R Observatory: Metrics for SIMplyBee version 0.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SIMplyBee

0.4.1Package record

'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes

0packages depend

3Kdownloads / year

45.6%test coverage

13/13flavors OK

Overview

About

Maintained by Jana ObšteterCRAN page ↗GitHub ↗

An extension of the 'AlphaSimR' package (https://cran.r-project.org/package=AlphaSimR) for stochastic simulations of honeybee populations and breeding programmes. 'SIMplyBee' enables simulation of individual bees that form a colony, which includes a queen, fathers (drones the queen mated with), virgin queens, workers, and drones. Multiple colony can be merged into a population of colonies, such as an apiary or a whole country of colonies. Functions enable operations on castes, colony, or colonies, to ease 'R' scripting of whole populations. All 'AlphaSimR' functionality with respect to genomes and genetic and phenotype values is available and further extended for honeybees, including haplo-diploidy, complementary sex determiner locus, colony events (swarming, supersedure, etc.), and colony phenotype values.

Changes in 0.4.1

2024-09-19

Bug fixes

locations of the colonies in the D_Crossing vignettes were previously

sampled by random. This caused that on some runs some queens were left unmated,

which caused an error. We now read in the locations from a csv file.

From NEWS.md in the release

Install

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

install.packages("SIMplyBee", 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("HighlanderLab/SIMplyBee")

Development version from HighlanderLab/SIMplyBee. 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-simplybee

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-SIMplyBee

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-SIMplyBee

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: 5.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-01
ERROR12 OK, 1 ERROR2026-08-30
OK13 OK2026-08-05
ERROR12 OK, 1 ERROR2026-07-30
OK13 OK2026-05-12

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-05-11
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-11
ERROR13 OK, 1 ERROR2026-04-10
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.1

READMEYes · 118 wordsVignettesYes · 8 · dynamicNEWSYes · 100% structured · mentions 0.4.1Citation fileYes · cites a publication

Help pages: 101 (1 internal)includes a package overview page
Examples that run: 100%88 run in a plain check
Exported functions with examples: 97%
Documented parameters: 99%
Return-value docs: 99%
Help pages citing references: 8%

Vignettes (8)

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #12,522 · ~8/day · ~249/mo

Releases R versions

Daily download trend is not available in this view yet.

33130 days

88890 days

3K1 year

Compare downloads with other packages →

Also on376 r2u7 autocran53 c2d4u

How downloads are counted

Repository

highlanderlab/simplybee ↗Organization: HighlanderLab

3Stars

6Forks

75Open issues

1Open PRs

2Releases

1,246Commits

7Commit identities

1,246 commits · Last activity 2024-09-19 · Discussions: 7 posts

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 367
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-13 · 32026-07-07 · 3

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/highlanderlab/simplybee on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (3)

pkgdown

GitHub Pages site last deployed 2024-09-19 · The repository has a site deploy workflow

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing SIMplyBee adds 9 packages (6 with compiled code, 19 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, rbibutils 1.1 MB.

Depends (2)

R >= 3.3.0AlphaSimR

Imports (7)

methodsR6statsutilsextraDistr RANN Rcpp

LinkingTo (3)

Rcpp RcppArmadillo BH

Suggests (5)

rmarkdown knitr ggplot2 testthatMatrix

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Jana Obšteter

Author, Maintainer since 0.3.0 (2022)

Jernej Bubnič

Author

Gregor Gorjanc

Author

Laura Strachan

Author

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.4.1Latest
record
2024-09-20 · current release · diff ↗
0.4.0
record
2024-08-26 · diff ↗ ·
removed 1 export
createRandomCrossPlan

added 6 exports
createCrossPlan, getMisc, isVirginQueenPresent, isVirginQueens, rcircle, setMisc
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.0
record
2022-12-15
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-15
Total releases: 3 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.3.0
Download size: 2.2 MB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("SIMplyBee")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1186/s12711-023-00798-y.

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 SIMplyBee version 0.4.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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