Rtreemix: Mutagenetic trees mixture models.


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Documentation for package ‘Rtreemix’ version 1.4.0

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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,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"