Rtreemix: Mutagenetic trees mixture models.

Documentation for package ‘Rtreemix’ version 1.52.0

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-- 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 --

Example of an RtreemixData object

-- I --

-- K --

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 --

-- N --

-- 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 --