| growthPheno-package |
Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits |
| 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 |
Deprecated Functions in the Package growthPheno |
| 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 |
| 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 |
Deprecated Functions in the Package growthPheno |
| intervalGRdiff |
Deprecated Functions in the Package growthPheno |
| 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 |
Deprecated Functions in the Package growthPheno |
| intervalWUI |
Deprecated Functions in the Package growthPheno |
| 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 |
Deprecated Functions in the Package growthPheno |
| 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 |
Deprecated Functions in the Package growthPheno |
| plotMedianDeviations |
Deprecated Functions in the Package growthPheno |
| 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 |
Deprecated Functions in the Package growthPheno |
| 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 |
Deprecated Functions in the Package growthPheno |
| splitSplines |
Deprecated Functions in the Package growthPheno |
| splitValueCalculate |
Deprecated Functions in the Package growthPheno |
| 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) |
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