Entry: distances
Aliases: L1.dist euclidian.dist cosin.dist rank.cor.dist
Keywords: misc
Description: Different distances between two given vectors
URL: ../../../library/Rtreemix/html/L1.dist.html

Entry: L2.norm
Aliases: L2.norm
Keywords: misc
Description: L2 norm of a given vector
URL: ../../../library/Rtreemix/html/L2.norm.html

Entry: Pval.dist
Aliases: Pval.dist
Keywords: misc
Description: p-value of a given similarity value
URL: ../../../library/Rtreemix/html/Pval.dist.html

Entry: RtreemixData-class
Aliases: RtreemixData-class Description Events Patients Sample eventsNum sampleSize Description<- Events<- Patients<- Description,RtreemixData-method Description<-,RtreemixData-method Events,RtreemixData-method Events<-,RtreemixData-method Patients,RtreemixData-method Patients<-,RtreemixData-method Sample,RtreemixData-method eventsNum,RtreemixData-method sampleSize,RtreemixData-method initialize,RtreemixData-method print,RtreemixData-method show,RtreemixData-method
Keywords: classes
Description: Class "RtreemixData"
URL: ../../../library/Rtreemix/html/RtreemixData-class.html

Entry: RtreemixGPS-class
Aliases: GPS Model SamplingMode SamplingParam gpsCI getData RtreemixGPS-class GPS,RtreemixGPS-method Model,RtreemixGPS-method SamplingMode,RtreemixGPS-method SamplingParam,RtreemixGPS-method getData,RtreemixGPS-method gpsCI,RtreemixGPS-method initialize,RtreemixGPS-method print,RtreemixGPS-method show,RtreemixGPS-method
Keywords: classes
Description: Class "RtreemixGPS"
URL: ../../../library/Rtreemix/html/RtreemixGPS-class.html

Entry: RtreemixModel-class
Aliases: CompleteMat Resp Star Trees Weights WeightsCI getTree getData,RtreemixModel numTrees Weights<- RtreemixModel-class CompleteMat,RtreemixModel-method Resp,RtreemixModel-method Star,RtreemixModel-method Trees,RtreemixModel-method Weights,RtreemixModel-method Weights<-,RtreemixModel-method WeightsCI,RtreemixModel-method getData,RtreemixModel-method getTree,RtreemixModel,numeric-method numTrees,RtreemixModel-method initialize,RtreemixModel-method print,RtreemixModel-method show,RtreemixModel-method plot,RtreemixModel-method, missing-method
Keywords: classes
Description: Class "RtreemixModel"
URL: ../../../library/Rtreemix/html/RtreemixModel-class.html

Entry: RtreemixSim-class
Aliases: SamplingMode,RtreemixSim SamplingParam,RtreemixSim SamplingTimes SimPatterns WaitingTimes getModel noDraws,RtreemixSim noDraws RtreemixSim-class SamplingMode,RtreemixSim-method SamplingParam,RtreemixSim-method SamplingTimes,RtreemixSim-method SimPatterns,RtreemixSim-method WaitingTimes,RtreemixSim-method getModel,RtreemixSim-method noDraws,RtreemixSim-method initialize,RtreemixSim-method print,RtreemixSim-method show,RtreemixSim-method
Keywords: classes
Description: Class "RtreemixSim"
URL: ../../../library/Rtreemix/html/RtreemixSim-class.html

Entry: RtreemixStats-class
Aliases: LogLikelihoods Model,RtreemixStats WLikelihoods getData,RtreemixStats getResp RtreemixStats-class LogLikelihoods,RtreemixStats-method Model,RtreemixStats-method WLikelihoods,RtreemixStats-method getData,RtreemixStats-method getResp,RtreemixStats-method initialize,RtreemixStats-method print,RtreemixStats-method show,RtreemixStats-method
Keywords: classes
Description: Class "RtreemixStats"
URL: ../../../library/Rtreemix/html/RtreemixStats-class.html

Entry: bootstrap-methods
Aliases: bootstrap bootstrap-methods bootstrap,RtreemixData,numeric-method
Keywords: methods datagen
Description: Method for fitting a mutagenetic trees mixture model and analyzing its variance
URL: ../../../library/Rtreemix/html/bootstrap-methods.html

Entry: Models
Aliases: comp.models comp.models.levels
Keywords: misc
Description: Functions for comparing the tree topologies of two mutagenetic trees mixture models
URL: ../../../library/Rtreemix/html/comp.models.html

Entry: comp.trees
Aliases: comp.trees comp.trees.levels
Keywords: misc
Description: Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model
URL: ../../../library/Rtreemix/html/comp.trees.html

Entry: confIntGPS-methods
Aliases: confIntGPS confIntGPS-methods confIntGPS,RtreemixData,numeric-method
Keywords: methods
Description: Method for calculating GPS values and their 95\% bootstrap confidence intervals
URL: ../../../library/Rtreemix/html/confIntGPS-methods.html

Entry: distribution-methods
Aliases: distribution distribution-methods distribution,RtreemixModel,missing,missing,missing-method distribution,RtreemixModel,character,numeric,numeric-method
Keywords: methods distribution
Description: Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model
URL: ../../../library/Rtreemix/html/distribution-methods.html

Entry: fit-methods
Aliases: fit fit-methods fit,RtreemixData,numeric-method
Keywords: methods
Description: Method for fitting mutagenetic trees mixture model to a given dataset
URL: ../../../library/Rtreemix/html/fit-methods.html

Entry: generate-methods
Aliases: generate generate-methods generate,numeric,numeric-method
Keywords: methods models
Description: Method for generating a random mutagenetic trees mixture model
URL: ../../../library/Rtreemix/html/generate-methods.html

Entry: get.tree.levels
Aliases: get.tree.levels
Keywords: misc
Description: Function for constructing level vectors
URL: ../../../library/Rtreemix/html/get.tree.levels.html

Entry: gps-methods
Aliases: gps gps-methods gps,RtreemixModel,RtreemixData-method gps,RtreemixModel,matrix-method gps,RtreemixModel,missing-method
Keywords: methods survival
Description: Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model
URL: ../../../library/Rtreemix/html/gps-methods.html

Entry: hiv.data
Aliases: hiv.data
Keywords: datasets
Description: Example of an RtreemixData object
URL: ../../../library/Rtreemix/html/hiv.data.html

Entry: kullback.leibler
Aliases: kullback.leibler
Keywords: misc
Description: Kullback-Leibler divergence
URL: ../../../library/Rtreemix/html/kullback.leibler.html

Entry: likelihoods-methods
Aliases: likelihoods likelihoods-methods likelihoods,RtreemixModel,RtreemixData-method
Keywords: methods
Description: Method for predicting the likelihoods of a set of samples with respect to a mutagenetic trees mixture model
URL: ../../../library/Rtreemix/html/likelihoods-methods.html

Entry: plot-methods
Aliases: plot plot-methods plot,RtreemixModel,missing-method
Keywords: methods
Description: Method for visualizing mutagenetic trees mixture models
URL: ../../../library/Rtreemix/html/plot-methods.html

Entry: sim-methods
Aliases: sim sim-methods sim,RtreemixModel,missing,missing-method sim,RtreemixModel,character,numeric-method
Keywords: methods misc
Description: Method for simulating data from a mutagenetic trees mixture model
URL: ../../../library/Rtreemix/html/sim-methods.html

Entry: stability.sim
Aliases: stability.sim
Keywords: misc
Description: Stability analysis of the mutagenetic trees mixture model
URL: ../../../library/Rtreemix/html/stability.sim.html
