R Observatory: Metrics for baker version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

baker

1.0.4Package record

"Nested Partially Latent Class Models"

0packages depend

3.5Kdownloads / year

0.3%test coverage

13/13flavors OK

Overview

About

Maintained by Zhenke WuCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides functions to specify, fit and visualize nested partially-latent class models ( Wu, Deloria-Knoll, Hammitt, and Zeger (2016) doi:10.1111/rssc.12101; Wu, Deloria-Knoll, and Zeger (2017) doi:10.1093/biostatistics/kxw037; Wu and Chen (2021) doi:10.1002/sim.8804) for inference of population disease etiology and individual diagnosis. In the motivating Pneumonia Etiology Research for Child Health (PERCH) study, because both quantities of interest sum to one hundred percent, the PERCH scientists frequently refer to them as population etiology pie and individual etiology pie, hence the name of the package.

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("zhenkewu/baker")

Development version from zhenkewu/baker. Installs pak first if it is not already available.

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-baker

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-baker

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-baker

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMEYes · 1,209 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 154 (1 internal)includes a package overview page
Examples that run: 88%44 run in a plain check · 6 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 2%

Vignettes (1)

Vignettes for baker: An R package for fitting nested partially latent class models

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #5,754 · ~10/day · ~292/mo

Releases R versions

Daily download trend is not available in this view yet.

76130 days

1.4K90 days

3.5K1 year

Compare downloads with other packages →

Also on124 r2u33 autocran

How downloads are counted

Repository

zhenkewu/baker ↗Account: zhenkewu

9Stars

9Forks

0Open issues

0Open PRs

4Releases

728Commits

10Commit identities

rrstatslatent-class-analysiscran-rcase-controlbayesian

728 commits · Last activity 2025-12-12 · 0% stars, 30d · Default branch at 1.0.4.9000, ahead of CRAN 1.0.4 (checked 2026-10-18) · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 53%
Median days to close, 50 most recently updated closed issues: 183
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2024-07-02 · 82026-07-07 · 9

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/zhenkewu/baker on 2026-10-18.

Continuous integration (3)

GitHub ActionsR CMD check workflowAppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-12-12 · The repository has a site deploy workflow

pkgdown site last built 2025-12-12

CRAN release process (2)

cran-comments.mdrevdep/

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing baker adds 142 packages (79 with compiled code, 139 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.3.0

Imports (17)

rjags R2jags lubridate binom(>= 1.1)coda robCompositions ggplot2(>= 1.0)ggpubr gridExtra reshape2mgcvmvbutils shinyFiles shinydashboardstatsutilsabind

LinkingTo (0)

none

Suggests (7)

spelling knitr testthat rmarkdown covr knitcitations sf

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Author

Contributor

Contributor

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-12-12
1.0.4Latest
record
2025-12-12 · current release · diff ↗
archivedRemoved from CRAN
2025-10-19
check issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.3
record
2024-01-30 · diff ↗
unarchivedReturned to CRAN
2023-12-21
1.0.2
record
2023-12-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-06-08
check problems were not corrected in time
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2022-02-02
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-02
Total releases: 4 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3.0
Bundled data: 12 KB / 4 files
Download size: 952 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("baker")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/rssc.12101, 10.1093/biostatistics/kxw037.

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 baker version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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