Package: binGroup2 1.3.1

binGroup2: Identification and Estimation using Group Testing

Methods for the group testing identification problem: 1) Operating characteristics (e.g., expected number of tests) for commonly used hierarchical and array-based algorithms, and 2) Optimal testing configurations for these same algorithms. Methods for the group testing estimation problem: 1) Estimation and inference procedures for an overall prevalence, and 2) Regression modeling for commonly used hierarchical and array-based algorithms.

Authors:Brianna Hitt [aut, cre], Christopher Bilder [aut], Frank Schaarschmidt [aut], Brad Biggerstaff [aut], Christopher McMahan [aut], Joshua Tebbs [aut], Boan Zhang [ctb], Michael Black [ctb], Peijie Hou [ctb], Peng Chen [ctb], Minh Nguyen [ctb]

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binGroup2.pdf |binGroup2.html✨
binGroup2/json (API)
NEWS

# Install 'binGroup2' in R:
install.packages('binGroup2', repos = c('https://bdhitt.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • hivsurv - Data from an HIV surveillance project

On CRAN:

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

2.48 score 1 packages 3 scripts 260 downloads 1 mentions 37 exports 38 dependencies

Last updated 1 years agofrom:c1965c4a56. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64OKNov 07 2024
R-4.5-linux-x86_64OKNov 07 2024
R-4.4-win-x86_64OKNov 07 2024
R-4.4-mac-x86_64OKNov 07 2024
R-4.4-mac-aarch64OKNov 07 2024
R-4.3-win-x86_64OKNov 07 2024
R-4.3-mac-x86_64OKNov 07 2024
R-4.3-mac-aarch64OKNov 07 2024

Exports:AccuracyCompareConfigConfigConfig.opCharConfig.OTCdesignEstdesignPowerexpectOrderBetaExpTestsExpTests.halvingExpTests.opCharExpTests.OTCExpTests.SterrettExpTests.TODGroupMembershipMatrixgtPowergtReggtRegControlgtSimgtTestgtWidthhalvingIndProbinformativeArrayProbopChar1opChar2operatingCharacteristics1operatingCharacteristics2OTC1OTC2pmfpmf.halvingpmf.SterrettpropCIpropDiffCISterrettTOD

Dependencies:clicolorspacefansifarverggplot2gluegmpgtableisobandlabelinglatticelifecyclemagrittrMASSmathjaxrMatrixmgcvmunsellnlmepartitionspillarpkgconfigpolynomR6rBeta2009rbibutilsRColorBrewerRcppRcppArmadilloRdpackrlangscalessetstibbleutf8vctrsviridisLitewithr

Identification-through-group-testing

Rendered fromIdentification-through-group-testing.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2023-11-14
Started: 2023-11-14

Readme and manuals

Help Manual

Help pageTopics
Extract the accuracy measures from group testing resultsAccuracy
binGroup2: Identification and Estimation using Group TestingbinGroup2-package binGroup2
Extract coefficients from a fitted group testing modelcoef.gtReg coefficients.gtReg
Compare group testing resultsCompareConfig
Access the testing configurations returned from an objectConfig
Extract the testing configuration from group testing resultsConfig.opChar
Extract the testing configuration from group testing resultsConfig.OTC
Optimal group size determination based on minimal MSE when estimating an overall prevalencedesignEst
Number of groups or group size needed to achieve a power level in one parameter group testingdesignPower
Determine a vector of probabilities for informative group testing algorithmsexpectOrderBeta
Access the expected number of tests from an objectExpTests
Extract the expected number of tests from testing configuration resultsExpTests.halving
Extract the expected number of tests from testing configuration resultsExpTests.opChar
Extract the expected number of tests from optimal testing configuration resultsExpTests.OTC
Extract the expected number of tests from testing configuration resultsExpTests.Sterrett
Extract the expected number of tests from testing configuration resultsExpTests.TOD
Extract the model formula from a fitted group testing modelformula.gtReg
Construct a group membership matrix for hierarchical algorithmsGroupMembershipMatrix
Power to reject a hypothesis for one proportion in group testinggtPower
Fitting group testing regression modelsgtReg
Auxiliary for controlling group testing regressiongtRegControl
Simulation function for group testing datagtSim
Hypothesis test for one proportion in group testinggtTest
Expected width of confidence intervals in group testinggtWidth
Probability mass function for halvinghalving
Data from an HIV surveillance projecthivsurv
Extract the individual probabilities used to calculate group testing resultsIndProb
Arrange a matrix of probabilities for informative array testinginformativeArrayProb
Calculate operating characteristics for group testing algorithms that use a single-disease assayopChar1 operatingCharacteristics1
Calculate operating characteristics for group testing algorithms that use a multiplex assay for two diseasesopChar2 operatingCharacteristics2
Find the optimal testing configuration for group testing algorithms that use a single-disease assayOTC1
Find the optimal testing configuration for group testing algorithms that use a multiplex assay for two diseasesOTC2
Plot method for optimal testing configuration resultsplot.OTC
Access the testing probability mass function returned from an objectpmf
Extract probability mass function (PMF) from group testing resultspmf.halving
Extract probability mass function (PMF) from group testing resultspmf.Sterrett
Predict method for 'gtReg'predict.gtReg
Print method for objects of class "designEst"print.designEst
Print method for objects of class "designPower"print.designPower
Print method for 'gtReg'print.gtReg
Print method for objects of class "gtTest"print.gtTest
Print method for objects of class "halving"print.halving
Print method for operating characteristics resultsprint.opChar
Print method for optimal testing configuration resultsprint.OTC
Print method for 'predict.gtReg'print.predict.gtReg
Print method for objects of class "propCI"print.propCI
Print method for objects of class "propDiffCI"print.propDiffCI
Print method for objects of class "Sterrett"print.Sterrett
Print method for 'summary.gtReg'print.summary.gtReg
Print method for 'TOD'print.TOD
Confidence intervals for one proportion in group testingpropCI
Confidence intervals for the difference of proportions in group testingpropDiffCI
Extract model residuals from a fitted group testing modelresiduals.gtReg
Summary measures for Sterrett algorithmsSterrett
Summary method for 'gtReg'summary.gtReg
Summary method for operating characteristics resultssummary.opChar
Summary method for optimal testing configuration resultssummary.OTC
Summary measures for the Thresholded Optimal Dorfman (TOD) algorithmTOD