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growthPheno (version 1.0-22)

Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data

Description

Assists in producing longitudinal or profile plots of measured traits. These allow checks to be made for anomalous data and growth patterns in the data to be explored. Smoothing of growth trends for individual plants using smoothing splines is available for removing transient effects. There are tools for diagnosing the adequacy of trait smoothing, either using this package or other packages, such as those that fit nonlinear growth models. A range of per-unit (pot, plant, plot) growth traits can be extracted from longitudinal data, including single time-point smoothed trait values and their growth rates, interval growth rates and other growth statistics, such as maximum growth. The package is particularly suited to preparing data from high-throughput phenotyping facilities, such as imaging data from a Lemna-Tec Scananalyzer (see for more information). The package 'growthPheno' can also be installed from .

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Version

Install

install.packages('growthPheno')

Monthly Downloads

353

Version

1.0-22

License

GPL (>= 2)

Maintainer

Chris Brien

Last Published

March 18th, 2020

Functions in growthPheno (1.0-22)

exampleData

A small data set to use in function examples
designFactors

Adds the factors and covariates for a blocked, split-plot design
anom

Tests if any values in a vector are anomalous in being outside specified limits
calcLagged

Replaces the values in a vector with the result of applying an operation to it and a lagged value
intervalGRaverage

Calculates the growth rates for a specified time interval by taking weighted averages of growth rates for times within the interval
importExcel

Imports an Excel imaging file and allows some renaming of variables
GrowthRates

Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
PVA

Selects a subset of variables using Principal Variable Analysis (PVA)
cumulate

Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUE
growthPheno-deprecated

Deprecated Functions in the Package asremlPlus
plotMedianDeviations

Calculates and plots the median of the deviations of the smoothed values from the observed values.
calcTimes

Calculates for a set of times, the time intervals after an origin time and the position of each within a time interval
RiceRaw.dat

Data for an experiment to investigate a rice germplasm panel
growthPheno-pkg

growthPheno
WUI

Calculates the Water Use Index (WUI)
probeDF

Compares, for a set of specified values of df, a response and the smooths of it, possibly along with growth rates calculated from the smooths
fitSpline

Produce the fits from a natural cubic smoothing spline applied to a response in a data.frame, and growth rates can be computed using derivatives
plotImagetimes

Plots the position of a time within an interval against the interval for each cart
getTimesSubset

Forms a subset of responses in data that contains their values for the nominated times
intervalGRdiff

Calculates the growth rates for a specified time interval
plotLongitudinal

Plots longitudinal data for a set of indiividuals
probeSmoothing

Compares, for a set of specified values of df and different smoothing methods, a response and the smooths of it, possibly along with growth rates calculated from the smooths
intervalWUI

Calculates water use indices (WUI) over a specified time interval to a data.frame
twoLevelOpcreate

Creates a data.frame formed by applying, for each response, a binary operation to the paired values of two different treatments
intervalPVA

Selects a subset of variables observed within a specified time interval using Principal Variable Analysis (PVA)
intervalValueCalculate

Calculates a single value that is a function of an individual's values for a response over a specified time interval
rcontrib

Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of them
longitudinalPrime

Selects a set variables to be retained in a data frame of longitudinal data
splitContGRdiff

Adds the growth rates calculated continuously over time for subsets of a response to a data.frame
plotCorrmatrix

Calculates and plots correlation matrices for a set of responses
splitSplines

Adds the fits, and optionally growth rates computed from derivatives, after fitting natural cubic smoothing splines to subsets of a response to a data.frame
plotDeviationsBoxes

Produces boxplots of the deviations of the observed values from the smoothed values over values of x.
splitValueCalculate

Calculates a single value that is a function of an individual's values for a response
tomato.dat

Longitudinal data for an experiment to investigate tomato response to mycorrhizal fungi and zinc
plotAnom

Identifies anomalous individuals and produces longitudinal plots without them and with just them