memgene (version 1.0.2)

mgMEM: Extraction of MEM eigenvectors given distances among sampling locations

Description

Extract MEM eigenvectors given a distance matrix among sampling locations of genetic material. This matrix could be Euclidean or otherwise. If truncation and/or transformation parameters are provided these operations occur. Truncation implies that distances that exceed a threshold amount are assigned to 4 * threshold. Minimum spanning tree truncation is the recommended default. Transformation performs an exponential or gaussian transformation of the distance matrix after truncation.

Usage

mgMEM(locD, truncation = NULL, transformation = NULL)

Arguments

locD

A symmetric distance matrix giving the distances (typically Euclidean) among the sampling locations of genetic material (e.g. of genotyped individuals or populations).

truncation

See details (EXPERIMENTAL)

transformation

Can be character "exponential" or "gaussian" or NULL for no transformation (EXPERIMENTAL)

Value

A list $valuesMEM gives the eigenvalues all MEM eigenvectors $vectorsMEM gives the MEM eigenvectors in columns

Details

If sampling locations are in longitude/latitude and are far apart, be sure to supply the geodesic distance as locD. (Note that mgQuick implements geodesic distances using the longlat=TRUE parameter when provided with sampling coordinates)

truncation

1. Can be numeric from 0 to 1 specifying the proportion of the maximum distance in locD to truncate following this a spanning tree is used to further truncate as in PCNM (aka dbMEM or classical MEM)

2. Can be NULL (default) indicating only the minimum spanning tree (MST) truncation where links that exceed the longest link in the MST (dMST) are replaced with 4 * dMST

3. Can be FALSE indicating that nothing is done to the distance matrix which is only suitable when locD is non-euclidean (i.e. will have negative eigenvectors

References

Legendre, P., and Legendre L. 2012. Numerical Ecology, 3rd. ed. Elsevier, Amsterdam.

Examples

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

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

# }