mgVarPart: Variation partitioning of the genetic distance matrix

In kkeenan02/memgeneMod: Spatial pattern detection in genetic distance data using Moran's Eigenvector Maps

Description

This function performs a variation partitioning of the genetic distance matrix using the supplied MEM eigenvectors and spatial coordinates. Randomization tests are conducted to determine the significance of the [a] fraction representing the MEM eigenvectors, the [c] fraction representing the spatial coordinates and the [abc] fraction representing the spatial genetic variation. It is called by mgLandscape.

Usage

mgVarPart(genD, vectorsMEM, coords, perm=1000)

Arguments

genD	A symmetrical distance matrix giving the genetic distances among individual genotypes or populations
vectorsMEM	A matrix giving a set of any number of MEM eigenvectors
coords	A two column matrix or data.frame of x and y coordinates of sampling locations of individual genotypes or populations.
perm	The number of permutations to use when testing the significance of the [a], [c] and [abc] fractions.

Details

See mgLandscape for explanation of the fractions.

Author(s)

Pedro Peres-Neto ([e-mail])
Paul Galpern ([e-mail])

Examples

## Not run: 
## Prepare the radial data for analysis
radialData <- read.csv(system.file("extdata/radial.csv", package="memgene"))
radialGen <- radialData[, -c(1,2)]
radialXY <- radialData[, 1:2]

if (require(adegenet)) {
  radialDM <- codomToPropShared(radialGen)
} else {
  stop("adegenent package required to produce genetic distance matrix in example.")
}


## Find MEM eigenvectors given sampling locations
## by first finding the Euclidean distance matrix
radialEuclid <- dist(radialXY)
radialMEM <- mgMEM(radialEuclid)

## Forward select significant MEM eigenvectors using RDA
## Positive MEM eigenvectors (positive spatial autocorrelation) first
radialPositive <- mgForward(radialDM,
    radialMEM$vectorsMEM[ , radialMEM$valuesMEM > 0])
## Negative MEM eigenvectors (negative spatial autocorrelation) second
radialNegative <- mgForward(radialDM,
    radialMEM$vectorsMEM[ , radialMEM$valuesMEM < 0])


## Summarize the selected MEM eigenvectors
allSelected <- cbind(radialMEM$vectorsMEM[, radialMEM$valuesMEM > 0][
                    , na.omit(radialPositive$selectedMEM)],
                 radialMEM$vectorsMEM[, radialMEM$valuesMEM < 0][
                    , na.omit(radialNegative$selectedMEM)])

## Use the selected MEM eigenvectors and coordinates in
## variation partitioning
radialVarPart <- mgVarPart(radialDM, allSelected, radialXY)

## End(Not run)

kkeenan02/memgeneMod documentation built on May 20, 2019, 10:46 a.m.