Rtreemix: Rtreemix: Mutagenetic trees mixture models.
Version 1.38.0

Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.

Browse man pages Browse package API and functions Browse package files

AuthorJasmina Bogojeska
Bioconductor views StatisticalMethod
Date of publicationNone
MaintainerJasmina Bogojeska <jasmina.bogojeska@gmail.com>
LicenseLGPL
Version1.38.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rtreemix")

Man pages

bootstrap-methods: Method for fitting a mutagenetic trees mixture model and...
comp.models: Functions for comparing the tree topologies of two...
comp.trees: Functions for quantifying the diversity of the nontrivial...
confIntGPS-methods: Method for calculating GPS values and their 95% bootstrap...
distribution-methods: Method for generating the (scaled) probablility distribution...
fit-methods: Method for fitting mutagenetic trees mixture model to a given...
generate-methods: Method for generating a random mutagenetic trees mixture...
get.tree.levels: Function for constructing level vectors
gps-methods: Methods for predicting the GPS of given dataset by using a...
hiv.data: Example of an RtreemixData object
kullback.leibler: Kullback-Leibler divergence
L1.dist: Different distances between two given vectors
L2.norm: L2 norm of a given vector
likelihoods-methods: Method for predicting the likelihoods of a set of samples...
Pval.dist: p-value of a given similarity value
RtreemixData-class: Class "RtreemixData"
RtreemixGPS-class: Class "RtreemixGPS"
RtreemixModel-class: Class "RtreemixModel"
RtreemixSim-class: Class "RtreemixSim"
RtreemixStats-class: Class "RtreemixStats"
sim-methods: Method for simulating data from a mutagenetic trees mixture...
stability.sim: Stability analysis of the mutagenetic trees mixture model

