Overlap Ratio Metric

Sim6 Co-occurrence Randomization Algorithm

PiankaVariance Niche Overlap Metric

CScore Co-occurrence Metric

Sim10 Co-occurrence Randomization Algorithm

SizeGamma Size Overlap Randomization Algorithm

SizeUniform Size Overlap Randomization Algorithm

Sim4 Co-occurrence Randomization Algorithm

West Indian Finches data This data frame is a binary presence-absence matrix for West Indies finches (Fringillidae). Each row is a different species of finch and each column is one of the 19 major islands in the West Indies. Entries indicate the presence (1) or absence (0) of a species on an island. Data from Gotelli and Abele (1982).

EcoSimR EcoSimR is a collection of functions for calculating community metrics and algorithms for randomizing community data for null model analysis. Current modules are included for the analysis of niche overlap, body size overlap, and species co-occurrence. EcoSimR also allows users to define their own functions and algorithms to develop new null models.

plot.nichenullmod

Niche Null Model Plot function

summary.nichenullmod

Generic function for calculating null model summary statistics

MacArthur's (1958) warbler data This data matrix is from MacArthur's classic (1958) paper on the coexistence of 5 species of New England warbler. Each row of the data matrix is a different species of warbler, and each column is one of 16 different subregions of a coniferous tree. Each entry is the percentage of time that each species was observed foraging in a different subregion of the tree (see Figures 2-4 in MacArthur 1958). Zeroes indicate subregions of the tree in which a species was not recorded foraging.

Checker Co-occurrence Metric

MinDiff Size Overlap Metric

Sim5 Co-occurrence Randomization Algorithm

summary.sizenullmod

Generic function for calculating null model summary statistics

Sim1 Co-occurrence Randomization Algorithm

CScoreVariance Co-occurrence Metric

summary.nullmod

Generic function for calculating null model summary statistics

plot.coocnullmod

Co-Occurrence Model Plot Function

size_uniform_user

SizeUser Size Overlap Randomization Algorithm

Sim3 Co-occurrence Randomization Algorithm

MinRatio Size Overlap Ratio Metric

Desert rodent data set This data vector is from Brown's (1975) study of the coexistence of desert rodent species. Each entry is the average adult body mass in grams of six co-occurring species of Sonoran Desert rodents.

reproduce_model

Reproduce a result

Sim9 Co-occurrence Randomization Algorithm

size_null_model

plot.sizenullmod

Size Ratio Plot Function

Pianka Niche Overlap Metric

czekanowski_skew

CzekanowskiSkew Niche Overlap Metric

niche_null_model

Niche overlap null models

PiankaSkew Niche Overlap Metric

Sim7 Co-occurrence Randomization Algorithm

Random Matrix Generator

size_source_pool

SizeSourcePoolDraw Size Overlap Randomization Algorithm

VarDiff Size Overlap Ratio Metric

CScoreSkew Co-occurrence Metric

null_model_engine

Sim8 Co-occurrence Randomization Algorithm

Vector Sample Function

SpeciesCombo Co-occurrence Metric