Package: Rtreemix 1.69.0

Jasmina Bogojeska

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.

Authors:Jasmina Bogojeska

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Rtreemix.pdf |Rtreemix.html✨
Rtreemix/json (API)

# Install 'Rtreemix' in R:

install.packages('Rtreemix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

hiv.data - Example of an RtreemixData object

On BioConductor:Rtreemix-1.69.0(bioc 3.21)Rtreemix-1.68.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

statisticalmethod

3.68 score 12 scripts 282 downloads 2 mentions 57 exports 68 dependencies

Last updated 23 days agofrom:45c317fa2c. Checks:OK: 1 NOTE: 1 ERROR: 2 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	WARNING	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-win-x86_64	WARNING	Oct 31 2024
R-4.4-mac-x86_64	WARNING	Oct 31 2024
R-4.4-mac-aarch64	ERROR	Oct 31 2024
R-4.3-win-x86_64	WARNING	Oct 31 2024
R-4.3-mac-x86_64	WARNING	Oct 31 2024
R-4.3-mac-aarch64	ERROR	Oct 31 2024

Exports:bootstrap comp.models comp.models.levels comp.trees comp.trees.levels CompleteMat confIntGPS cosin.dist Description Description<-distribution euclidian.dist Events Events<-eventsNum fit generate get.tree.levels getData getModel getResp getTree gps GPS gpsCI initialize kullback.leibler L1.dist L2.norm likelihoods LogLikelihoods Model noDraws numTrees Patients Patients<-plot print Pval.dist rank.cor.dist Resp Sample sampleSize SamplingMode SamplingParam SamplingTimes show sim SimPatterns stability.sim Star Trees WaitingTimes Weights Weights<-WeightsCI WLikelihoods

Dependencies:backports base64enc Biobase BiocGenerics bslib cachem checkmate cli cluster colorspace data.table digest evaluate fansi farver fastmap fontawesome foreign Formula fs ggplot2 glue graph gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme nnet pillar pkgconfig R6 rappdirs RColorBrewer rlang rmarkdown rpart rstudioapi sass scales stringi stringr tibble tinytex utf8 vctrs viridis viridisLite withr xfun yaml

Rtreemix

Rendered fromRtreemix.Rnwusingutils::Sweaveon Oct 31 2024.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Method for fitting a mutagenetic trees mixture model and analyzing its variance	bootstrap bootstrap,RtreemixData,numeric-method bootstrap-methods
Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model	comp.trees comp.trees.levels
Method for calculating GPS values and their 95% bootstrap confidence intervals	confIntGPS confIntGPS,RtreemixData,numeric-method confIntGPS-methods
Different distances between two given vectors	cosin.dist euclidian.dist L1.dist rank.cor.dist
Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model	distribution distribution,RtreemixModel,character,numeric,numeric-method distribution,RtreemixModel,missing,missing,missing-method distribution-methods
Method for fitting mutagenetic trees mixture model to a given dataset	fit fit,RtreemixData,numeric-method fit-methods
Method for generating a random mutagenetic trees mixture model	generate generate,numeric,numeric-method generate-methods
Function for constructing level vectors	get.tree.levels
Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model	gps gps,RtreemixModel,matrix-method gps,RtreemixModel,missing-method gps,RtreemixModel,RtreemixData-method gps-methods
Example of an RtreemixData object	hiv.data
Kullback-Leibler divergence	kullback.leibler
L2 norm of a given vector	L2.norm
Method for predicting the likelihoods of a set of samples with respect to a mutagenetic trees mixture model	likelihoods likelihoods,RtreemixModel,RtreemixData-method likelihoods-methods
Functions for comparing the tree topologies of two mutagenetic trees mixture models	comp.models comp.models.levels
p-value of a given similarity value	Pval.dist
Class "RtreemixData"	Description Description,RtreemixData-method Description<- Description<-,RtreemixData-method Events Events,RtreemixData-method Events<- Events<-,RtreemixData-method eventsNum eventsNum,RtreemixData-method initialize,RtreemixData-method Patients Patients,RtreemixData-method Patients<- Patients<-,RtreemixData-method print,RtreemixData-method RtreemixData-class Sample Sample,RtreemixData-method sampleSize sampleSize,RtreemixData-method show,RtreemixData-method
Class "RtreemixGPS"	getData getData,RtreemixGPS-method GPS GPS,RtreemixGPS-method gpsCI gpsCI,RtreemixGPS-method initialize,RtreemixGPS-method Model Model,RtreemixGPS-method print,RtreemixGPS-method RtreemixGPS-class SamplingMode SamplingMode,RtreemixGPS-method SamplingParam SamplingParam,RtreemixGPS-method show,RtreemixGPS-method
Class "RtreemixModel"	CompleteMat CompleteMat,RtreemixModel-method getData,RtreemixModel getData,RtreemixModel-method getTree getTree,RtreemixModel,numeric-method initialize,RtreemixModel-method numTrees numTrees,RtreemixModel-method plot,RtreemixModel,missing-method print,RtreemixModel-method Resp Resp,RtreemixModel-method RtreemixModel-class show,RtreemixModel-method Star Star,RtreemixModel-method Trees Trees,RtreemixModel-method Weights Weights,RtreemixModel-method Weights<- Weights<-,RtreemixModel-method WeightsCI WeightsCI,RtreemixModel-method
Class "RtreemixSim"	getModel getModel,RtreemixSim-method initialize,RtreemixSim-method noDraws noDraws,RtreemixSim noDraws,RtreemixSim-method print,RtreemixSim-method RtreemixSim-class SamplingMode,RtreemixSim SamplingMode,RtreemixSim-method SamplingParam,RtreemixSim SamplingParam,RtreemixSim-method SamplingTimes SamplingTimes,RtreemixSim-method show,RtreemixSim-method SimPatterns SimPatterns,RtreemixSim-method WaitingTimes WaitingTimes,RtreemixSim-method
Class "RtreemixStats"	getData,RtreemixStats getData,RtreemixStats-method getResp getResp,RtreemixStats-method initialize,RtreemixStats-method LogLikelihoods LogLikelihoods,RtreemixStats-method Model,RtreemixStats Model,RtreemixStats-method print,RtreemixStats-method RtreemixStats-class show,RtreemixStats-method WLikelihoods WLikelihoods,RtreemixStats-method
Method for simulating data from a mutagenetic trees mixture model	sim sim,RtreemixModel,character,numeric-method sim,RtreemixModel,missing,missing-method sim-methods
Stability analysis of the mutagenetic trees mixture model	stability.sim