# Rtreemix: Mutagenetic trees mixture models.

## Documentation for package ‘Rtreemix’ version 1.60.0

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

## Help Pages

B C D E F G H I K L M N P R S T W

## -- B --

bootstrap | Method for fitting a mutagenetic trees mixture model and analyzing its variance
bootstrap-method | Method for fitting a mutagenetic trees mixture model and analyzing its variance
bootstrap-methods | Method for fitting a mutagenetic trees mixture model and analyzing its variance

## -- C --

comp.models | Functions for comparing the tree topologies of two mutagenetic trees mixture models
comp.models.levels | Functions for comparing the tree topologies of two mutagenetic trees mixture models
comp.trees | Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model
comp.trees.levels | Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model
CompleteMat | Class "RtreemixModel"
CompleteMat-method | Class "RtreemixModel"
confIntGPS | Method for calculating GPS values and their 95% bootstrap confidence intervals
confIntGPS-method | Method for calculating GPS values and their 95% bootstrap confidence intervals
confIntGPS-methods | Method for calculating GPS values and their 95% bootstrap confidence intervals
cosin.dist | Different distances between two given vectors

## -- D --

Description | Class "RtreemixData"
Description-method | Class "RtreemixData"
Description<- | Class "RtreemixData"
Description<--method | Class "RtreemixData"
distribution | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model
distribution-method | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model
distribution-methods | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model

## -- E --

euclidian.dist | Different distances between two given vectors
Events | Class "RtreemixData"
Events-method | Class "RtreemixData"
Events<- | Class "RtreemixData"
Events<--method | Class "RtreemixData"
eventsNum | Class "RtreemixData"
eventsNum-method | Class "RtreemixData"

## -- F --

fit | Method for fitting mutagenetic trees mixture model to a given dataset
fit-method | Method for fitting mutagenetic trees mixture model to a given dataset
fit-methods | Method for fitting mutagenetic trees mixture model to a given dataset

## -- G --

generate | Method for generating a random mutagenetic trees mixture model
generate-method | Method for generating a random mutagenetic trees mixture model
generate-methods | Method for generating a random mutagenetic trees mixture model
get.tree.levels | Function for constructing level vectors
getData | Class "RtreemixGPS"
getData,RtreemixModel | Class "RtreemixModel"
getData,RtreemixStats | Class "RtreemixStats"
getData-method | Class "RtreemixGPS"
getData-method | Class "RtreemixModel"
getData-method | Class "RtreemixStats"
getModel | Class "RtreemixSim"
getModel-method | Class "RtreemixSim"
getResp | Class "RtreemixStats"
getResp-method | Class "RtreemixStats"
getTree | Class "RtreemixModel"
getTree-method | Class "RtreemixModel"
GPS | Class "RtreemixGPS"
gps | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
GPS-method | Class "RtreemixGPS"
gps-method | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
gps-methods | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
gpsCI | Class "RtreemixGPS"
gpsCI-method | Class "RtreemixGPS"

## -- H --

hiv.data | Example of an RtreemixData object

## -- I --

initialize-method | Class "RtreemixData"
initialize-method | Class "RtreemixGPS"
initialize-method | Class "RtreemixModel"
initialize-method | Class "RtreemixSim"
initialize-method | Class "RtreemixStats"

## -- K --

kullback.leibler | Kullback-Leibler divergence

## -- L --

L1.dist | Different distances between two given vectors
L2.norm | L2 norm of a given vector
likelihoods | Method for predicting the likelihoods of a set of samples with respect to a mutagenetic trees mixture model
likelihoods-method | Method for predicting the likelihoods of a set of samples with respect to 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
LogLikelihoods | Class "RtreemixStats"
LogLikelihoods-method | Class "RtreemixStats"

## -- M --

Model | Class "RtreemixGPS"
Model,RtreemixStats | Class "RtreemixStats"
Model-method | Class "RtreemixGPS"
Model-method | Class "RtreemixStats"

## -- N --

noDraws | Class "RtreemixSim"
noDraws,RtreemixSim | Class "RtreemixSim"
noDraws-method | Class "RtreemixSim"
numTrees | Class "RtreemixModel"
numTrees-method | Class "RtreemixModel"

## -- P --

Patients | Class "RtreemixData"
Patients-method | Class "RtreemixData"
Patients<- | Class "RtreemixData"
Patients<--method | Class "RtreemixData"
plot-method | Class "RtreemixModel"
print-method | Class "RtreemixData"
print-method | Class "RtreemixGPS"
print-method | Class "RtreemixModel"
print-method | Class "RtreemixSim"
print-method | Class "RtreemixStats"
Pval.dist | p-value of a given similarity value

## -- R --

rank.cor.dist | Different distances between two given vectors
Resp | Class "RtreemixModel"
Resp-method | Class "RtreemixModel"
RtreemixData-class | Class "RtreemixData"
RtreemixGPS-class | Class "RtreemixGPS"
RtreemixModel-class | Class "RtreemixModel"
RtreemixSim-class | Class "RtreemixSim"
RtreemixStats-class | Class "RtreemixStats"

## -- S --

Sample | Class "RtreemixData"
Sample-method | Class "RtreemixData"
sampleSize | Class "RtreemixData"
sampleSize-method | Class "RtreemixData"
SamplingMode | Class "RtreemixGPS"
SamplingMode,RtreemixSim | Class "RtreemixSim"
SamplingMode-method | Class "RtreemixGPS"
SamplingMode-method | Class "RtreemixSim"
SamplingParam | Class "RtreemixGPS"
SamplingParam,RtreemixSim | Class "RtreemixSim"
SamplingParam-method | Class "RtreemixGPS"
SamplingParam-method | Class "RtreemixSim"
SamplingTimes | Class "RtreemixSim"
SamplingTimes-method | Class "RtreemixSim"
show-method | Class "RtreemixData"
show-method | Class "RtreemixGPS"
show-method | Class "RtreemixModel"
show-method | Class "RtreemixSim"
show-method | Class "RtreemixStats"
sim | Method for simulating data from a mutagenetic trees mixture model
sim-method | Method for simulating data from a mutagenetic trees mixture model
sim-methods | Method for simulating data from a mutagenetic trees mixture model
SimPatterns | Class "RtreemixSim"
SimPatterns-method | Class "RtreemixSim"
stability.sim | Stability analysis of the mutagenetic trees mixture model
Star | Class "RtreemixModel"
Star-method | Class "RtreemixModel"

## -- T --

Trees | Class "RtreemixModel"
Trees-method | Class "RtreemixModel"

## -- W --

WaitingTimes | Class "RtreemixSim"
WaitingTimes-method | Class "RtreemixSim"
Weights | Class "RtreemixModel"
Weights-method | Class "RtreemixModel"
Weights<- | Class "RtreemixModel"
Weights<--method | Class "RtreemixModel"
WeightsCI | Class "RtreemixModel"
WeightsCI-method | Class "RtreemixModel"
WLikelihoods | Class "RtreemixStats"
WLikelihoods-method | Class "RtreemixStats"