R Observatory: Metrics for biometryassist version 1.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biometryassist

1.5.1Package record

Functions to Assist Design and Analysis of Agronomic Experiments

0packages depend

7.1Kdownloads / year

99.0%test coverage

13/13flavors OK

Overview

About

Maintained by Sam RogersCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Adelaide University and Grains Research and Development Corporation

Provides functions to aid in the design and analysis of agronomic and agricultural experiments through easy access to documentation and helper functions, especially for users who are learning these concepts. While not required for most functionality, this package enhances the `asreml` package which provides a computationally efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It is a commercial package that can be purchased as 'ASReml-R' from 'VSNi' https://vsni.co.uk/, who will supply a zip file for local installation/updating (see https://asreml.kb.vsni.co.uk/).

Changes in 1.5.1

Minor Changes

Added citation information: citation("biometryassist") now gives the package citation, including its CRAN DOI, and the repository includes a CITATION.cff generated from the package metadata. (#194, #196)
reference_comparisons() now uses the exact Dunnett test whenever all comparisons share a common degrees of freedom (e.g. single-stratum aovlist and balanced lmer() models), instead of falling back to Holm for any model that reports degrees of freedom per comparison.
The package startup message, licence and documentation now refer to Adelaide University.
multiple_comparisons(), pairwise_comparisons() and reference_comparisons() now work with asreml models whose terms use ASReml-R special functions, such as at() in the fixed model or diag(), fa(), us() and vm() in the random model. (#198)
The predictions returned by multiple_comparisons() no longer include a df column for aov and lm models, so the output is the same for every model type.

Bug Fixes

use_template() now copies the requested package template as expected. Previously it always copied mixed_model_template.R. (#188)
Fixed the argument order in the export_design_to_excel() examples, which are now runnable. (#189, #197)
multiple_comparisons(), pairwise_comparisons() and reference_comparisons() now use the correct pairwise contrast degrees of freedom for nlme::lme() models rather than those of the individual means. In multiple_comparisons() this gave too-large HSD values; results now match equivalent aov() and lmer() fits. (#190)
Fixed the standard errors of difference (and degrees of freedom) being assigned to the wrong pairs for models with four or more treatment levels that use emmeans (aovlist, lmer(), nlme::lme(), afex and glmmTMB). This affected the p-values, HSD and letter groups from multiple_comparisons() for unbalanced data; balanced designs were not affected. (#193)
multiple_comparisons() no longer errors when a treatment level is aliased in models that use emmeans (aovlist, lmer(), nlme::lme(), afex and glmmTMB). (#195)

Show all changes in 1.5.1Hide the rest of the changes in 1.5.1

The warning given when the comparison functions fall back to the residual degrees of freedom for an asreml model now always names the classify term; previously the term name could be missing.
multiple_comparisons() no longer errors with "subscript out of bounds" when ASReml-R's levels argument is used to predict a subset of levels for an asreml model.
multiple_comparisons() confidence intervals (int.type = "ci") now use the degrees of freedom of each predicted mean, rather than the largest pairwise-comparison degrees of freedom, and int.type = "tukey" now uses the smallest comparison degrees of freedom for each mean. Intervals were too narrow for multi-stratum models (aovlist, afex, lmer(), nlme::lme() and asreml at() terms); single-stratum models are not affected. (#199)

From NEWS.md in the release

Install

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

install.packages("biometryassist", 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("biometryhub/biometryassist")

Development version from biometryhub/biometryassist. 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-biometryassist

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-biometryassist

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-biometryassist

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: 8.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-08
ERROR12 OK, 1 ERROR2026-10-05
OK13 OK2026-08-21
ERROR12 OK, 1 ERROR2026-08-17
OK13 OK2026-08-05

Show 5 earlier changesHide 5 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.1

README· In the repository, left out of the releaseVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.5.1Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 67 (49 internal)includes a package overview page
Examples that run: 76%13 run in a plain check (1 of them under a condition) · 4 never run
Exported functions with examples: 76%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 3%

Vignettes (3)

How these are measured

Downloads

7.1K

CRAN downloads in the past year

Rank #5,268 · ~19/day · ~592/mo

Releases R versions

Daily download trend is not available in this view yet.

