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:
Rtreemix_1.69.0.tar.gz
Rtreemix_1.69.0.zip(r-4.5)Rtreemix_1.69.0.zip(r-4.4)Rtreemix_1.69.0.zip(r-4.3)
Rtreemix_1.69.0.tgz(r-4.4-x86_64)Rtreemix_1.69.0.tgz(r-4.4-arm64)Rtreemix_1.69.0.tgz(r-4.3-x86_64)Rtreemix_1.69.0.tgz(r-4.3-arm64)
Rtreemix_1.69.0.tar.gz(r-4.5-noble)Rtreemix_1.69.0.tar.gz(r-4.4-noble)
Rtreemix_1.69.0.tgz(r-4.4-emscripten)Rtreemix_1.69.0.tgz(r-4.3-emscripten)
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')) |
- 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.
Last updated 2 months agofrom:45c317fa2c. Checks:ERROR: 7 NOTE: 1 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Dec 03 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 | ERROR | Dec 03 2024 |
| R-4.4-mac-x86_64 | ERROR | Dec 03 2024 |
| R-4.4-mac-aarch64 | ERROR | Dec 03 2024 |
| R-4.3-win-x86_64 | ERROR | Dec 03 2024 |
| R-4.3-mac-x86_64 | ERROR | Dec 03 2024 |
| R-4.3-mac-aarch64 | ERROR | Dec 03 2024 |
Exports:bootstrapcomp.modelscomp.models.levelscomp.treescomp.trees.levelsCompleteMatconfIntGPScosin.distDescriptionDescription<-distributioneuclidian.distEventsEvents<-eventsNumfitgenerateget.tree.levelsgetDatagetModelgetRespgetTreegpsGPSgpsCIinitializekullback.leiblerL1.distL2.normlikelihoodsLogLikelihoodsModelnoDrawsnumTreesPatientsPatients<-plotprintPval.distrank.cor.distRespSamplesampleSizeSamplingModeSamplingParamSamplingTimesshowsimSimPatternsstability.simStarTreesWaitingTimesWeightsWeights<-WeightsCIWLikelihoods
Dependencies:backportsbase64encBiobaseBiocGenericsbslibcachemcheckmatecliclustercolorspacedata.tabledigestevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2gluegraphgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmennetpillarpkgconfigR6rappdirsRColorBrewerrlangrmarkdownrpartrstudioapisassscalesstringistringrtibbletinytexutf8vctrsviridisviridisLitewithrxfunyaml
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 |
