R Observatory: Metrics for BayesPocket version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BayesPocket

0.1.0

Bayesian Causal Inference for Periodontal Diseases in Longitudinal Studies

0packages depend

1.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Qingyang LiuFirst published 2026-05-131 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("BayesPocket", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bayespocket

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-BayesPocket

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-BayesPocket

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.1 min · r-release-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

8

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-14
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.2K

CRAN downloads in the past year

Rank #9,552 · ~3/day · ~98/mo

Releases R versions

Daily download trend is not available in this view yet.

23330 days

97690 days

1.2K1 year

Compare downloads with other packages →

Also on24 r2u10 autocran

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (8)

statsGIGrvg truncnorm progress stochtree SoftBartparallelpbmcapply

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Qingyang Liu

Author, Maintainer

Authors (4)

Qingyang Liu

Author, Maintainer

Dipankar Bandyopadhyay

Author

Yang Ni

Author

Debdeep Pati

Author

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-05-13 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-13
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5
Download size: 17 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BayesPocket")

Format

Liu, Q., Bandyopadhyay, D., Ni, Y., & Pati, D. (2026). BayesPocket: Bayesian Causal Inference for Periodontal Diseases in Longitudinal Studies (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.BayesPocket

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for BayesPocket version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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