msr.varipart: Moran spectral randomization for variation partitioning

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/msr.varipart.R

Description

The functions allows to evaluate the significance and estimate parts in variation partitioning using Moran Spectral Randomization (MSR) as a spatially-constrained null model to account for spatial autocorrelation in table X. Hence, this function provides a variation partioning adujsted for spurious correlation due to spatial autocorrelation in both the response and one explanatory matrix.

Usage

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## S3 method for class 'varipart'
msr(x, listwORorthobasis, nrepet = x$test$rep[1],
  method = c("pair", "triplet", "singleton"), ...)

Arguments

x

An object generated by the varipart function.

listwORorthobasis

an object of the class listw (spatial weights) created by the functions of the spdep package or an object of class orthobasis

nrepet

an integer indicating the number of replicates

method

an character specifying which algorithm should be used to produce spatial replicates (see codemsr.default).

...

further arguments of the codemsr.default function.

Details

The function corrects the biases due to spatial autocorrelation by using MSR procedure to produce environmental predictors that preserve the spatial autocorrelation and the correlation structures of the original environmental variables while being generated independently of species distribution.

Value

An object of class varipart randomized replicates.

Author(s)

(s) Stephane Dray [email protected] and Sylvie Clappe [email protected]

References

Sylvie Clappe, Stephane Dray and Pedro R. Peres-Neto (in preparation) Beyond neutrality: using a null model to disentangle the effects of niche dynamics and spurious correlations in variation partitioning.

Wagner, H. H., and S. Dray, 2015. Generating spatially constrained null models for irregularly spaced data using Moran spectral randomization methods. Methods in Ecology and Evolution 6:1169–1178.

See Also

msr.default, varipart

Examples

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library(ade4)
library(spdep)
data(mafragh)
## Performing standard variation partitioning
dudiY <- dudi.pca(mafragh$flo, scannf = FALSE, scale = FALSE)
mafragh.lw <- nb2listw(mafragh$nb)
me <- mem(mafragh.lw, MEM.autocor = "positive")
vprda <- varipart(dudiY, mafragh$env, me, type = "parametric")

## Adjust estimation and compute p-value by msr methods
vprda.msr <- msr(vprda, mafragh.lw, nrepet=99)
vprda.msr

Example output

Attaching package: 'ade4'

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

    multispati

Loading required package: sp
Loading required package: Matrix

Attaching package: 'spdep'

The following object is masked from 'package:ade4':

    mstree

$test
Monte-Carlo test
Call: msr.varipart(x = vprda, listwORorthobasis = mafragh.lw, nrepet = 99)

Observation: 0.2366554 

Based on 99 replicates
Simulated p-value: 0.02 
Alternative hypothesis: greater 

     Std.Obs  Expectation     Variance 
2.6216833285 0.1742386390 0.0005668156 

$R2
         a          b          c          d 
0.06295763 0.17369775 0.42438794 0.33895668 

$R2.adj.msr
         a          b          c          d 
-0.0139170  0.0895039  0.2565338  0.6678793 

attr(,"class")
[1] "varipart" "list"    

adespatial documentation built on May 23, 2018, 5:04 p.m.