Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data


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Documentation for package ‘growthPheno’ version 1.0-34

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AGRdiff Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
anom Tests if any values in a vector are anomalous in being outside specified limits
anomPlot Deprecated Functions in the Package asremlPlus
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
cart.dat A small data set to use in function examples
corrPlot Deprecated Functions in the Package asremlPlus
cumulate Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUE
designFactors Adds the factors and covariates for a blocked, split-plot design
exampleData A small data set to use in function examples
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
getDates Deprecated Functions in the Package asremlPlus
getTimesSubset Forms a subset of 'responses' in 'data' that contains their values for the nominated times
growthPheno Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data
growthPheno-deprecated Deprecated Functions in the Package asremlPlus
growthPheno-pkg Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data
GrowthRates Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
imagetimesPlot Deprecated Functions in the Package asremlPlus
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
intervalGRdiff Calculates the growth rates for a specified time interval
intervalPVA Selects a subset of variables using Principal Variable Analysis (PVA), based on the observed values within a specified time interval
intervalPVA.data.frame Selects a subset of variables using Principal Variable Analysis (PVA), based on the observed values within a specified time interval
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
longi.dat A small data set to use in function examples
longi.prime.dat A small data set to use in function examples
longiPlot Deprecated Functions in the Package asremlPlus
longitudinalPrime Selects a set variables to be retained in a data frame of longitudinal data
PGR Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
plotAnom Identifies anomalous individuals and produces longitudinal plots without them and with just them
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.
plotImagetimes Plots the position of a time within an interval against the interval for each cart
plotLongitudinal Plots longitudinal data for a set of indiividuals
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
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
PVA Selects a subset of variables using Principal Variable Analysis (PVA)
PVA.data.frame Selects a subset of variables stored in a data.frame using Principal Variable Analysis (PVA)
PVA.matrix Selects a subset of variables using Principal Variable Analysis (PVA) based on a correlation matrix
raw.dat A small data set to use in function examples
rcontrib Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of them
rcontrib.data.frame Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of them
rcontrib.matrix Computes a measure of how correlated each variable in a set is with the other variable, conditional on a nominated subset of them
RGRdiff Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
RiceRaw.dat Data for an experiment to investigate a rice germplasm panel
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'
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
twoLevelOpcreate Creates a data.frame formed by applying, for each response, a binary operation to the paired values of two different treatments
WUI Calculates the Water Use Index (WUI)