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 |

http://www.r-project.org, http://webpages.icav.up.pt/pessoas/ptarroso/phylin/phylin.html, https://github.com/ptarroso/phylin |

**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.

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
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.