# Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

## Documentation for package ‘growthPheno’ version 2.1.19

- 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 growthPheno
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
cart.dat | A small data set to use in function examples
corrPlot | Deprecated Functions in the Package growthPheno
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
getDates | Deprecated Functions in the Package growthPheno
getTimesSubset | Forms a subset of 'responses' in 'data' that contains their values for the nominated times
growthPheno | Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
growthPheno-deprecated | Deprecated Functions in the Package growthPheno
growthPheno-pkg | Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
GrowthRates | Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
imagetimesPlot | Deprecated Functions in the Package growthPheno
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
is.smooths.frame | Tests whether an object is of class smooths.frame
longi.dat | A small data set to use in function examples
longiPlot | Deprecated Functions in the Package growthPheno
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 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
probeDF | Deprecated Functions in the Package growthPheno
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.
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
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
smooths.frame | Description of a smooths.frame object
smooths.frame-class | Description of a smooths.frame object
smoothSpline | Fit a spline to smooth the relationship between a 'response' and an 'x' in a 'data.frame', optionally computing growth rates using derivatives.
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'.
WUI | Calculates the Water Use Index (WUI)