R Observatory: Metrics for hmde version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hmde

1.4.0Package record

Hierarchical Methods for Differential Equations

0packages depend

3.2Kdownloads / year

72.8%test coverage

13/13flavors OK

Overview

About

Maintained by Tess O'BrienCRAN page ↗GitHub ↗Website ↗Issues ↗

Wrapper for 'Stan' that offers a number of in-built models to implement a hierarchical Bayesian longitudinal model for repeat observation data. Model choice selects the differential equation that is fit to the observations. Single and multi-individual models are available. O'Brien et al. (2024) doi:10.1111/2041-210X.14463.

Install

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

install.packages("hmde", 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("traitecoevo/hmde")

Development version from traitecoevo/hmde. 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-hmde

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-hmde

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-hmde

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: 32.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.0

READMEYes · 534 wordsVignettesYes · 6 · dynamicNEWSYes · 67% structured · does not mention 1.4.0Citation fileNoWebsiteYes · pkgdown

Help pages: 31 (2 internal)includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 42%
Documented parameters: 99%
Return-value docs: 58%
Help pages citing references: 6%

Vignettes (6)

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #11,833 · ~9/day · ~270/mo

Releases R versions

Daily download trend is not available in this view yet.

41030 days

92790 days

3.2K1 year

Compare downloads with other packages →

Also on457 r2u5 autocran

How downloads are counted

Repository

traitecoevo/hmde ↗Organization: traitecoevo

5Stars

4Forks

2Open issues

0Open PRs

9Releases

67Commits

3Commit identities

bayesian-inverse-problemsbayesian-methodsdifferential-equationshierarchical-modelsrrstanstan

67 commits · Last activity 2026-05-06

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 24
Median days to close, 50 most recently updated closed PRs: 1

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/traitecoevo/hmde on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-07 · The repository has a site deploy workflow

pkgdown site last built 2026-05-07

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing hmde adds 57 packages (27 with compiled code, 47 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, loo 2.7 MB.

Depends (1)

R >= 4.1.0

Imports (12)

methodsdplyr ggplot2 Rcpp RcppParallel (>= 5.0.1)rlang rstan rstantools tibble cowplot knitr purrr

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (9)

rmarkdown testthat withr mnormt here patchwork deSolve mixtoolsMASS

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

Author, Contributor

Contributor

Releases (5)

Pick two releases to compare their code metrics.

1.4.0Latest
record
2026-05-04 · current release · diff ↗ ·
removed 2 exports
hmde_assign_data, hmde_extract_estimates

added 26 exports
error_ests<-, fit_summary<-, individual_ests<-, measurement_ests<-, method<-, model_level<-, model_name<-, obs_data<-, par_names<-, population_ests<-, prior_pars<-, runtime<-, error_ests, fit_summary, hmde_data_template, hmde_estimates, individual_ests, measurement_ests, method, model_level, model_name, obs_data, par_names, population_ests, prior_pars, runtime
R
R 4.6.0 released · 2026-04-24
1.3.1
record
2025-12-23 · diff ↗
1.3
record
2025-11-27 · diff ↗ ·
added 2 exports
hmde_extract_Rhat, hmde_plot_Rhat_hist
1.2.2
record
2025-10-02 · diff ↗
1.2.1
record
2025-07-04
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-04
Total releases: 5 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 18 KB / 4 files
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hmde")

Format

O'Brien, T., Falster, D., Kar, F., & Warton, D. (2026). hmde: Hierarchical Methods for Differential Equations (Version 1.4.0) [Computer software]. https://doi.org/10.32614/CRAN.package.hmde

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 hmde version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →