growthPheno v1.0-13

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Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data

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 <http://www.lemnatec.com/products/hardware-solutions/scanalyzer-3d> for more information). The package 'growthPheno' can also be installed from <http://chris.brien.name/rpackages/>.

Functions in growthPheno

Name Description
growthPheno-deprecated Deprecated Functions in the Package asremlPlus
intervalGRdiff Calculates the growth rates for a specified time interval
plotAnom Identifies anomalous individuals and produces longitudinal plots without them and with just them
tomato.dat Longitudinal data for an experiment to investigate tomato response to mycorrhizal fungi and zinc
splitValueCalculate Calculates a single value that is a function of an individual's values for a response
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
plotLongitudinal Plots longitudinal data for a set of indiividuals
longitudinalPrime Selects a set variables to be retained in a data frame of longitudinal data
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
intervalPVA Selects a subset of variables observed within a specified time interval using Principal Variable Analysis (PVA)
splitContGRdiff Adds the growth rates calculated continuously over time for subsets of a response to a data.frame
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
intervalValueCalculate Calculates a single value that is a function of an individual's values for a response over a specified time interval
intervalWUI Calculates water use indices (WUI) over a specified time interval to a data.frame
growthPheno-pkg growthPheno
rcontrib Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of them
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
twoLevelOpcreate Creates a data.frame formed by applying, for each response, a binary operation to the paired values of two different treatments
plotMedianDeviations Calculates and plots the median of the deviations of the smoothed values from the observed values.
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
exampleData A small data set to use in function examples
importExcel Imports an Excel imaging file and allows some renaming of variables
intervalGRaverage Calculates the growth rates for a specified time interval by taking weighted averages of growth rates for times within the interval
plotCorrmatrix Calculates and plots correlation matrices for a set of responses
plotDeviationsBoxes Produces boxplots of the deviations of the observed values from the smoothed values over values of x.
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
calcTimes Calculates for a set of times, the time intervals after an origin time and the position of each within a time interval
cumulate Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUE
PVA Selects a subset of variables using Principal Variable Analysis (PVA)
GrowthRates Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
designFactors Adds the factors and covariates for a blocked, split-plot design
RiceRaw.dat Data for an experiment to investigate a rice germplasm panel
WUI Calculates the Water Use Index (WUI)
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Vignettes of growthPheno

Name
Rice.pdf.asis
growthPheno-manual.pdf.asis
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Details

Date 2019-05-12
VignetteBuilder R.rsp
License GPL (>= 2)
URL http://chris.brien.name
RoxygenNote 5.0.1
NeedsCompilation no
Packaged 2019-05-12 08:51:31 UTC; briencj
Repository CRAN
Date/Publication 2019-05-14 14:20:07 UTC

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