NicheBarcoding (version 1.0)

spe.mantel.test: Mantel test between interspecific pairwise genetic distance and ecological distance

Description

Determine the independence between genetic distance and ecological distance for a reference dataset at the level of species.

Usage

spe.mantel.test(
  fas,
  dna.model = "raw",
  ecol.dist.method = "euclidean",
  mantel.method = "spearman",
  permutations = 999,
  en.vir = NULL
)

Arguments

fas

DNAbin, reference dataset containing sample IDs, taxon information, longitude and latitude, and barcode sequences of samples.

dna.model

Character, specifying the evolutionary model to be used; must be one of "raw" (default), "N", "TS", "TV", "JC69", "K80", "F81", "K81", "F84", "BH87", "T92", "TN93", "GG95", "logdet", "paralin", "indel", or "indelblock".

ecol.dist.method

Character, distance measure to be used; must be one of "euclidean" (default), "maximum", "manhattan", "canberra", "binary" or "minkowski".

mantel.method

Character, correlation method, as accepted by cor: "pearson","spearman" (default) or "kendall".

permutations

Numeric, the number of permutations required.

en.vir

RasterBrick, the global bioclimate data output from "raster::getData" function.

Value

The Mantel statistic.

The empirical significance level from permutations.

A matrix of interspecific pairwise genetic distance.

A matrix of interspecific pairwise ecological distance.

References

Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Can. Res. 27:209-220.

Oksanen J., F.G. Blanchet, M. Friendly, R. Kindt, P. Legendre, D. McGlinn, P.R. Minchin, R.B. O'Hara, G.L. Simpson, P. Solymos, M.H.H. Stevens, E. Szoecs and H Wagner. 2016. vegan: Community Ecology Package https://CRAN.R-project.org/package=vegan. r package version 2.5-6.

Examples

# NOT RUN {
data(en.vir)
#envir<-raster::getData("worldclim",download=FALSE,var="bio",res=2.5)
#en.vir<-raster::brick(envir)

library(ape)
data(LappetMoths)
ref.seq<-LappetMoths$ref.seq

spe.mantel<-spe.mantel.test(fas=ref.seq,en.vir=en.vir)
spe.mantel$MantelStat.r
spe.mantel$p.value
# }