# Plotting, Smoothing and Growth Trait Extraction for Longitudinal Data

## Documentation for package ‘growthPheno’ version 1.0-34

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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)