pcvr

1.4.1

Plant Phenotyping and Bayesian Statistics

0packages depend

6.2Kdownloads / year

80.7%test coverage

12/13checks pass

Overview

About

Maintained by Josh SumnerFirst published 2024-09-055 releasesCRAN page ↗GitHub ↗

Analyse common types of plant phenotyping data, provide a simplified interface to longitudinal growth modeling and select Bayesian statistics, and streamline use of 'PlantCV' output. Several Bayesian methods and reporting guidelines for Bayesian methods are described in Kruschke (2018) doi:10.1177/2515245918771304, Kruschke (2013) doi:10.1037/a0029146, and Kruschke (2021) doi:10.1038/s41562-021-01177-7.

Install

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

install.packages("pcvr", 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("danforthcenter/pcvr")

Development version from danforthcenter/pcvr. 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-pcvr

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-pcvr

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-pcvr

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: 15.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.32

80.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 144 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 75%
Documented parameters: 98%
Return-value docs: 98%
References docs: 0%

Downloads

6.2K

CRAN downloads in the past year

Rank #7,176 · ~17/day · ~513/mo

Releases R versions

Daily download trend is not available in this view yet.

25530 days

1.3K90 days

6.2K1 year

Compare downloads with other packages →

Also on164 r2u

Repository

GitHub ↗ danforthcenter/pcvr

5Stars

0Forks

0Open issues

1Open PRs

0Releases

1,696Commits

1Contributors

1,696 commits · Last activity 2026-06-24 · +25% stars, 30d

Stars over time

2025-06-28 · 42026-07-07 · 5

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/danforthcenter/pcvr on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (24)

FactoMineR rlangstatsutilsmethodsdata.table ggplot2 ggridges igraph jsonlite lme4 patchwork extraDistrparallelbayestestR viridismgcvquantregnlmesplineslmeSplines scalessurvivalcar

LinkingTo (0)

none

Suggests (11)

knitr rmarkdown brms flexsurv curl cmdstanr rstan caret vctrs plyr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Josh Sumner

Author, Maintainer

Authors (2)

Josh Sumner

Author, Maintainer

Jeffrey Berry

Author

Donald Danforth Plant Science Center

Reviewers (1)

Noah Fahlgren

Reviewer

Package Timeline

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

1.4.1Latest
2026-06-23 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.3.1
2025-08-18 · diff ↗
1.2.0
2025-04-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.1.0
2024-11-06 · diff ↗
1.0.0
2024-09-05
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-05
Total releases: 5 / 2 yrs
License: GPL-2 OSI
Additional repositories: stan-dev.r-universe.dev
Minimum R: ≥ 3.5.0
Download size: 2.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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