Detect and Remove Outliers in Phylogenomics Datasets

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Documentation for package ‘phylter’ version 0.9.11

• 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
medcouple	A robust measure of skewness for univariate data
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)