biogeom

1.5.2

Biological Geometries

0packages depend

4Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Peijian ShiFirst published 2022-05-1219 releasesCRAN page ↗

Is used to simulate and fit biological geometries. 'biogeom' incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) doi:10.3732/ajb.90.3.333; Shi et al. (2020) doi:10.3390/sym12040645), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) doi:10.1016/j.ecolmodel.2017.01.012; Shi et al. (2021) doi:10.3390/sym13081524). The optimization method proposed by Nelder and Mead (1965) doi:10.1093/comjnl/7.4.308 was used to estimate model parameters. 'biogeom' includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. 'biogeom' can quantify the conspecific or interspecific similarity of natural outlines, and provides information with important ecological and evolutionary implications for the growth and form of living organisms. Please see Shi et al. (2022) doi:10.1111/nyas.14862 for details.

Install

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

install.packages("biogeom", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-biogeom

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-biogeom

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-biogeom

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.0 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 100%

Downloads

CRAN downloads in the past year

Rank #6,162 · ~11/day · ~335/mo

Releases R versions

Daily download trend is not available in this view yet.

28830 days

1.5K90 days

4K1 year

Compare downloads with other packages →

Also on201 r2u4 autocran

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (2)

bmp spatstat.geom

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Peijian Shi

Author, Maintainer

Authors (3)

Peijian Shi

Author, Maintainer

Johan Gielis

Author

Brady K. Quinn

Author

Listed in earlier versions (2)

Gielis

no longer listed · 1.0.5 to 1.5.2

Quinn

no longer listed · 1.0.5 to 1.5.2

Package Timeline

19 releases. Pick two to compare their code metrics. R releases are shown for context.

1.5.2Latest
2026-07-11 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.5.1
2026-04-16 · diff ↗
1.5.0
2025-08-24 · diff ↗
1.4.4
2025-07-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.4.3
2024-03-29 · diff ↗
1.4.2
2024-03-13 · diff ↗
1.4.1
2024-01-09 · diff ↗
1.3.7
2023-10-22 · diff ↗
unarchivedReturned to CRAN
2023-10-22
archivedRemoved from CRAN
2023-10-20
policy violation HTML mail, denied the error
1.3.6
2023-08-10 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.3.5
2022-12-22 · diff ↗

Show 10 earlier events

1.2.1
2022-10-26 · diff ↗
1.2.0
2022-10-20 · diff ↗
1.1.4
2022-10-03 · diff ↗
1.1.2
2022-09-29 · diff ↗
1.1.1
2022-08-18 · diff ↗
1.0.9
2022-08-07 · diff ↗
1.0.7
2022-07-17 · diff ↗
1.0.6
2022-07-03 · diff ↗
1.0.5
2022-05-12
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-12
Total releases: 19 / 4 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3.0
Bundled data: 927 KB / 11 files
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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