Package: CopulaREMADA 1.7.3

Aristidis K. Nikoloulopoulos

CopulaREMADA: Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy Studies

The bivariate copula mixed model for meta-analysis of diagnostic test accuracy studies in Nikoloulopoulos (2015) <doi:10.1002/sim.6595> and Nikoloulopoulos (2018) <doi:10.1007/s10182-017-0299-y>. The vine copula mixed model for meta-analysis of diagnostic test accuracy studies accounting for disease prevalence in Nikoloulopoulos (2017) <doi:10.1177/0962280215596769> and also accounting for non-evaluable subjects in Nikoloulopoulos (2020) <doi:10.1515/ijb-2019-0107>. The hybrid vine copula mixed model for meta-analysis of diagnostic test accuracy case-control and cohort studies in Nikoloulopoulos (2018) <doi:10.1177/0962280216682376>. The D-vine copula mixed model for meta-analysis and comparison of two diagnostic tests in Nikoloulopoulos (2019) <doi:10.1177/0962280218796685>. The multinomial quadrivariate D-vine copula mixed model for meta-analysis of diagnostic tests with non-evaluable subjects in Nikoloulopoulos (2020) <doi:10.1177/0962280220913898>. The one-factor copula mixed model for joint meta-analysis of multiple diagnostic tests in Nikoloulopoulos (2022) <doi:10.1111/rssa.12838>. The multinomial six-variate 1-truncated D-vine copula mixed model for meta-analysis of two diagnostic tests accounting for within and between studies dependence in Nikoloulopoulos (2024) <doi:10.1177/09622802241269645>. The 1-truncated D-vine copula mixed models for meta-analysis of diagnostic accuracy studies without a gold standard (Nikoloulopoulos, 2024).

Authors:Aristidis K. Nikoloulopoulos [aut, cre]

CopulaREMADA_1.7.3.tar.gz
CopulaREMADA_1.7.3.tar.gz(r-4.5-noble)CopulaREMADA_1.7.3.tar.gz(r-4.4-noble)
CopulaREMADA_1.7.3.tgz(r-4.4-emscripten)CopulaREMADA_1.7.3.tgz(r-4.3-emscripten)
CopulaREMADA.pdf |CopulaREMADA.html
CopulaREMADA/json (API)

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

Peer review:

Datasets:
  • CT - The computing tomography data
  • Down - The down syndrome data
  • LAG - The lymphangiography data
  • MK2016 - The coronary CT angiography data in Menke and Kowalski (2016).
  • MRI - The magnetic resonance imaging data
  • OGT - The orale glucose tolerance data
  • Pap - The Pap test data
  • arthritis - The rheumatoid arthritis data
  • betaDG - The beta-D-Glucan-data
  • coronary - The coronary CT angiography data
  • mgrid - A list containing four-dimensional arrays
  • mgrid15 - A list containing four-dimensional arrays
  • mgrid30 - A list containing four-dimensional arrays
  • mgrid50 - A list containing four-dimensional arrays
  • mgrid5d15 - A list containing five-dimensional arrays
  • mgrid5d30 - A list containing five-dimensional arrays
  • telomerase - The telomerase data

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

1.60 score 2 stars 10 scripts 474 downloads 1 mentions 90 exports 73 dependencies

Last updated 1 months agofrom:7f7d5607eb. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-linuxOKNov 17 2024