71030 days

1.5K90 days

7.1K1 year

Compare downloads with other packages →

Also on474 r2u37 autocran37 c2d4u

How downloads are counted

Repository

biometryhub/biometryassist ↗Organization: biometryhub

12Stars

7Forks

7Open issues

2Open PRs

12Releases

913Commits

9Commit identities

rstatsrstats-packagerpackageexperimental-designteachingbiometry

913 commits · Last activity 2026-10-07 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 72
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-10-10 · 72026-07-07 · 12

How these are measured

PracticesBeta

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

Checks run against github.com/biometryhub/biometryassist on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (2)

Code of conductContributing guide

Docs source (4)

README.qmdpkgdown

GitHub Pages site last deployed 2026-10-07 · The repository has a site deploy workflow

pkgdown site last built 2026-10-07

Coverage (2)

Coverage reporting (Codecov).covrignore

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

CITATION.cff

Lint, format, editor (3)

Lint workflowAirVS Code

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-08-18
Seen in the repository: .github/copilot-instructions.md
Pull request: opened by its own account
Commits: 33 by its own account
Claude Codefirst seen 2026-05-01
Seen in the repository: CLAUDE.md
Named in .Rbuildignore: .claude, CLAUDE.md
Commits: at least 2 crediting it in the message

Models named in its commits

Claude Opus 4.82 commits · Jun 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing biometryassist adds 29 packages (12 with compiled code, 34 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, patchwork 3.2 MB.

Depends (1)

R >= 4.1.0

Imports (12)

agricolae curl emmeans ggplot2 jsonlitelatticemultcompView pracma patchwork rlang scales stringi

LinkingTo (0)

none

Suggests (13)

covr crayon ggspatial knitrMatrixmockery mvtnorm openxlsx2 quarto rmarkdown testthat vdiffr withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (6)

Sam Rogers

Author, Maintainer since 1.0.0 (2022)

Annie Conway

Author

Sharon Nielsen

Author

Michael Mumford

Contributor · added in 1.5.0

Adelaide University

Copyright holder, Funder · added in 1.5.1

https://adelaide.edu.au/

Grains Research and Development Corporation

Copyright holder, Funder

https://grdc.com.au/

Listed in earlier versions (1)

University of Adelaide

no longer listed · 1.0.0 to 1.5.0

Releases (15)

Pick two releases to compare their code metrics.

1.5.1Latest
record
2026-10-07 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-07 14:07 UTC, so it stayed less than the time between readings.
1.5.0
record
2026-06-17 · diff ↗ ·
added 2 exports
pairwise_comparisons, reference_comparisons
R
R 4.6.0 released · 2026-04-24
1.4.0
record
2026-02-03 · diff ↗
1.3.3
record
2025-09-15 · diff ↗
1.3.2
record
2025-09-11 · diff ↗
1.3.1
record
2025-07-04 · diff ↗
1.3.0
record
2025-06-11 · diff ↗ ·
removed 1 export
get_predictions

added 4 exports
add_buffers, export_design_to_excel, list_templates, use_template
unarchivedReturned to CRAN
2025-04-23
1.2.2
record
2025-04-23 · diff ↗ ·
added 1 export
get_predictions
archivedRemoved from CRAN
2025-04-19
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
1.2.1
record
2024-06-05 · diff ↗ ·
added 1 export
summary_graph
1.2.0
record
2024-05-31 · diff ↗ ·
added 1 export
heat_map
R
R 4.4.0 released · 2024-04-24
1.1.3
record
2023-07-19 · diff ↗

Show 7 earlier eventsHide 7 earlier events

R
R 4.3.0 released · 2023-04-21
1.1.2
record
2022-11-25 · diff ↗
1.1.1
record
2022-10-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
record
2022-04-14 · diff ↗
1.0.0
record
2022-01-28
R
R 4.1.0 released · 2021-05-18

Across CRAN, the median accepted release of the past year spent 19 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2022-01-28
Total releases: 15 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 1.9 MB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("biometryassist")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

The repository also keeps a CITATION.cff.

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 biometryassist version 1.5.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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