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Rtreemix (version 1.34.0)

Rtreemix: Mutagenetic trees mixture models.

Description

Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.

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Version

Version

1.34.0

License

LGPL

Maintainer

Jasmina Bogojeska

Last Published

February 15th, 2017

Functions in Rtreemix (1.34.0)

bootstrap-methods

Method for fitting a mutagenetic trees mixture model and analyzing its variance
Pval.dist

p-value of a given similarity value
kullback.leibler

Kullback-Leibler divergence
L2.norm

L2 norm of a given vector
fit-methods

Method for fitting mutagenetic trees mixture model to a given dataset
confIntGPS-methods

Method for calculating GPS values and their 95% bootstrap confidence intervals
distribution-methods

Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model
sim-methods

Method for simulating data from a mutagenetic trees mixture model
RtreemixData-class

Class "RtreemixData"
distances

Different distances between two given vectors
RtreemixStats-class

Class "RtreemixStats"
gps-methods

Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
stability.sim

Stability analysis of the mutagenetic trees mixture model
comp.trees

Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model
likelihoods-methods

Method for predicting the likelihoods of a set of samples with respect to a mutagenetic trees mixture model
hiv.data

Example of an RtreemixData object
Models

Functions for comparing the tree topologies of two mutagenetic trees mixture models
generate-methods

Method for generating a random mutagenetic trees mixture model
RtreemixGPS-class

Class "RtreemixGPS"
RtreemixModel-class

Class "RtreemixModel"
RtreemixSim-class

Class "RtreemixSim"
get.tree.levels

Function for constructing level vectors