Exports:CopulaREMADA.betaCopulaREMADA.normcountermonotonicCopulaREMADA.betacountermonotonicCopulaREMADA.normcountermonotonicity.vuongcvinesimdbvndclndcln180dcln270dcln90dfrkdtrvinesimdvine6dsimdvinesimFactorCopulaREMADA.betaFactorCopulaREMADA.normhybridCopulaREMADA.betahybridCopulaREMADA.normimperfect.fivevariateVineCopulaREMADA.beta.comprehensiveimperfect.fivevariateVineCopulaREMADA.norm.comprehensiveimperfect.quadrivariateVineCopulaREMADA.beta.comprehensiveimperfect.quadrivariateVineCopulaREMADA.norm.comprehensiveimperfect.trivariateVineCopulaREMADA.betaimperfect.trivariateVineCopulaREMADA.beta.comprehensiveimperfect.trivariateVineCopulaREMADA.normimperfect.trivariateVineCopulaREMADA.norm.comprehensiveimperfectCopulaREMADA.betaimperfectCopulaREMADA.normimperfectREMADA.betaimperfectREMADA.normmultinom6dVineCopulaREMADA.betamultinom6dVineCopulaREMADA.normmultinomVineCopulaREMADA.betamultinomVineCopulaREMADA.normpcondbvnpcondclnpcondcln180pcondcln270pcondcln90pcondfrkqcondbvnqcondclnqcondcln180qcondcln270qcondcln90qcondfrkquadVineCopulaREMADA.betaquadVineCopulaREMADA.normquadVineCopulaREMADA.norm.betarclnrcln180rcln270rcln90rCopulaREMADA.betarCopulaREMADA.normrFactorCopulaREMADA.betarFactorCopulaREMADA.normrfrkrimperfect.trivariateVineCopulaREMADA.betarimperfect.trivariateVineCopulaREMADA.normrmultinom6dVineCopulaREMADA.betarmultinom6dVineCopulaREMADA.normrmultinomVineCopulaREMADA.betarmultinomVineCopulaREMADA.normrVineCopulaREMADA.betarVineCopulaREMADA.normSROCSROC.betaSROC.normtau2par.bvntau2par.clntau2par.cln180tau2par.cln270tau2par.cln90tau2par.frktmultinomVineCopulaREMADA.betatmultinomVineCopulaREMADA.normtvine.vuong.betatvine.vuong.normtvine2.vuong.betatvine2.vuong.normtVineCopulaREMADA.betatVineCopulaREMADA.normvine.vuong.betavine.vuong.normVineCopulaREMADA.betaVineCopulaREMADA.normvuong.betavuong.norm

