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evobiR (version 1.0)

evobiR: evolutionary biology in R.

Description

evobiR is a collection of tools for use in evolutionary biology

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Version

Install

install.packages('evobiR')

Monthly Downloads

235

Version

1.0

License

GPL (>= 2)

Maintainer

Heath Blackmon

Last Published

October 21st, 2013

Functions in evobiR (1.0)

PPSDiscrete

Create Simulated Datasets via PPS
ResSel

Selection on Residuals
FuzzyMatch

Find Close Matches in a tree and dataset
SampleTrees

Select a random sample of trees
CalcD

Calculate Patterson's D-statistic
1.fasta

simulated SNP data
hym.tree

Phylogenetic tree
evobiR-package

evobiR: Evolutionary Biology in R
taxa.table

A table with taxonomic information
horn.beetle.csv

Gnatocerus measurements
3.fasta

simulated SNP data
GetTaxonomy

Create a taxonomy table
species.tree

Species Phylogenetic tree
trees.nex

100 Phylogenetic trees
mcmc3

mcmc log file
AnalyzeAssembly

Analyze Genome Assembly
HetLevels

Calculates heterozygosity based on ambigous IUPAC nucleotide codes
data.taxonomy

taxonomic table
trees

10 Phylogenetic trees
HighLevelTree

Prune a phylogeny to a higher taxonomic levels.
ReplTable

Maximize Retained Tips
GenomeSym

Genome Simulation
mite.data

cytogenetic mite data
mite.tree

phylogenetic tree of mites
tree.taxonomy

taxonomic table
assembly.fasta

a sample of a genome
2.fasta

simulated SNP data
CoalSim

Coalescence Simulations
DriftSim

Simulate Allele Frequencies
genome

A small portion of the genome of Tribolium confusum
mcmc2

mcmc log file