Rtreemix: Rtreemix: Mutagenetic trees mixture models.

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.

Author
Jasmina Bogojeska
Date of publication
None
Maintainer
Jasmina Bogojeska <jasmina.bogojeska@gmail.com>
License
LGPL
Version
1.36.0

View on Bioconductor

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

Files in this package

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