phylin: Spatial Interpolation of Genetic Data

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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.

Author
Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Date of publication
2015-11-04 02:00:17
Maintainer
Pedro Tarroso <ptarroso@cibio.up.pt>
License
GPL (>= 2)
Version
1.1.1
URLs

View on CRAN

Man pages

d.gen
Genetic distance matrix between vipers and lineages.
extract.var
Extact pairwise values from a matrix in a specified order.
gen.variogram
Semi-variogram with the genetic distance matrix
grid
Grid centroids for the Iberian Peninsula.
grid.image
Simple plot of interpolated grid.
gv.model
Fit a model to the semi-variogram.
idw
Inverse Distance Weighting interpolation
intgen.idw
Interpolation of genetic distances to a a grid of points.
krig
Simple and ordinary kriging.
midpoints
Midpoints between pairs of coordinates
mpinv
Generalized inverse of a matrix
mtest.gv
Tests if a 'gv' object has a model.
multispecies
Summarizes data from multiple species.
phylin-package
Phylogenetic Landscape Interpolation.
plot.gv
Plot a 'gv' object
predict.gv
Predict method for 'gen.variogram' object with model.
real.dist
Real distance matrix for samples and interpolation locations.
summary.gv
Summary for 'gv' object
vipers
Vipers sample locations for 'd.gen' dataset.

Files in this package

phylin
phylin/inst
phylin/inst/doc
phylin/inst/doc/phylin_tutorial.R
phylin/inst/doc/phylin_tutorial.pdf
phylin/inst/doc/phylin_tutorial.Snw
phylin/NAMESPACE
phylin/data
phylin/data/d.gen.rda
phylin/data/vipers.rda
phylin/data/grid.rda
phylin/R
phylin/R/predict.gv.R
phylin/R/extract.val.R
phylin/R/midpoints.R
phylin/R/gen.variogram.single.R
phylin/R/gen.variogram.R
phylin/R/gv.model.R
phylin/R/plot.gv.R
phylin/R/mpinv.R
phylin/R/gen.variogram.multi.R
phylin/R/plot.gv_WITHMULTI.R
phylin/R/krig.R
phylin/R/summary.gv.R
phylin/R/real.dist.R
phylin/R/grid.image.R
phylin/R/idw.R
phylin/R/multispecies.R
phylin/R/intgen.idw.R
phylin/R/mtest.gv.R
phylin/vignettes
phylin/vignettes/references.bib
phylin/vignettes/phylin_tutorial.Snw
phylin/MD5
phylin/build
phylin/build/vignette.rds
phylin/DESCRIPTION
phylin/man
phylin/man/real.dist.Rd
phylin/man/idw.Rd
phylin/man/multispecies.Rd
phylin/man/d.gen.Rd
phylin/man/summary.gv.Rd
phylin/man/predict.gv.Rd
phylin/man/krig.Rd
phylin/man/midpoints.Rd
phylin/man/mpinv.Rd
phylin/man/mtest.gv.Rd
phylin/man/phylin-package.Rd
phylin/man/grid.Rd
phylin/man/intgen.idw.Rd
phylin/man/extract.var.Rd
phylin/man/gv.model.Rd
phylin/man/grid.image.Rd
phylin/man/gen.variogram.Rd
phylin/man/vipers.Rd
phylin/man/plot.gv.Rd