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:Kevin R. Coombes, Jiexin Zhang, Caitlin E. Coombes

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

3.54 score 58 scripts 259 downloads 2 mentions 37 exports 74 dependencies

Last updated 4 years agofrom:46c5342920. Checks:OK: 1 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 09 2024
R-4.5-linux	NOTE	Nov 09 2024

Exports:addControl alterMean alterSD BlockHyperParameters blur CancerEngine CancerModel ClinicalEngine ClinicalNoiseModel correl covar Engine EngineWithActivity getDaisyTypes getDataTypes IndependentLogNormal IndependentNormal invGammaMultiple makeBlockStructure makeDataTypes MixedTypeEngine MVN ncol nComponents nHitsPerPattern NoiseModel normalOffset NormalVsCancerEngine NormalVsCancerModel nPatterns nPossibleHits nrow outcomeCoefficients rand summary survivalCoefficients SurvivalModel

Dependencies:abind backports BimodalIndex boot broom car carData cli cluster colorspace corrplot cowplot cpp11 Deriv doBy dplyr fansi farver Formula generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable isoband labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mc2d mclust mgcv microbenchmark minqa modelr munsell mvtnorm nlme nloptr nnet numDeriv oompaBase pbkrtest pillar pkgconfig polynom purrr quantreg R6 RColorBrewer Rcpp RcppEigen rlang rstatix scales SparseM stringi stringr survival tibble tidyr tidyselect utf8 vctrs viridisLite withr

Umpire 2.0: Clinically Realistic Simulations

Kevin R. Coombes and Caitlin E. Coombes

Rendered fromUmpire2.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2020-08-02
Started: 2020-04-14

Umpire Primer

Rendered fromUmpire.Rnwusingutils::Sweaveon Nov 09 2024.

Last update: 2017-07-11
Started: 2017-07-11

Umpire 2.0: Simulating Associated Survival

Kevin R. Coombes and Caitlin E. Coombes

Rendered fromsurv.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2020-06-01
Started: 2020-06-01

Citation

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