Package: phylin 2.0.2

phylin: Spatial Interpolation of Genetic Data

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.

Authors:Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho

phylin_2.0.2.tar.gz
phylin_2.0.2.zip(r-4.7-any)phylin_2.0.2.zip(r-4.6-any)phylin_2.0.2.zip(r-4.5-any)
phylin_2.0.2.tgz(r-4.6-any)phylin_2.0.2.tgz(r-4.5-any)
phylin_2.0.2.tar.gz(r-4.7-any)phylin_2.0.2.tar.gz(r-4.6-any)
phylin_2.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
phylin/json (API)

# Install 'phylin' in R:
install.packages('phylin', repos = c('https://ptarroso.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ptarroso/phylin/issues

Datasets:
  • d.gen - Genetic distance matrix between vipers and lineages.
  • grid - Grid centroids for the Iberian Peninsula.
  • simul.env - Simulated environments.
  • simul.gen.dist - Simulated genetic distances.
  • simul.sample - Random samples from simulation.
  • vipers - Vipers sample locations for 'd.gen' dataset.

On CRAN:

Conda:

3.06 score 57 scripts 262 downloads 1 mentions 16 exports 0 dependencies

Last updated from:6e407da85a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK129
source / vignettesOK323
linux-releaseOK216
macos-releaseOK146
macos-oldrelOK170
windows-develOK80
windows-releaseOK77
windows-oldrelOK98
wasm-releaseOK105

Exports:extract.valgen.variogramgeo.distgrid.imagegv.modelidwintgen.idwkrigmidpointsmpinvmtest.gvmultispeciesplot.gvpredict.gvprint.gvsummary.gv

Dependencies:

Phylin with resistance
Preamble | Example data | Distance calculation | Building the variograms | Distance functions | Spatial interpolation
Rendered fromresistance_tutorial.Snwusingutils::Sweave

Last update: 2019-11-19
Started: 2019-03-13

Phylin: a step-by-step tutorial
Installation | Example data | Variogram | Spatial interpolation of lineage occurrence | Potential contact zones | Other methods in phylin
Rendered fromphylin_tutorial.Snwusingutils::Sweave

Last update: 2019-11-19
Started: 2015-11-04