Learn R Programming

phylin (version 2.0.2)

Spatial Interpolation of Genetic Data

Description

The spatial interpolation of genetic distances between samples 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.

Copy Link

Version

Install

install.packages('phylin')

Monthly Downloads

183

Version

2.0.2

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Maintainer

Pedro Tarroso

Last Published

December 12th, 2019

Functions in phylin (2.0.2)

grid.image

Simple plot of interpolated grid.
krig

Simple and ordinary kriging.
intgen.idw

Interpolation of genetic distances to a a grid of points.
grid

Grid centroids for the Iberian Peninsula.
plot.gv

Plot a 'gv' object
phylin-package

Phylogenetic Landscape Interpolation.
vipers

Vipers sample locations for 'd.gen' dataset.
d.gen

Genetic distance matrix between vipers and lineages.
predict.gv

Predict method for 'gen.variogram' object with model.
extract.val

Extact pairwise values from a matrix in a specified order.
print.gv

Prints details of a 'gv' object
gv.model

Fit a model to the semi-variogram.
idw

Inverse Distance Weighting interpolation
mtest.gv

Tests if a 'gv' object has a model.
gen.variogram

Semi-variogram with the genetic distance matrix
geo.dist

Geographical distance matrix for samples and interpolation locations.
multispecies

Summarizes data from multiple species.
simul.sample

Random samples from simulation.
simul.env

Simulated environments.
midpoints

Midpoints between pairs of coordinates
summary.gv

Summary for 'gv' object
simul.gen.dist

Simulated genetic distances.
mpinv

Generalized inverse of a matrix