Package: BayesPocket
Type: Package
Title: Bayesian Causal Inference for Periodontal Diseases in
        Longitudinal Studies
Version: 0.1.0
Authors@R: c(
    person("Qingyang", "Liu", email = "rh8liuqy@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3265-6330")),
    person("Debdeep", "Pati", email = "dpati2@wisc.edu", role = c("aut")),
    person("Yang", "Ni", email = "yang.ni@austin.utexas.edu", role = c("aut")),
    person("Dipankar", "Bandyopadhyay", email = "dbandyop@vcu.edu", role = "aut")
  )
Description: Implements the Mixed Treatment-State Causal Model (MTSCM), a Bayesian 
    framework for estimating causal effects of clinical interventions on bounded 
    continuous outcomes in longitudinal observational studies with irregular visits. 
    The methodology is specifically designed for periodontal disease research, where 
    discrete treatments and continuous disease states (e.g., proportion of periodontal 
    pockets exceeding 3 mm) reciprocally influence one another under dynamic feedback. 
    The package integrates a double-censored Tobit likelihood to handle boundary mass 
    at zero and one, subject-specific random effects to capture within-subject 
    correlation, and flexible tree-based ensemble priors (standard BART and Soft BART) 
    to model complex nonlinear interactions without parametric restrictions. Causal 
    identification is established under the potential outcomes framework via the 
    G-computation formula, with key estimands including the Mixed Average Potential 
    Outcome (MAPO) and the Mixed Probability of Disease Resolution (MPDR). The 
    package provides functions for model fitting, posterior inference, and causal estimand 
    estimation.
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: stats (>= 4.4.2), GIGrvg(>= 0.8), truncnorm(>= 1.0-9),
        progress(>= 1.2.3), stochtree(>= 0.1.1), SoftBart(>= 1.0.3),
        parallel(>= 4.4.2), pbmcapply(>= 1.5.1)
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2026-05-08 20:31:34 UTC; kevin_liu
Author: Qingyang Liu [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3265-6330>),
  Debdeep Pati [aut],
  Yang Ni [aut],
  Dipankar Bandyopadhyay [aut]
Maintainer: Qingyang Liu <rh8liuqy@gmail.com>
Repository: CRAN
Date/Publication: 2026-05-13 08:10:22 UTC
Built: R 4.5.2; ; 2026-05-13 11:23:31 UTC; unix
