growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

Assists in the plotting and functional smoothing of traits measured over time and the extraction of features from these traits, implementing the SET (Smoothing and Extraction of Traits) method described in Brien et al. (2020) Plant Methods, 16. Smoothing of growth trends for individual plants using natural cubic smoothing splines or P-splines is available for removing transient effects and segmented smoothing is available to deal with discontinuities in growth trends. There are graphical tools for assessing the adequacy of trait smoothing, both when using this and other packages, such as those that fit nonlinear growth models. A range of per-unit (plant, pot, plot) growth traits or features can be extracted from the data, including single time points, interval growth rates and other growth statistics, such as maximum growth or days to maximum growth. The package also has tools adapted to inputting data from high-throughput phenotyping facilities, such from a Lemna-Tec Scananalyzer 3D (see <https://www.youtube.com/watch?v=MRAF_mAEa7E/> for more information). The package 'growthPheno' can also be installed from <http://chris.brien.name/rpackages/>.

Version: 2.1.16
Depends: R (≥ 3.5.0)
Imports: dae, GGally, ggplot2, grDevices, Hmisc, JOPS, methods, RColorBrewer, readxl, reshape, stats, stringi, utils
Suggests: testthat, nlme, R.rsp, scales, WriteXLS
Published: 2022-11-15
Author: Chris Brien ORCID iD [aut, cre]
Maintainer: Chris Brien <chris.brien at adelaide.edu.au>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://chris.brien.name
NeedsCompilation: no
CRAN checks: growthPheno results

Documentation:

Reference manual: growthPheno.pdf
Vignettes: Rice: an example illustrating the first five steps for Smoothing and Extracting Traits (SET)
Tomato: an example of the Smoothing and Extraction of Traits (SET) process
growthPheno-manual

Downloads:

Package source: growthPheno_2.1.16.tar.gz
Windows binaries: r-devel: growthPheno_2.1.16.zip, r-release: growthPheno_2.1.16.zip, r-oldrel: growthPheno_2.1.16.zip
macOS binaries: r-release (arm64): growthPheno_2.1.16.tgz, r-oldrel (arm64): growthPheno_2.1.16.tgz, r-release (x86_64): growthPheno_2.1.16.tgz, r-oldrel (x86_64): growthPheno_2.1.16.tgz
Old sources: growthPheno archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=growthPheno to link to this page.