Package: Umpire 2.0.10
Kevin R. Coombes
Umpire: Simulating Realistic Gene Expression and Clinical Data
The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.
Authors:
Umpire_2.0.10.tar.gz
Umpire_2.0.10.tar.gz(r-4.5-noble)Umpire_2.0.10.tar.gz(r-4.4-noble)
Umpire_2.0.10.tgz(r-4.4-emscripten)Umpire_2.0.10.tgz(r-4.3-emscripten)
Umpire.pdf |Umpire.html✨
Umpire/json (API)
# Install 'Umpire' in R: |
install.packages('Umpire', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/oompa
Last updated 4 years agofrom:46c5342920. Checks:OK: 1 NOTE: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 09 2024 |
R-4.5-linux | NOTE | Dec 09 2024 |
Exports:addControlalterMeanalterSDBlockHyperParametersblurCancerEngineCancerModelClinicalEngineClinicalNoiseModelcorrelcovarEngineEngineWithActivitygetDaisyTypesgetDataTypesIndependentLogNormalIndependentNormalinvGammaMultiplemakeBlockStructuremakeDataTypesMixedTypeEngineMVNncolnComponentsnHitsPerPatternNoiseModelnormalOffsetNormalVsCancerEngineNormalVsCancerModelnPatternsnPossibleHitsnrowoutcomeCoefficientsrandsummarysurvivalCoefficientsSurvivalModel
Dependencies:abindbackportsBimodalIndexbootbroomcarcarDatacliclustercolorspacecorrplotcowplotcpp11DerivdoBydplyrfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmc2dmclustmgcvmicrobenchmarkminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivoompaBasepbkrtestpillarpkgconfigpolynompurrrquantregR6RColorBrewerRcppRcppEigenrlangrstatixscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr
Umpire 2.0: Clinically Realistic Simulations
Rendered fromUmpire2.Rmd
usingknitr::rmarkdown
on Dec 09 2024.Last update: 2020-08-02
Started: 2020-04-14
Umpire Primer
Rendered fromUmpire.Rnw
usingutils::Sweave
on Dec 09 2024.Last update: 2017-07-11
Started: 2017-07-11
Umpire 2.0: Simulating Associated Survival
Rendered fromsurv.Rmd
usingknitr::rmarkdown
on Dec 09 2024.Last update: 2020-06-01
Started: 2020-06-01
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Method "addControl" | addControl addControl,ANY-method addControl,CancerEngine-method addControl,CancerModel-method addControl-method |
Methods "alterMean" and "alterSD" | alterMean alterMean,ANY-method alterMean-method alterSD alterSD,ANY-method alterSD-method |
The "BlockHyperParameters" Class | BlockHyperParameters BlockHyperParameters-class makeBlockStructure |
Method "blur" | blur blur,ANY-method blur-method |
The "CancerEngine" Class | CancerEngine CancerEngine-class ClinicalEngine nComponents,CancerEngine-method nrow,CancerEngine-method rand,CancerEngine-method summary,CancerEngine-method |
The "CancerModel" Class | CancerModel CancerModel-class ncol,CancerModel-method nHitsPerPattern nPatterns nPossibleHits nrow,CancerModel-method outcomeCoefficients rand,CancerModel-method summary,CancerModel-method survivalCoefficients |
A Noise Model for Clinical Data | ClinicalNoiseModel |
The "Engine" Class | alterMean,Engine-method alterSD,Engine-method Engine Engine-class nComponents,Engine-method nrow,Engine-method rand,Engine-method summary,Engine-method |
The "EngineWithActivity" Class | EngineWithActivity EngineWithActivity-class rand,EngineWithActivity-method summary,EngineWithActivity-method |
The "IndependentLogNormal" Class | alterMean,IndependentLogNormal-method alterSD,IndependentLogNormal-method IndependentLogNormal IndependentLogNormal-class nrow,IndependentLogNormal-method rand,IndependentLogNormal-method summary,IndependentLogNormal-method |
The "IndependentNormal" Class | alterMean,IndependentNormal-method alterSD,IndependentNormal-method IndependentNormal IndependentNormal-class nrow,IndependentNormal-method rand,IndependentNormal-method summary,IndependentNormal-method |
Discretize a Continuous Data Set to Mixed Types | getDaisyTypes getDataTypes makeDataTypes |
The "MixedTypeEngine" Class | MixedTypeEngine MixedTypeEngine-class rand,MixedTypeEngine-method summary,MixedTypeEngine-method |
The "MVN" Class | alterMean,MVN-method alterSD,MVN-method correl covar MVN MVN-class nrow,MVN-method rand,MVN-method summary,MVN-method |
Method "nComponents" | nComponents nComponents,ANY-method nComponents-method |
The "NoiseModel" Class | blur,NoiseModel-method NoiseModel NoiseModel-class summary,NoiseModel-method |
Simulating Cancer Versus Normal Datasets | NormalVsCancerEngine NormalVsCancerModel |
Method "rand" | rand rand,ANY-method rand-method |
The "SurvivalModel" Class | rand,SurvivalModel-method SurvivalModel SurvivalModel-class |
Transform functions | invGammaMultiple normalOffset |