evobiR: Comparative and Population Genetic Analyses

Comparative analysis of continuous traits influencing discrete states, and utility tools to facilitate comparative analyses. Implementations of ABBA/BABA type statistics to test for introgression in genomic data. Wright-Fisher, phylogenetic tree, and statistical distribution Shiny interactive simulations for use in teaching.

Author
Heath Blackmon and Richard H. Adams
Date of publication
2015-09-06 19:30:55
Maintainer
Heath Blackmon <coleoguy@gmail.com>
License
GPL (>= 2)
Version
1.1
URLs

View on CRAN

Man pages

1.fasta
simulated SNP data
AICc
Computes an AICc score
AncCond
Calculate the mean of a continuous character at the origin of...
CalcD
Calculate Patterson's D-statistic
Even
Tests whether a number is even
evobiR-package
evobiR: Evolutionary Biology in R
FuzzyMatch
Find Close Matches in a tree and dataset
horn.beetle
Gnatocerus measurements
hym.tree
Phylogenetic tree
mcmc2
mcmc log file
mite.trait
phenotype data for mites
Mode
Calcualtes the mode of a numeric vector
PPSDiscrete
Create Simulated Datasets via PPS
ReorderData
Reorders trait data to match the order of tips in a tree
ResSel
Selection on Residuals
SampleTrees
Select a random sample of trees
SlidingWindow
Sliding window analysis
SuperMatrix
creates a supermatrix from multiple gene alignments
trees
10 Phylogenetic trees
trees.mite
10 Phylogenetic trees
trees.nex
100 Phylogenetic trees
ViewEvo
Learning Resources
WinCalcD
Calculate Patterson's D-statistic in sliding windows

Files in this package

evobiR
evobiR/inst
evobiR/inst/2.fasta
evobiR/inst/horn.beetle.csv
evobiR/inst/3.fasta
evobiR/inst/wf.model
evobiR/inst/wf.model/ui.R
evobiR/inst/wf.model/server.R
evobiR/inst/dist.model
evobiR/inst/dist.model/ui.R
evobiR/inst/dist.model/server.R
evobiR/inst/bd.model
evobiR/inst/bd.model/ui.R
evobiR/inst/bd.model/server.R
evobiR/inst/1.fasta
evobiR/inst/trees.nex
evobiR/NAMESPACE
evobiR/data
evobiR/data/trees.mite.rda
evobiR/data/trees.rda
evobiR/data/mite.trait.rda
evobiR/data/mcmc3.rda
evobiR/data/mcmc2.rda
evobiR/data/hym.tree.rda
evobiR/R
evobiR/R/ViewEvo.R
evobiR/R/AICc.R
evobiR/R/CalcD.R
evobiR/R/SampleTrees.R
evobiR/R/SlidingWindow.R
evobiR/R/AncCond.R
evobiR/R/ReorderData.R
evobiR/R/Even.R
evobiR/R/PPSDiscrete.R
evobiR/R/ResSel.R
evobiR/R/WinCalcD.R
evobiR/R/Mode.R
evobiR/R/FuzzyMatch.R
evobiR/R/SuperMatrix.R
evobiR/MD5
evobiR/DESCRIPTION
evobiR/man
evobiR/man/FuzzyMatch.Rd
evobiR/man/horn.beetle.Rd
evobiR/man/AICc.Rd
evobiR/man/ResSel.Rd
evobiR/man/CalcD.Rd
evobiR/man/PPSDiscrete.Rd
evobiR/man/mite.trait.Rd
evobiR/man/SampleTrees.Rd
evobiR/man/AncCond.Rd
evobiR/man/Mode.Rd
evobiR/man/SlidingWindow.Rd
evobiR/man/hym.tree.Rd
evobiR/man/ViewEvo.Rd
evobiR/man/trees.Rd
evobiR/man/trees.mite.Rd
evobiR/man/mcmc2.Rd
evobiR/man/evobiR-package.Rd
evobiR/man/ReorderData.Rd
evobiR/man/1.fasta.Rd
evobiR/man/trees.nex.Rd
evobiR/man/SuperMatrix.Rd
evobiR/man/WinCalcD.Rd
evobiR/man/Even.Rd