| phylin-package {phylin} | R Documentation |
Phylogenetic Landscape Interpolation.
Description
This package provides functions for the spatial interpolation of genetic distances between samples. The interpolation is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.
Details
| Package: | phylin |
| Type: | Package |
| Version: | 2.0 |
| Date: | 2016-04-27 |
| License: | GPL-2 |
The kriging algorithm uses a model fitted to the semi-variogram to weight the values of the samples. Here the variogram was modified to fit a model with pairwise comparison between genetic and real distances, describing the spatial dependence in the genetic distance between samples. A map for the lineage can be generated using only a vector that define if each point belong to the a lineage or not.
Since version 2.0, the kriging interpolation can be performed taking into consideration a cost distance instead of simple geographical distances between points. This can help in cases where a landscape resistance explains better the genetic distances between samples than the geographic distances alone.
The IDW can be used to interpolate the genetic distance of each sample against the others, or to interpolate genetic diverge at midpoints between samples. The interpolated value at certain location is obtained by weighting with the distances to the avaialable samples. Similarly to kriging, these distance can be based on a cost distance calculation.
Author(s)
Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Maintainer: Pedro Tarroso <ptarroso@cibio.up.pt>
References
Tarroso, P., Velo-Anton, G., & Carvalho, S.B. (2015). PHYLIN: an R package for phylogeographic interpolation. Molecular Ecology Resources, 15(2), 349-357.
Tarroso, P., Carvalho, S.B. & Velo-Anton, G. (2019). PHYLIN 2.0: Extending the phylogeographic interpolation method to include uncertainty and user-defined distance metrics. Molecular Ecology Resources, in press.
Examples
## See examples for the included functions.