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
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
intervalPVA.data.frame
                        Selects a subset of variables using Principal
                        Variable Analysis (PVA), based on the observed
                        values within a specified time interval
is.smooths.frame        Tests whether an object is of class
                        smooths.frame
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 image
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
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
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'.