Functions

CompleteMat Man page
CompleteMat,RtreemixModel-method Man page
Description Man page
Description,RtreemixData-method Man page
Description<- Man page
Description<-,RtreemixData-method Man page
Events Man page
Events,RtreemixData-method Man page
Events<- Man page
Events<-,RtreemixData-method Man page
GPS Man page
GPS,RtreemixGPS-method Man page
L1.dist Man page Source code
L2.norm Man page Source code
LogLikelihoods Man page
LogLikelihoods,RtreemixStats-method Man page
Model Man page
Model,RtreemixGPS-method Man page
Model,RtreemixStats Man page
Model,RtreemixStats-method Man page
Patients Man page
Patients,RtreemixData-method Man page
Patients<- Man page
Patients<-,RtreemixData-method Man page
Pval.dist Man page Source code
Resp Man page
Resp,RtreemixModel-method Man page
RtreemixData-class Man page
RtreemixGPS-class Man page
RtreemixModel-class Man page
RtreemixSim-class Man page
RtreemixStats-class Man page
Sample Man page
Sample,RtreemixData-method Man page
SamplingMode Man page
SamplingMode,RtreemixGPS-method Man page
SamplingMode,RtreemixSim Man page
SamplingMode,RtreemixSim-method Man page
SamplingParam Man page
SamplingParam,RtreemixGPS-method Man page
SamplingParam,RtreemixSim Man page
SamplingParam,RtreemixSim-method Man page
SamplingTimes Man page
SamplingTimes,RtreemixSim-method Man page
SimPatterns Man page
SimPatterns,RtreemixSim-method Man page
Star Man page
Star,RtreemixModel-method Man page
Trees Man page
Trees,RtreemixModel-method Man page
WLikelihoods Man page
WLikelihoods,RtreemixStats-method Man page
WaitingTimes Man page
WaitingTimes,RtreemixSim-method Man page
Weights Man page
Weights,RtreemixModel-method Man page
Weights<- Man page
Weights<-,RtreemixModel-method Man page
WeightsCI Man page
WeightsCI,RtreemixModel-method Man page
bootstrap Man page
bootstrap,RtreemixData,numeric-method Man page
bootstrap-methods Man page
comp.models Man page Source code
comp.models.levels Man page Source code
comp.trees Man page Source code
comp.trees.levels Man page Source code
confIntGPS Man page
confIntGPS,RtreemixData,numeric-method Man page
confIntGPS-methods Man page
cosin.dist Man page Source code
distribution Man page
distribution,RtreemixModel,character,numeric,numeric-method Man page
distribution,RtreemixModel,missing,missing,missing-method Man page
distribution-methods Man page
euclidian.dist Man page Source code
eventsNum Man page
eventsNum,RtreemixData-method Man page
fit Man page
fit,RtreemixData,numeric-method Man page
fit-methods Man page
generate Man page
generate,numeric,numeric-method Man page
generate-methods Man page
get.tree.levels Man page Source code
getData Man page
getData,RtreemixGPS-method Man page
getData,RtreemixModel Man page
getData,RtreemixModel-method Man page
getData,RtreemixStats Man page
getData,RtreemixStats-method Man page
getModel Man page
getModel,RtreemixSim-method Man page
getResp Man page
getResp,RtreemixStats-method Man page
getTree Man page
getTree,RtreemixModel,numeric-method Man page
gps Man page
gps,RtreemixModel,RtreemixData-method Man page
gps,RtreemixModel,matrix-method Man page
gps,RtreemixModel,missing-method Man page
gps-methods Man page
gpsCI Man page
gpsCI,RtreemixGPS-method Man page
hiv.data Man page
initialize,RtreemixData-method Man page
initialize,RtreemixGPS-method Man page
initialize,RtreemixModel-method Man page
initialize,RtreemixSim-method Man page
initialize,RtreemixStats-method Man page
kullback.leibler Man page Source code
likelihoods Man page
likelihoods,RtreemixModel,RtreemixData-method Man page
likelihoods-methods Man page
noDraws Man page
noDraws,RtreemixSim Man page
noDraws,RtreemixSim-method Man page
numTrees Man page
numTrees,RtreemixModel-method Man page
onUnload Source code
plot,RtreemixModel,missing-method Man page
plotRes Source code
plott1 Source code
plott2 Source code
print,RtreemixData-method Man page
print,RtreemixGPS-method Man page
print,RtreemixModel-method Man page
print,RtreemixSim-method Man page
print,RtreemixStats-method Man page
printRtreemixData Source code
printRtreemixGPS Source code
printRtreemixModel Source code
printRtreemixSim Source code
printRtreemixStats Source code
rank.cor.dist Man page Source code
sampleSize Man page
sampleSize,RtreemixData-method Man page
show,RtreemixData-method Man page
show,RtreemixGPS-method Man page
show,RtreemixModel-method Man page
show,RtreemixSim-method Man page
show,RtreemixStats-method Man page
sim Man page
sim,RtreemixModel,character,numeric-method Man page
sim,RtreemixModel,missing,missing-method Man page
sim-methods Man page
stability.sim Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/ClassMethods.R
R/RtreemixMethods.R
R/StabilityFunctions.R
R/zzz.R
build
build/vignette.rds
data
data/hiv.data.RData
inst
inst/doc
inst/doc/Rtreemix.R
inst/doc/Rtreemix.Rnw
inst/doc/Rtreemix.pdf
inst/examples
inst/examples/script.R
inst/examples/treemix.pat
man
man/L1.dist.Rd
man/L2.norm.Rd
man/Pval.dist.Rd
man/RtreemixData-class.Rd
man/RtreemixGPS-class.Rd
man/RtreemixModel-class.Rd
man/RtreemixSim-class.Rd
man/RtreemixStats-class.Rd
man/bootstrap-methods.Rd
man/comp.models.Rd
man/comp.trees.Rd
man/confIntGPS-methods.Rd
man/distribution-methods.Rd
man/fit-methods.Rd
man/generate-methods.Rd
man/get.tree.levels.Rd
man/gps-methods.Rd
man/hiv.data.Rd
man/kullback.leibler.Rd
man/likelihoods-methods.Rd
man/sim-methods.Rd
man/stability.sim.Rd
src
src/Makevars
src/Makevars.win
src/Rtreemix.cc
src/Rtreemix_patch.cc
src/WrapGraph.cc
src/cfunctions.cc
src/include
src/include/Array.hh
src/include/Edge.hh
src/include/Edge_Array.hh
src/include/Graph.hh
src/include/List.hh
src/include/Map.hh
src/include/Matrix.hh
src/include/Node.hh
src/include/NodeN.hh
src/include/Node_Array.hh
src/include/Queue.hh
src/include/RefCounted.hh
src/include/Rtreemix_patch.h
src/include/Set.hh
src/include/Vector.hh
src/include/WrapGraph.hh
src/include/cfunctions.h
src/include/kmeans.h
src/include/max_weight_branch.h
src/include/mtree.h
src/include/mtreemix.h
src/include/replaceleda.hh
src/kmeans.cc
src/max_weight_branch.cc
src/mtree.cc
src/mtreemix.cc
src/replaceleda.cc
vignettes
vignettes/ClassDiagram.pdf
vignettes/ExtendedVignette.pdf
vignettes/Rtreemix.Rnw
vignettes/Rtreemix.bib
vignettes/topologies.pdf
vignettes/treemix.pat
Rtreemix documentation built on May 20, 2017, 10:17 p.m.