R Observatory: Metrics for flocker version 1.1-0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

flocker

1.1-0Package record

Flexible Occupancy Estimation with Stan

0packages depend

3.1Kdownloads / year

93.6%test coverage

13/13flavors OK

Overview

About

Maintained by Jacob B. SocolarCRAN page ↗GitHub ↗Website ↗Issues ↗

Fit occupancy models in 'Stan' via 'brms'. The full variety of 'brms' formula-based effects structures are available to use in multiple classes of occupancy model, including single-season models, models with data augmentation for never-observed species, dynamic (multiseason) models with explicit colonization and extinction processes, and dynamic models with autologistic occupancy dynamics. Formulas can be specified for all relevant distributional terms, including detection and one or more of occupancy, colonization, extinction, and autologistic depending on the model type. Several important forms of model post-processing are provided. References: Bürkner (2017) doi:10.18637/jss.v080.i01; Carpenter et al. (2017) doi:10.18637/jss.v076.i01; Socolar & Mills (2023) doi:10.1101/2023.10.26.564080.

Changes in 1.1-0

Added the twolevel_single model family for single-season occupancy models in which groups of closure units may themselves be structurally absent. Users specify the grouping factor with level2_group, may supply a separate table of group-level predictors with level2_covs, and model group-level occupancy with f_meta.
Refactored the data-augmented model as a special case of the general two-level model, with shared data formatting, likelihood, fitting, and post-processing machinery.
Breaking change for augmented models: every species supplied in the original obs array must have at least one detection. Never-observed pseudospecies must instead be added through n_aug.
Breaking change for augmented models: get_Z() now returns a list containing unit states for species-site combinations and level2 states for species. Generic two-level models use the same return structure. Joint samples from the two levels are mutually consistent.

Show all changes in 1.1-0Hide the rest of the changes in 1.1-0

Two-level outputs from get_Z(), log_lik_flocker(), and loo_flocker() now retain user-supplied group names. Augmented models similarly retain supplied species names and assign stable names to augmented pseudospecies.
Improved the numerical stability of two-level log-likelihood calculations by evaluating occupancy mixtures in log space.
Corrected backward smoothing and backward sampling of latent states from multiseason models so that both use the appropriate transition probabilities and future-data likelihoods.
Corrected history-conditioned get_Z() calculations for augmented models and when using new_data, including rep-constant models. Augmented group-level probabilities now marginalize over unit occupancy and incorporate the fitted group-level occupancy probability.
Fixed expansion of user-supplied unit and event covariates in simulate_flocker_data() so that values are shared across species at each unit or visit, and allowed make_flocker_data() to accept data-frame observation inputs as documented.
Fixed reconstruction of maximally ragged observation and covariate arrays, including multiseason data with a final season that is unobserved in every series, and made post-processing robust when exactly one posterior draw is requested.
Fitted models and formatted data objects are now tagged with the version of flocker that created them. Two-level packing metadata is stored separately from the underlying brmsfit data.

From NEWS.md in the release

Install

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

install.packages("flocker", 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("jsocolar/flocker")

Development version from jsocolar/flocker. 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-flocker

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-flocker

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-flocker

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: 15.3 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-10-20
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
WARNING12 OK, 1 WARNING2026-05-09
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1-0

READMEYes · 348 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 1.1-0Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Description cites a JSS article

Help pages: 21
Examples that run: 50%8 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 7 never run
Exported functions with examples: 84%
Documented parameters: 100%
Return-value docs: 95%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #8,280 · ~8/day · ~257/mo

Releases R versions

Daily download trend is not available in this view yet.

40930 days

1.1K90 days

3.1K1 year

Compare downloads with other packages →

Also on112 r2u2 autocran

How downloads are counted

Repository

jsocolar/flocker ↗Account: jsocolar

33Stars

7Forks

8Open issues

2Open PRs

0Releases

615Commits

7Commit identities

615 commits · Last activity 2026-10-16 · 0% stars, 30d · Default branch at 1.1-1, ahead of CRAN 1.1-0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 36
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-29 · 312026-08-08 · 33

How these are measured

PracticesBeta

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

Checks run against github.com/jsocolar/flocker on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-16 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 1 practice

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing flocker adds 73 packages (35 with compiled code, 75 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (10)

abind assertthatbootbrms looMASSmatrixStatsstatsutilswithr

LinkingTo (0)

none

Suggests (8)

BH knitr RcppEigen rmarkdown rstan spelling testthat tibble

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 (3)

Jacob B. Socolar

Simon C. Mills

Author

Paul-Christian Bürkner

Contributor

Releases (3)

Pick two releases to compare their code metrics.

1.1-0Latest
record
2026-10-16 · current release · diff ↗ ·
added 1 export
make_flocker_data_twolevel_single
·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-16 02:28 UTC, so it stayed less than the time between readings.
1.0-2
record
2026-06-22 · diff ↗ ·
added 1 export
example_flocker_model_single
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0-0
record
2024-02-05
R
R 4.3.0 released · 2023-04-21

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2024-02-05
Total releases: 3 / 2 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 3.8 KB / 1 file
Download size: 6.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("flocker")

Format

Socolar, J. B., Bürkner, P., & Mills, S. C. (2026). flocker: Flexible Occupancy Estimation with Stan (Version 1.1-0) [Computer software]. https://doi.org/10.32614/CRAN.package.flocker

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 flocker version 1.1-0 [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 →