Package: COMBO
Title: Correcting Misclassified Binary Outcomes in Association Studies
Version: 1.2.0
Authors@R: 
    person("Kimberly", "Hochstedler Webb",
           email = "kah343@cornell.edu", role = c("aut", "cre"))
Author: Kimberly Hochstedler Webb [aut, cre]
Maintainer: Kimberly Hochstedler Webb <kah343@cornell.edu>
Description: Use frequentist and Bayesian methods to estimate
        parameters from a binary outcome misclassification model. These
        methods correct for the problem of "label switching" by
        assuming that the sum of outcome sensitivity and specificity is
        at least 1. A description of the analysis methods is available
        in Hochstedler and Wells (2023)
        <doi:10.48550/arXiv.2303.10215>.
Depends: R (>= 4.2.0)
Imports: dplyr (>= 1.0.10), tidyr (>= 1.2.1), Matrix (> 1.4-1), rjags
        (>= 4-13), turboEM (>= 2021.1), SAMBA (>= 0.9.0), utils (>=
        4.2.0)
Suggests: knitr (>= 1.40), testthat (>= 3.0.0), devtools (>= 2.4.5),
        xtable (>= 1.8.0)
SystemRequirements: JAGS (http://mcmc-jags.sourceforge.net)
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Collate: 'sum_every_n1.R' 'sum_every_n.R' 'pistar_compute.R'
        'pi_compute.R' 'COMBO_data.R' 'expit.R'
        'perfect_sensitivity_EM.R' 'w_j.R' 'q_gamma_f.R' 'q_beta_f.R'
        'em_function.R' 'loglik.R' 'COMBO_EM.R' 'pitilde_compute.R'
        'COMBO_data_2stage.R' 'w_j_2stage.R' 'q_delta_f.R'
        'em_function_2stage.R' 'loglik_2stage.R' 'COMBO_EM_2stage.R'
        'COMBO_EM_data.R' 'label_switch.R' 'check_and_fix_chains.R'
        'mean_pistarjj_compute.R' 'pistar_compute_for_chains.R'
        'pistar_by_chain.R' 'naive_jags_picker.R'
        'naive_model_picker.R' 'jags_picker.R' 'model_picker.R'
        'COMBO_MCMC.R' 'model_picker_2stage.R' 'COMBO_MCMC_2stage.R'
        'LSAC_data.R' 'VPRAI_synthetic_data.R'
        'check_and_fix_chains_2stage.R' 'jags_picker_2stage.R'
        'label_switch_2stage.R' 'misclassification_prob.R'
        'misclassification_prob2.R' 'naive_jags_picker_2stage.R'
        'naive_loglik_2stage.R' 'naive_model_picker_2stage.R'
        'pistar_by_chain_2stage.R' 'pistar_compute_for_chains_2stage.R'
        'pitilde_by_chain.R' 'pitilde_compute_for_chains.R'
        'true_classification_prob.R'
LazyData: true
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make jags libicu-dev
Repository: https://kimberlywebb.r-universe.dev
Date/Publication: 2025-02-25 16:36:29 UTC
RemoteUrl: https://github.com/kimberlywebb/combo
RemoteRef: HEAD
RemoteSha: 9385fedf396d1f7d153d20b64b40a62ee5d9b4a2
NeedsCompilation: no
Packaged: 2026-06-14 07:31:56 UTC; root