RADami: R Package for Phylogenetic Analysis of RADseq Data

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This package implements import, export, manipulation, visualization, and downstream (post-clustering) analysis of RADseq data, integrating with the pyRAD package by Deren Eaton.

Author
Andrew L. Hipp <ahipp@mortonarb.org>
Date of publication
2014-03-03 12:10:23
Maintainer
Andrew L. Hipp <ahipp@mortonarb.org>
License
GPL-3
Version
1.0-3

View on CRAN

Man pages

compare.all.trees
Compare all trees in a treeset, and return a matrix (lower...
consensus.pyRAD
Generate a consensus sequence for each of the loci in a...
filter.by
Identify names of loci for which at the requested taxa are...
gen.RAD.loci.datasets
Generate datasets for partitioned RAD analysis
genTrees
Generate permuted trees using rNNI or rtree, and check for...
get.raxml.siteLikelihoods
Read likelihoods from a RAxML_perSiteLLs file
get.raxml.treeLikelihoods
Extract likelihoods from a RAxML info file
lengths.report
Return the lengths of all loci in a pyRAD.loci object
locus.dist
Generate a pairwise similarity matrix for individuals based...
match.lnL.to.trees
Match the likelihoods returned on a subset of trees for...
oak.rads
101-locus RAD dataset, in 'pyRAD.loci' format
oak.tree
28-tip oak phylogeny, in 'phylo' format
overlap.report
Generates a report on locus overlap between pairs of samples...
plot.locus.dist
Plot a phylogeny with a graphical representation of locus...
plot.partitionedRAD
Plot a 'partitionedRAD' object
plot.rankedPartitionedRAD
Plot a 'rankedPartitionedRAD' object
print.pyRAD.loci
Print method for 'pyRAD.loci' objects
rad2mat
Generates a matrix of sequences from a 'pyRAD.loci' object
rad2phy
Export a 'rad.mat' object to a phylip file
RADami-package
R Package for Phylogenetic Analysis of RADseq Data
rank.partitionedRAD
Bin trees into 'suppported' or 'disfavored' by locus.
read.pyRAD
Read in data from pyRAD
rtreePhylo
Generate random trees using an input tree to get taxon names...
subset.pyRAD.loci
Subsets a 'pyRAD.loci' object
summary.pyRAD.loci
Summary method for 'pyRAD.loci' objects
write.DNAStringSet
Writes a sequence matrix to phylip format

Files in this package

RADami
RADami/NAMESPACE
RADami/data
RADami/data/oak.rads.rda
RADami/data/oak.tree.rda
RADami/R
RADami/R/filter.by.R
RADami/R/rank.partitionedRAD.R
RADami/R/write.DNAStringSet.R
RADami/R/rtreePhylo.R
RADami/R/get.raxml.treeLikelihoods.R
RADami/R/plot.partitionedRAD.R
RADami/R/get.raxml.siteLikelihoods.R
RADami/R/print.pyRAD.loci.R
RADami/R/genTrees.R
RADami/R/rad2mat.R
RADami/R/gen.RAD.loci.datasets.R
RADami/R/plot.rankedPartitionedRAD.R
RADami/R/compare.all.trees.R
RADami/R/consensus.pyRAD.R
RADami/R/lengths.report.R
RADami/R/summary.pyRAD.loci.R
RADami/R/subset.pyRAD.loci.R
RADami/R/locus.dist.R
RADami/R/plot.locus.dist.R
RADami/R/unique.multiPhylo.R
RADami/R/read.pyRAD.R
RADami/R/overlap.report.R
RADami/R/match.lnL.to.trees.R
RADami/R/rad2phy.R
RADami/MD5
RADami/DESCRIPTION
RADami/man
RADami/man/rtreePhylo.Rd
RADami/man/oak.tree.Rd
RADami/man/rad2phy.Rd
RADami/man/rad2mat.Rd
RADami/man/overlap.report.Rd
RADami/man/gen.RAD.loci.datasets.Rd
RADami/man/get.raxml.siteLikelihoods.Rd
RADami/man/consensus.pyRAD.Rd
RADami/man/summary.pyRAD.loci.Rd
RADami/man/write.DNAStringSet.Rd
RADami/man/locus.dist.Rd
RADami/man/subset.pyRAD.loci.Rd
RADami/man/match.lnL.to.trees.Rd
RADami/man/RADami-package.Rd
RADami/man/compare.all.trees.Rd
RADami/man/plot.locus.dist.Rd
RADami/man/genTrees.Rd
RADami/man/lengths.report.Rd
RADami/man/filter.by.Rd
RADami/man/rank.partitionedRAD.Rd
RADami/man/print.pyRAD.loci.Rd
RADami/man/read.pyRAD.Rd
RADami/man/oak.rads.Rd
RADami/man/get.raxml.treeLikelihoods.Rd
RADami/man/plot.partitionedRAD.Rd
RADami/man/plot.rankedPartitionedRAD.Rd