Rtreemix: Mutagenetic trees mixture models.


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Documentation for package ‘Rtreemix’ version 1.32.0

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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"