# Null Model Analysis for Ecological Data

## Documentation for package ‘EcoSimR’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

EcoSimR-package | 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.
checker | Checker Co-occurrence Metric
cooc_null_model | Co-Occurrence Null model
czekanowski | Czekanowski Niche Overlap Metric
czekanowski_skew | CzekanowskiSkew Niche Overlap Metric
czekanowski_var | CzekanowskiVariance Niche Overlap Metric
c_score | CScore Co-occurrence Metric
c_score_skew | CScoreSkew Co-occurrence Metric
c_score_var | CScoreVariance Co-occurrence Metric
dataMacWarb | 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.
dataRodents | 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.
dataWiFinches | 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 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.
min_diff | MinDiff Size Overlap Metric
min_ratio | MinRatio Size Overlap Ratio Metric
niche_null_model | Niche overlap null models
null_model_engine | Run null model
pianka | Pianka Niche Overlap Metric
pianka_skew | PiankaSkew Niche Overlap Metric
pianka_var | PiankaVariance Niche Overlap Metric
plot.coocnullmod | Co-Occurrence Model Plot Function
plot.nichenullmod | Niche Null Model Plot function
plot.nullmod | plot a histogram null model
plot.sizenullmod | Size Ratio Plot Function
ra1 | RA1 Niche Overlap Randomization Algorithm
ra2 | RA2 Niche Overlap Randomization Algorithm
ra3 | RA3 Niche Overlap Randomization Algorithm
ra4 | RA4 Niche Overlap Randomization Algorithm
ranMatGen | Random Matrix Generator
reproduce_model | Reproduce a result
sim1 | Sim1 Co-occurrence Randomization Algorithm
sim10 | Sim10 Co-occurrence Randomization Algorithm
sim2 | Sim2 Co-occurrence Randomization Algorithm
sim3 | Sim3 Co-occurrence Randomization Algorithm
sim4 | Sim4 Co-occurrence Randomization Algorithm
sim5 | Sim5 Co-occurrence Randomization Algorithm
sim6 | Sim6 Co-occurrence Randomization Algorithm
sim7 | Sim7 Co-occurrence Randomization Algorithm
sim8 | Sim8 Co-occurrence Randomization Algorithm
sim9 | Sim9 Co-occurrence Randomization Algorithm
sim9_single | sim9_single
size_gamma | SizeGamma Size Overlap Randomization Algorithm
size_null_model | Size Ratio
size_source_pool | SizeSourcePoolDraw Size Overlap Randomization Algorithm
size_uniform | SizeUniform Size Overlap Randomization Algorithm
size_uniform_user | SizeUser Size Overlap Randomization Algorithm
species_combo | SpeciesCombo Co-occurrence Metric
summary.coocnullmod | Generic function for calculating null model summary statistics.
summary.nichenullmod | Generic function for calculating null model summary statistics
summary.nullmod | Generic function for calculating null model summary statistics
summary.sizenullmod | Generic function for calculating null model summary statistics
var_diff | VarDiff Size Overlap Ratio Metric
var_ratio | VarRatio Size Overlap Ratio Metric
vector_sample | Vector Sample Function
v_ratio | SchlutersVRatio Co-occurrence Metric