R Observatory: Metrics for statgenHTP version 1.0.9.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

statgenHTP

1.0.9.5Package record

High Throughput Phenotyping (HTP) Data Analysis

0packages depend

4.8Kdownloads / year

85.8%test coverage

13/13flavors OK

Overview

About

Maintained by Bart-Jan van RossumCRAN page ↗GitHub ↗Website ↗Issues ↗

Phenotypic analysis of data coming from high throughput phenotyping (HTP) platforms, including different types of outlier detection, spatial analysis, and parameter estimation. The package is being developed within the EPPN2020 project (https://cordis.europa.eu/project/id/731013). Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (https://vsni.co.uk/software/asreml-r/).

Changes in 1.0.9.5

No user visual changes.

From NEWS.md in the release

Install

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

install.packages("statgenHTP", 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("Biometris/statgenHTP")

Development version from Biometris/statgenHTP. 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-statgenhtp

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-statgenHTP

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-statgenHTP

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: 11.7 min · r-oldrel-macos-x86_64

Status changes

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

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.9.5

READMEYes · 79 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.9.5Citation fileNoWebsiteYes · pkgdown

Help pages: 38 (1 internal)includes a package overview page
Examples that run: 59%17 run in a plain check · 12 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 16%

Vignettes (1)

Overview

How these are measured

Downloads

4.8K

CRAN downloads in the past year

Rank #6,004 · ~13/day · ~404/mo

Releases R versions

Daily download trend is not available in this view yet.

64630 days

1.4K90 days

4.8K1 year

Compare downloads with other packages →

Also on141 r2u1 autocran68 c2d4u

How downloads are counted

Repository

biometris/statgenhtp ↗Organization: Biometris

9Stars

2Forks

0Open issues

0Open PRs

0Releases

876Commits

3Commit identities

geneticscranhigh-troughput-phenotypingr-package

876 commits · Last activity 2026-09-24 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 11
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-08-19 · 72026-07-07 · 9

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/biometris/statgenhtp on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowGitLab CI

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 2026-09-24 · The repository has a site deploy workflow

pkgdown site last built 2026-09-24

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing statgenHTP adds 42 packages (27 with compiled code, 48 MB of source tarballs). Heaviest: LMMsolver 7.1 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.6

Imports (15)

animation ggforce ggplot2 ggnewscalegridgridExtraMatrixmethodsLMMsolver locfit lubridate rlang scales spam SpATS

LinkingTo (0)

none

Suggests (4)

asreml knitr rmarkdown tinytest

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 (8)

Bart-Jan van Rossum

Author, Maintainer since 1.0.0 (2021)

Martin Boer

Author

Nadine Hilgert

Author

Emilie J Millet

Author

Diana Marcela Perez Valencia

Author

Maria Xose Rodriguez Alvarez

Author

Isabelle Sanchez

Author

Fred van Eeuwijk

Author

Releases (16)

Pick two releases to compare their code metrics.

1.0.9.5Latest
record
2026-09-24 · current release · diff ↗
1.0.9.4
record
2026-07-06 · diff ↗
1.0.9.3
record
2026-05-21 · diff ↗
1.0.9.2
record
2026-05-21 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.9.1
record
2025-07-03 · diff ↗
1.0.9
record
2025-07-02 · diff ↗
1.0.8
record
2025-04-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.7
record
2024-10-14 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.6.1
record
2023-04-14 · diff ↗
1.0.6
record
2022-12-13 · diff ↗ ·
added 1 export
fitSplineHDM
R
R 4.2.0 released · 2022-04-22
1.0.5
record
2021-09-15 · diff ↗

Show 7 earlier eventsHide 7 earlier events

1.0.4
record
2021-08-20 · diff ↗
1.0.3
record
2021-06-18 · diff ↗
1.0.2
record
2021-06-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.1
record
2021-03-09 · diff ↗
1.0.0
record
2021-03-05
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-05
Total releases: 16 / 5 yrs
License: GPL
Minimum R: ≥ 3.6
Bundled data: 3.2 MB / 7 files
Download size: 3.7 MB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("statgenHTP")

Format

van Rossum, B., Boer, M., Hilgert, N., Millet, E. J., Perez Valencia, D. M., Rodriguez Alvarez, M. X., Sanchez, I., & van Eeuwijk, F. (2026). statgenHTP: High Throughput Phenotyping (HTP) Data Analysis (Version 1.0.9.5) [Computer software]. https://doi.org/10.32614/CRAN.package.statgenHTP

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 statgenHTP version 1.0.9.5 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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