| 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) |