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growthPheno
View on CRAN: Click
here
Download and install growthPheno package within the R console
Install from CRAN:
install.packages("growthPheno")
Install from Github:
library("remotes")
install_github("cran/growthPheno")
Install by package version:
library("remotes")
install_version("growthPheno", "2.1.24")
Attach the package and use:
library("growthPheno")
Maintained by
Chris Brien
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-05-14
Latest Update: 2024-02-29
Description:
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
for more information). The package 'growthPheno' can also be
installed from .
How to cite:
Chris Brien (2019). growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits. R package version 2.1.24, https://cran.r-project.org/web/packages/growthPheno
Previous versions and publish date:
1.0-13 (2019-05-14 16:20), 1.0-15 (2019-07-15 10:10), 1.0-21 (2020-01-12 15:40), 1.0-22 (2020-03-18 07:10), 1.0-26 (2020-07-09 15:00), 1.0-30 (2020-12-12 09:20), 1.0-34 (2021-10-14 12:30), 2.1.16 (2022-11-15 19:30), 2.1.17 (2023-01-13 23:40), 2.1.19 (2023-03-15 06:00), 2.1.21 (2023-08-22 18:00), 2.1.23 (2023-10-24 15:40)
Other packages that cited growthPheno R package
View growthPheno citation profile
Other R packages that growthPheno depends,
imports, suggests or enhances
Functions, R codes and Examples using
the growthPheno R package
Some associated functions: GrowthRates . PVA.data.frame . PVA.matrix . PVA . RicePrepped.dat . RiceRaw.dat . WUI . anom . args4chosen_plot . args4chosen_smooth . args4devnboxes_plot . args4meddevn_plot . args4profile_plot . args4smoothing . as.smooths.frame . byIndv4Intvl_GRsAvg . byIndv4Intvl_GRsDiff . byIndv4Intvl_ValueCalc . byIndv4Intvl_WaterUse . byIndv4Times_GRsDiff . byIndv4Times_SplinesGRs . byIndv_ValueCalc . calcLagged . calcTimes . cumulate . designFactors . exampleData . fitSpline . getTimesSubset . growthPheno-deprecated . growthPheno-pkg . importExcel . intervalGRaverage . intervalGRdiff . intervalPVA.data.frame . intervalValueCalculate . intervalWUI . is.smooths.frame . longitudinalPrime . plotAnom . plotCorrmatrix . plotDeviationsBoxes . plotImagetimes . plotLongitudinal . plotMedianDeviations . plotProfiles . plotSmoothsComparison . plotSmoothsDevnBoxplots . plotSmoothsMedianDevns . prepImageData . probeSmoothing . probeSmooths . rcontrib.data.frame . rcontrib.matrix . rcontrib . smoothSpline . smooths.frame . splitContGRdiff . splitSplines . splitValueCalculate . tomato.dat . traitExtractFeatures . traitSmooth . twoLevelOpcreate . validSmoothsFrame .
Some associated R codes: Full growthPheno package functions and examples
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