# Detect and Remove Outliers in Phylogenomics Datasets

## Documentation for package ‘phylter’ version 0.9.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

carnivora | 125 genes trees for 53 carnivora species
detect.outliers | Detection of outliers in 1D and 2D data
detect.outliers.array | Detection of outliers in 1D and 2D data
Dist2WR | Compute gene x species matrix from the result of Distatis
DistatisFast | Fast implementation the multivariate analysis method Distatis
impMean | Imputation of missing values in a collection of matrices
normalize | Median normalization of 2D matrix by row or by colomn
phylter | Filter phylogenomics datasets
plot.phylter | Plot phylter objects
plot2WR | Plot phylter objects
plotDispersion | Plot phylter objects
plotopti | Plot phylter objects
plotRV | Plot phylter objects
PreparePhylterData | Prepare data for phylter analysis
print.phylter | Print phylter objects
print.phylterfinal | print objects of class phylterfinal
print.phylterinitial | print objects of class phylterinitial
print.summary.phylter | print summary of phylter objects
rename.genes | Name or rename a list of gene trees or matrices
simtrees | Simplistic simulation of gene trees with outliers
summary.phylter | Get summary for phylter objects
trees2matrices | Convert phylogenetic trees to distance matrices
write.phylter | Write summary of phyter analysis to file(s)