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11DerivdoBydplyrfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4magrittrMASSmatlabMatrixMatrixModelsmc2dmgcvmicrobenchmarkminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynompurrrquantregR6RColorBrewerRcppRcppEigenrlangrstatixscalesSparseMstatmodstringistringrsurvivaltensortibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy StudiesCopulaREMADA-package
The rheumatoid arthritis dataarthritis
The beta-D-Glucan-databetaDG
Maximum likelhood estimation for copula mixed models for diagnostic test accurracy studiesCopulaREMADA CopulaREMADA.beta CopulaREMADA.norm countermonotonicCopulaREMADA countermonotonicCopulaREMADA.beta countermonotonicCopulaREMADA.norm
The coronary CT angiography datacoronary
The computing tomography dataCT
Simulation from a trivariate C-vine copulacvinesim
Bivariate copula densitiesdbvn dcln dcln180 dcln270 dcln90 dcop dfrk
The down syndrome dataDown
Simulation from a six-variate 1-truncated D-vine copuladvine6dsim
Simulation from a (truncated) quadrivariate D-vine copuladtrvinesim dvinesim
Maximum likelihood estimation of 1-factor copula mixed models for joint meta-analysis of T diagnostic testsFactorCopulaREMADA FactorCopulaREMADA.beta FactorCopulaREMADA.norm
Maximum likelhood estimation for hybrid copula mixed models for combining case-control and cohort studies in meta-analysis of diagnostic testshybridCopulaREMADA hybridCopulaREMADA.beta hybridCopulaREMADA.norm
Maximum likelihood estimation of 5-variate 1-truncated D-vine copula mixed models for meta-analysis of diagnostic accuracy studies without a gold standardimperfect.fivevariateVineCopulaREMADA.beta.comprehensive imperfect.fivevariateVineCopulaREMADA.norm.comprehensive
Maximum likelihood estimation of quadrivariate 1-truncated D-vine copula mixed models for meta-analysis of diagnostic accuracy studies without a gold standardimperfect.quadrivariateVineCopulaREMADA.beta.comprehensive imperfect.quadrivariateVineCopulaREMADA.norm.comprehensive
Maximum likelihood estimation of trivariate 1-truncated D-vine copula mixed models for meta-analysis of diagnostic accuracy studies without a gold standardimperfect.trivariateVineCopulaREMADA imperfect.trivariateVineCopulaREMADA.beta imperfect.trivariateVineCopulaREMADA.beta.comprehensive imperfect.trivariateVineCopulaREMADA.norm imperfect.trivariateVineCopulaREMADA.norm.comprehensive
Maximum likelihood estimation of bivariate copula mixed models for meta-analysis of diagnostic accuracy studies without a gold standardimperfectCopulaREMADA imperfectCopulaREMADA.beta imperfectCopulaREMADA.norm
Maximum likelihood estimation of univariate mixed models for meta-analysis of diagnostic accuracy studies without a gold standardimperfectREMADA imperfectREMADA.beta imperfectREMADA.norm
The lymphangiography dataLAG
A list containing four-dimensional arraysmgrid mgrid15 mgrid30 mgrid50
A list containing five-dimensional arraysmgrid5d mgrid5d15 mgrid5d30
A list containing six-dimensional arraysmgrid6d
The coronary CT angiography data in Menke and Kowalski (2016).MK2016
The magnetic resonance imaging dataMRI
Maximum likelhood estimation for multinomial six-variate 1-truncated D-vine copula mixed models for meta-analysis of two diagnostic tests accounting for within and between studies dependencemultinom6dVineCopulaREMADA multinom6dVineCopulaREMADA.beta multinom6dVineCopulaREMADA.norm
Maximum likelhood estimation for multinomial quadrivariate (truncated) D-vine copula mixed models for diagnostic test accurracy studies accounting for non-evaluable outcomesmultinomVineCopulaREMADA multinomVineCopulaREMADA.beta multinomVineCopulaREMADA.norm tmultinomVineCopulaREMADA tmultinomVineCopulaREMADA.beta tmultinomVineCopulaREMADA.norm
The orale glucose tolerance dataOGT
The Pap test dataPap
Bivariate copula conditional distribution functionspcondbvn pcondcln pcondcln180 pcondcln270 pcondcln90 pcondcop pcondfrk
Bivariate copula conditional quantile functionsqcondbvn qcondcln qcondcln180 qcondcln270 qcondcln90 qcondcop qcondfrk
Maximum likelihood estimation of quadrivariate D-vine copula mixed models for joint meta-analysis and comparison of two diagnostic testsquadVineCopulaREMADA quadVineCopulaREMADA.beta quadVineCopulaREMADA.norm quadVineCopulaREMADA.norm.beta
Simulation from parametric bivariate copula familiesrbvn rcln rcln180 rcln270 rcln90 rcop rfrk
Simulation from copula mixed models for diagnostic test accuaracy studiesrCopulaREMADA rCopulaREMADA.beta rCopulaREMADA.norm
Simulation from 1-factor copula mixed models for joint meta-analysis of T diagnostic testsrFactorCopulaREMADA rFactorCopulaREMADA.beta rFactorCopulaREMADA.norm
Simulation from trivariate 1-truncated D-vine copula mixed models for meta-analysis of diagnostic accuracy studies without a gold standardrimperfect.trivariateVineCopulaREMADA rimperfect.trivariateVineCopulaREMADA.beta rimperfect.trivariateVineCopulaREMADA.norm
Simulation from multinomial six-variate 1-truncated D-vine copula mixed models for meta-analysis of two diagnostic tests accounting for within and between studies dependencermultinom6dVineCopulaREMADA rmultinom6dVineCopulaREMADA.beta rmultinom6dVineCopulaREMADA.norm
Simulation from multinomial quadrivariate (truncated) D-vine copula mixed models for diagnostic test accurracy studies accounting for non-evaluable outcomesrmultinomVineCopulaREMADA rmultinomVineCopulaREMADA.beta rmultinomVineCopulaREMADA.norm
Simulation from trivariate vine copula mixed models for diagnostic test accuaracy studies accounting for disease prevalence and non-evaluable resultsrVineCopulaREMADA rVineCopulaREMADA.beta rVineCopulaREMADA.norm
Summary receiver operating characteristic curves for copula mixed effect models for bivariate meta-analysis of diagnostic test accuracy studiesSROC SROC.beta SROC.norm
Mapping of Kendall's tau and copula parametertau2par tau2par.bvn tau2par.cln tau2par.cln180 tau2par.cln270 tau2par.cln90 tau2par.frk
The telomerase datatelomerase
Vuong's test for the comparison of non-nested vine copula mixed models for diagnostic test accuaracy studiestvine.vuong.beta tvine.vuong.norm tvine2.vuong.beta tvine2.vuong.norm vine.vuong vine.vuong.beta vine.vuong.norm
Maximum likelhood estimation for (truncated) vine copula mixed models for diagnostic test accurracy studies accounting for disease prevalence and non-evaluable outcomestVineCopulaREMADA tVineCopulaREMADA.beta tVineCopulaREMADA.norm VineCopulaREMADA VineCopulaREMADA.beta VineCopulaREMADA.norm
Vuong's test for the comparison of non-nested copula mixed models for diagnostic test accuaracy studiescountermonotonicity.vuong vuong vuong.beta vuong.norm