plotCorr: plot the predicted values against the observed values

In Traitspace: A Predictive Model for Trait Based Community Assembly of Plant Species

Description

Plots the results for each species/site in a separate window and finds the correlation between the predicted and the observed values. Plots the predicted relative abundances against the observed relative abundances (by default) or the predicted species distributions against the observed species distributions if byrow=FALSE.

Usage

plotCorr(result, obs = NULL, byrow = TRUE)

Arguments

result	The output from the traitspace function (class traitspace)
obs	The observed matrix - where, each row corresponds to a site and each column to a species - the order of sites and species should match with the order in which they appear in the predicted matrix. By default, NULL, will generate the observed matrix using the supplied trait data using the trueP function. See the trueP function for details.
byrow	By default, TRUE, will plot the relative abundances. If FALSE, will plot the species distribution.

Value

Traitspace plots.

References

Laughlin, D. C., Joshi, C., Richardson, S. J., Peltzer, D. A., Mason, N. W. H., & Wardle, D. A. (2015). Quantifying multimodal trait distributions improves trait-based predictions of species abundances and functional diversity. Journal of Vegetation Science, 26(1), 45-57.

Laughlin, D. C., Joshi, C., Bodegom, P. M., Bastow, Z. A., & Fule, P. Z. (2012). A predictive model of community assembly that incorporates intraspecific trait variation. Ecology Letters, 15(11), 1291-1299.

See Also

plotComb, plotEach,Traitspace, TraitspaceMod, trueP

Examples

data(spdata)
species<-spdata$species  #species column
trt<-cbind(spdata$t1,spdata$t2) #two traits
env<-spdata$env     #one env gradient
site<-spdata$site   #site information
result1<-Traitspace(species, trt, env, site)
plotCorr(result1)

Example output

Loading required package: permute
Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: 'Traitspace'

The following object is masked from 'package:permute':

    check

** Warning **: the observed relative abundances/species distributions are calculated from the trait data! 
 This may not be the correct value. Please refer to the documentation for details! 

Traitspace documentation built on May 2, 2019, 4:10 a.m.