A software package to fit ecological null models

Overview

EcoSimR is an open source R version of the EcoSim software project, it is a package to fit null models of ecological data. It 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. Details about the package can be found in the full documentation.

Filing a bug

EcoSimR is still in its early days. If you find a bug please file an issue

Quickstart

install.packages("EcoSimR")

Niche overlap null model

Run the niche overlap model

warbMod <- niche_null_model(dataMacWarb)
summary(warbMod)
## Time Stamp:  Tue Mar 31 22:27:54 2015 
## Reproducible:  FALSE 
## Number of Replications:  1000 
## Elapsed Time:  0.46 secs 
## Metric:  pianka 
## Algorithm:  ra3 
## Observed Index:  0.55514 
## Mean Of Simulated Index:  0.38881 
## Variance Of Simulated Index:  0.0021625 
## Lower 95% (1-tail):  0.32172 
## Upper 95% (1-tail):  0.47547 
## Lower 95% (2-tail):  0.30999 
## Upper 95% (2-tail):  0.49656 
## Lower-tail P =  0.995 
## Upper-tail P =  0.005 
## Observed metric > 995 simulated metrics 
## Observed metric < 5 simulated metrics 
## Observed metric = 0 simulated metrics 
## Standardized Effect Size (SES):  3.5767

Get a standard histogram plot of output

plot(warbMod, type="hist")