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)
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
RicePrepped.dat         Prepped data from an experiment to investigate
                        a rice germplasm panel.
RiceRaw.dat             Data for an experiment to investigate a rice
                        germplasm panel
WUI                     Calculates the Water Use Index (WUI)
anom                    Tests if any values in a vector are anomalous
                        in being outside specified limits
args4chosen_plot        Creates a 'list' of the values for the options
                        of profile plots for the chosen smooth
args4chosen_smooth      Creates a 'list' of the values for the
                        smoothing parameters for which a smooth is to
                        be extracted
args4devnboxes_plot     Creates a 'list' of the values for the options
                        of profile plots for comparing smooths
args4meddevn_plot       Creates a 'list' of the values for the options
                        of median deviations plots for smooths
args4profile_plot       Creates a 'list' of the values for the options
                        of profile plots for comparing smooths
args4smoothing          Creates a 'list' of the values for the
                        smoothing parameters to be passed to a
                        smoothing function
as.smooths.frame        Forms a 'smooths.frame' from a 'data.frame',
                        ensuring that the correct columns are present.
byIndv4Intvl_GRsAvg     Calculates the growth rates for a specified
                        time interval for individuals in a 'data.frame'
                        in long format by taking weighted averages of
                        growth rates for times within the interval.
byIndv4Intvl_GRsDiff    Calculates the growth rates for a specified
                        time interval for individuals in a 'data.frame'
                        in long format by differencing the values for a
                        response within the interval.
byIndv4Intvl_ValueCalc
                        Calculates a single value that is a 'function'
                        of the values of an individual for a response
                        in a 'data.frame' in long format over a
                        specified time interval.
byIndv4Intvl_WaterUse   Calculates, water use traits (WU, WUR, WUI)
                        over a specified time interval for each
                        individual in a 'data.frame' in long format.
byIndv4Times_GRsDiff    Adds, to a 'data.frame', the growth rates
                        calculated for consecutive times for
                        individuals in a 'data.frame' in long format by
                        differencing response values.
byIndv4Times_SplinesGRs
                        For a response in a 'data.frame' in long
                        format, computes, for a single set of smoothing
                        parameters, smooths of the response, possibly
                        along with growth rates calculated from the
                        smooths.
byIndv_ValueCalc        Calculates a single value that is a function of
                        an individual's values for a response.
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
designFactors           Adds the factors and covariates for a blocked,
                        split-unit design
exampleData             A small data set to use in function examples
fitSpline               Fits a spline to a 'response' in a
                        'data.frame', and growth rates can be computed
                        using derivatives
getTimesSubset          Forms a subset of 'responses' in 'data' that
                        contains their values for the nominated times
growthPheno-deprecated
                        Deprecated Functions in the Package growthPheno
growthPheno-package     Functional Analysis of Phenotypic Growth Data
                        to Smooth and Extract Traits
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.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
is.smooths.frame        Tests whether an object is of class
                        smooths.frame
longitudinalPrime       Selects a set variables to be retained in a
                        data frame of longitudinal data
plotAnom                Identifies anomalous individuals and produces
                        profile 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        Produces profile plots of longitudinal data for
                        a set of individuals
plotMedianDeviations    Calculates and plots the median of the
                        deviations of the smoothed values from the
                        observed values.
plotProfiles            Produces profile plots of longitudinal data for
                        a set of individuals
plotSmoothsComparison   Plots several sets of smoothed values for a
                        response, possibly along with growth rates and
                        optionally including the unsmoothed values, as
                        well as deviations boxplots.
plotSmoothsDevnBoxplots
                        Produces boxplots for several sets of
                        deviations of the smoothed values from a
                        response, possibly along with growth rates.
plotSmoothsMedianDevns
                        Calculates and plots the medians of the
                        deviations from the observed values for several
                        sets of smoothed values stored in a
                        'data.frame' in long format.
prepImageData           Prepares raw imaging data for further
                        processing
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
probeSmooths            For a response in a 'data.frame' in long
                        format, computes and compares, for sets of
                        smoothing parameters, smooths of the response,
                        possibly along with growth rates calculated
                        from the smooths.
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
smoothSpline            Fit a spline to smooth the relationship between
                        a 'response' and an 'x' in a 'data.frame',
                        optionally computing growth rates using
                        derivatives.
smooths.frame           Description of a smooths.frame object
splitContGRdiff         Adds, to a 'data.frame', the growth rates for
                        individuals calculated continuously over time
                        by differencing response values.
splitSplines            Adds the fits, and optionally growth rates
                        computed from derivatives, after fitting
                        splines to a response for an individual stored
                        in a 'data.frame' in long format
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
traitExtractFeatures    Extract features, that are single-valued for
                        each individual, from traits observed over
                        time.
traitSmooth             Obtain smooths for a trait by fitting spline
                        functions and, having compared several smooths,
                        allows one of them to be chosen and returned in
                        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
validSmoothsFrame       Checks that an object is a valid
                        'smooths.frame'.
