Traitspace: Traitspace Model

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

Description

Implements a predictive model of community assembly called the Traitspace.

Usage

Traitspace(level_1, level_2, level_3, site, N = 100, linear = FALSE)

Arguments

level_1	The data column containing species names.
level_2	The data column/s containing the trait values for one/multiple traits. One column per trait.
level_3	The data column/s containing the value of the enviroment gradient/s. One column per gradient.
site	The data column containing names of the sites
N	Size of the simulated trait sample per site
linear	Determines whether the trait-environment regression model is linear or quadratic. By default, FALSE, i.e. fits a quadratic model by default.

Value

A list which is an object of the 'traitspace' class.

r.squared TE	The R-squared values for the Trait environment relgression models fitted in step 1A. A separate model is fitted for each trait.
BIC_TS	The BIC value for the best gaussian mixture model fitted (using package mclust) for each species in step 1B.
Predicted relative abundances	A matrix containing the predicted relative abundances
Predicted species distribution	A matrix containing the predicted species distribution

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

Traitspace, TraitspaceMod

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)
result1

Example output

Loading required package: permute
Loading required package: mclust
Package 'mclust' version 5.3
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! 
$r.squard_TE
$r.squard_TE[[1]]
[1] 0.9332171

$r.squard_TE[[2]]
[1] 0.7778034


$BIC_TS
$BIC_TS[[1]]
[1] 23.15617

$BIC_TS[[2]]
[1] 64.1483

$BIC_TS[[3]]
[1] 125.2897

$BIC_TS[[4]]
[1] 104.5073

$BIC_TS[[5]]
[1] 100.8812

$BIC_TS[[6]]
[1] 146.4007


Predicted relative abundances: 
          S1      S2      S3      S4      S5      S6
-3   0.95334 0.04666 0.00000 0.00000 0.00000 0.00000
-1.5 0.01512 0.91756 0.06674 0.00058 0.00000 0.00000
0    0.00011 0.03949 0.63807 0.20099 0.12133 0.00000
1.5  0.00000 0.00023 0.00597 0.11476 0.83131 0.04772
3    0.00000 0.00000 0.00000 0.00530 0.33823 0.65648
Predicted species distributions: 
          S1      S2      S3      S4      S5      S6
-3   0.98376 0.04518 0.00000 0.00000 0.00000 0.00000
-1.5 0.01613 0.91862 0.10224 0.00200 0.00000 0.00000
0    0.00011 0.03599 0.88958 0.62879 0.09474 0.00000
1.5  0.00000 0.00020 0.00817 0.35238 0.63710 0.06565
3    0.00000 0.00000 0.00000 0.01682 0.26816 0.93435

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