Package: COMMA 1.0.0

COMMA: Correcting Misclassified Mediation Analysis

Use three methods to estimate parameters from a mediation analysis with a binary misclassified mediator. These methods correct for the problem of "label switching" using Youden's J criteria. A detailed description of the analysis methods is available in Webb and Wells (2024), "Effect estimation in the presence of a misclassified binary mediator" <doi:10.48550/arXiv.2407.06970>.

Authors:Kimberly Webb [aut, cre]

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COMMA/json (API)

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

Peer review:

Bug tracker:https://github.com/kimberlywebb/comma/issues

On CRAN:

6 exports 1.46 score 13 dependencies 10 scripts 171 downloads

Last updated 2 months agofrom:4ce3ba127c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 29 2024
R-4.5-winOKAug 29 2024
R-4.5-linuxOKAug 29 2024
R-4.4-winOKAug 29 2024
R-4.4-macOKAug 29 2024
R-4.3-winOKAug 29 2024
R-4.3-macOKAug 29 2024

Exports:COMMA_dataCOMMA_EMCOMMA_OLSCOMMA_PVWmisclassification_probtrue_classification_prob

Dependencies:codetoolsdoParallelforeachiteratorslatticeMASSMatrixMatrixModelsnumDerivquantregSparseMsurvivalturboEM

COMMA Notation Guide

Rendered fromCOMMA_Notation_Guide.Rmdusingknitr::knitron Aug 29 2024.

Last update: 2024-06-18
Started: 2024-06-05

Demonstration of the COMMA R Package

Rendered fromCOMMA_demo.Rmdusingknitr::knitron Aug 29 2024.

Last update: 2024-07-06
Started: 2024-06-05

Readme and manuals

Help Manual

Help pageTopics
EM-Algorithm Estimation of the Binary Outcome Misclassification ModelCOMBO_EM_algorithm
EM-Algorithm Function for Estimation of the Misclassification ModelCOMBO_EM_function
Compute E-step for Binary Outcome Misclassification Model Estimated With the EM-AlgorithmCOMBO_weight
Generate Data to use in COMMA FunctionsCOMMA_data
EM Algorithm Estimation of the Binary Mediator Misclassification ModelCOMMA_EM
Ordinary Least Squares Estimation of the Binary Mediator Misclassification ModelCOMMA_OLS
Predictive Value Weighting Estimation of the Binary Mediator Misclassification ModelCOMMA_PVW
EM Algorithm Function for Estimation of the Misclassification ModelEM_function_bernoulliY
EM Algorithm Function for Estimation of the Misclassification ModelEM_function_bernoulliY_XM
EM Algorithm Function for Estimation of the Misclassification ModelEM_function_normalY
EM Algorithm Function for Estimation of the Misclassification ModelEM_function_normalY_XM
EM Algorithm Function for Estimation of the Misclassification ModelEM_function_poissonY
EM Algorithm Function for Estimation of the Misclassification ModelEM_function_poissonY_XM
Compute Conditional Probability of Observed Mediator Given True Mediator, for Every Subjectmisclassification_prob
Compute Probability of Each True Outcome, for Every Subjectpi_compute
Compute Conditional Probability of Each Observed Outcome Given Each True Outcome, for Every Subjectpistar_compute
Sum Every "n"th Elementsum_every_n
Sum Every "n"th Element, then add 1sum_every_n1
Likelihood Function for Normal Outcome Mechanism with a Binary Mediatortheta_optim
Likelihood Function for Normal Outcome Mechanism with a Binary Mediator and an Interaction Termtheta_optim_XM
Compute Probability of Each True Mediator, for Every Subjecttrue_classification_prob
Compute E-step for Binary Mediator Misclassification Model Estimated With the EM Algorithmw_m_binaryY
Compute E-step for Binary Mediator Misclassification Model Estimated With the EM Algorithmw_m_normalY
Compute E-step for Binary Mediator Misclassification Model Estimated With the EM Algorithmw_m_poissonY