# Rtreemix: Mutagenetic trees mixture models.

## Documentation for package ‘Rtreemix’ version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## 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,RtreemixData,numeric-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.trees | Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model
CompleteMat | Class "RtreemixModel"
CompleteMat,RtreemixModel-method | Class "RtreemixModel"
confIntGPS | Method for calculating GPS values and their 95% bootstrap confidence intervals
confIntGPS,RtreemixData,numeric-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,RtreemixData-method | Class "RtreemixData"
Description<-,RtreemixData-method | Class "RtreemixData"
distribution | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model
distribution,RtreemixModel,character,numeric,numeric-method | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model
distribution,RtreemixModel,missing,missing,missing-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,RtreemixData-method | Class "RtreemixData"
Events<-,RtreemixData-method | Class "RtreemixData"
eventsNum | Class "RtreemixData"
eventsNum,RtreemixData-method | Class "RtreemixData"

## -- F --

fit | Method for fitting mutagenetic trees mixture model to a given dataset
fit,RtreemixData,numeric-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,numeric,numeric-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,RtreemixGPS-method | Class "RtreemixGPS"
getData,RtreemixModel | Class "RtreemixModel"
getData,RtreemixModel-method | Class "RtreemixModel"
getData,RtreemixStats | Class "RtreemixStats"
getData,RtreemixStats-method | Class "RtreemixStats"
getModel | Class "RtreemixSim"
getModel,RtreemixSim-method | Class "RtreemixSim"
getResp | Class "RtreemixStats"
getResp,RtreemixStats-method | Class "RtreemixStats"
getTree | Class "RtreemixModel"
getTree,RtreemixModel,numeric-method | Class "RtreemixModel"
GPS | Class "RtreemixGPS"
gps | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
GPS,RtreemixGPS-method | Class "RtreemixGPS"
gps,RtreemixModel,matrix-method | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
gps,RtreemixModel,missing-method | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
gps,RtreemixModel,RtreemixData-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,RtreemixGPS-method | Class "RtreemixGPS"

## -- H --

hiv.data | Example of an RtreemixData object

## -- I --

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

## -- M --

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

## -- N --

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

## -- P --

Patients | Class "RtreemixData"
Patients,RtreemixData-method | Class "RtreemixData"
Patients<-,RtreemixData-method | Class "RtreemixData"
plot | Method for visualizing mutagenetic trees mixture models
plot,RtreemixModel,missing-method | Method for visualizing mutagenetic trees mixture models
plot,RtreemixModel-method, missing-method | Class "RtreemixModel"
plot-methods | Method for visualizing mutagenetic trees mixture models
print,RtreemixData-method | Class "RtreemixData"
print,RtreemixGPS-method | Class "RtreemixGPS"
print,RtreemixModel-method | Class "RtreemixModel"
print,RtreemixSim-method | Class "RtreemixSim"
print,RtreemixStats-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,RtreemixModel-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,RtreemixData-method | Class "RtreemixData"
sampleSize | Class "RtreemixData"
sampleSize,RtreemixData-method | Class "RtreemixData"
SamplingMode | Class "RtreemixGPS"
SamplingMode,RtreemixGPS-method | Class "RtreemixGPS"
SamplingMode,RtreemixSim | Class "RtreemixSim"
SamplingMode,RtreemixSim-method | Class "RtreemixSim"
SamplingParam | Class "RtreemixGPS"
SamplingParam,RtreemixGPS-method | Class "RtreemixGPS"
SamplingParam,RtreemixSim | Class "RtreemixSim"
SamplingParam,RtreemixSim-method | Class "RtreemixSim"
SamplingTimes | Class "RtreemixSim"
SamplingTimes,RtreemixSim-method | Class "RtreemixSim"
show,RtreemixData-method | Class "RtreemixData"
show,RtreemixGPS-method | Class "RtreemixGPS"
show,RtreemixModel-method | Class "RtreemixModel"
show,RtreemixSim-method | Class "RtreemixSim"
show,RtreemixStats-method | Class "RtreemixStats"
sim | Method for simulating data from a mutagenetic trees mixture model
sim,RtreemixModel,character,numeric-method | Method for simulating data from a mutagenetic trees mixture model
sim,RtreemixModel,missing,missing-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,RtreemixSim-method | Class "RtreemixSim"
stability.sim | Stability analysis of the mutagenetic trees mixture model
Star | Class "RtreemixModel"
Star,RtreemixModel-method | Class "RtreemixModel"

## -- T --

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

## -- W --

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