R Observatory: Metrics for LDATS version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LDATS

0.3.0Package record

Latent Dirichlet Allocation Coupled with Time Series Analyses

1packages depend

8Kdownloads / year

97.7%test coverage

0/13flavors OK

Overview

About

Maintained by Juniper L. SimonisCRAN page ↗GitHub ↗Website ↗Issues ↗

Combines Latent Dirichlet Allocation (LDA) and Bayesian multinomial time series methods in a two-stage analysis to quantify dynamics in high-dimensional temporal data. LDA decomposes multivariate data into lower-dimension latent groupings, whose relative proportions are modeled using generalized Bayesian time series models that include abrupt changepoints and smooth dynamics. The methods are described in Blei et al. (2003) doi:10.1162/jmlr.2003.3.4-5.993, Western and Kleykamp (2004) doi:10.1093/pan/mph023, Venables and Ripley (2002, ISBN-13:978-0387954578), and Christensen et al. (2018) doi:10.1002/ecy.2373.

Changes in 0.3.0

*2023-09-16*

Patching CRAN issues with vignette building

The paper comparison vignette is now pre-computed to avoid needing to access internet resources during cran build (see https://ropensci.org/blog/2019/12/08/precompute-vignettes/).

Converting from travis ci to github actions

Travis CI no longer works, so shifting to github actions for builds

From NEWS.md in the release

Install

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

install.packages("LDATS", 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("weecology/LDATS")

Development version from weecology/LDATS. 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-ldats

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-LDATS

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

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

Health

CRAN checks

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) TS_diagnostics_plot.Rd:19: Lost braces
    19 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^
checkRd: (-1) plot.TS_fit.Rd:29: Lost braces
    29 | \item{interactive}{\code{logical} input, should be code{TRUE} unless
       |                                                        ^

CRAN check page ↗

Slowest check: 4.1 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 674 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.3.0Citation fileNoWebsiteYes · pkgdown

Help pages: 89includes a package overview page
Examples that run: 62%53 run in a plain check · 33 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 96%
Help pages citing references: 16%

Vignettes (3)

Comparison to Christensen et al. 2018 HTML
LDATS Codebase HTML
Rodents Example HTML

How these are measured

Downloads

8K

CRAN downloads in the past year

Rank #7,356 · ~22/day · ~668/mo

Releases R versions

Daily download trend is not available in this view yet.

40530 days

1.2K90 days

8K1 year

Compare downloads with other packages →

Also on66 r2u

How downloads are counted

Repository

weecology/ldats ↗Organization: weecology

25Stars

5Forks

20Open issues

2Open PRs

8Releases

766Commits

6Commit identities

ldaportalchangepointsoftmaxparallel-tempering

766 commits · Last activity 2020-03-19 · 0% stars, 30d · The default branch showed an older version (0.2.7) than CRAN on 2026-10-18

Responsiveness

How these are sampled

PRs merged (all time): 99%
Median days to close, 50 most recently updated closed issues: 28
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-02-05 · 252026-07-07 · 25

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/weecology/ldats on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

Governance and community (2)

Code of conductContributing guide

Docs source (2)

pkgdown

GitHub Pages site last deployed 2020-03-19

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Research and citation (1)

Zenodo

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing LDATS adds 44 packages (21 with compiled code, 38 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, viridis 2.9 MB.

Depends (1)

R >= 3.5.0

Imports (15)

coda digest extraDistrgraphicsgrDeviceslubridate magrittr memoisemethodsmvtnormnnetprogressstatstopicmodels viridis

LinkingTo (0)

none

Suggests (5)

knitr pkgdown rmarkdown testthat vdiffr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

argminCS

How these are counted

Code & Tests

Datasets

People & History

People (8)

Juniper L. Simonis

Author, Maintainer since 0.2.4 (2019)

Author

Author

Author

Author

Author

Author

Copyright holder

Listed in earlier versions (6)

Show 6 peopleHide 6 people

David J.