Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
Tests if any values in a vector are anomalous in being outside specifi...
Creates a list of the values for the options of profile plots for th...
Creates a list of the values for the smoothing parameters for which ...
Creates a list of the values for the options of profile plots for co...
Creates a list of the values for the options of median deviations pl...
Creates a list of the values for the options of profile plots for co...
Creates a list of the values for the smoothing parameters to be pass...
Forms a smooths.frame from a data.frame, ensuring that the correct...
Calculates a single value that is a function of an individual's values...
Calculates the growth rates for a specified time interval for individu...
Calculates the growth rates for a specified time interval for individu...
Calculates a single value that is a function of the values of an ind...
Calculates, water use traits (WU, WUR, WUI) over a specified time inte...
Adds, to a data.frame, the growth rates calculated for consecutive t...
For a response in a data.frame in long format, computes, for a singl...
Replaces the values in a vector with the result of applying an operati...
Calculates for a set of times, the time intervals after an origin time...
Calculates the cumulative sum, ignoring the first element if exclude.1...
Adds the factors and covariates for a blocked, split-unit design
Forms a subset of responses in data that contains their values for...
Deprecated Functions in the Package growthPheno
tools:::Rd_package_title("growthPheno")
Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in...
Imports an Excel imaging file and allows some renaming of variables
Selects a subset of variables using Principal Variable Analysis (PVA),...
Tests whether an object is of class smooths.frame
Identifies anomalous individuals and produces profile plots without th...
Calculates and plots correlation matrices for a set of responses
Produces boxplots of the deviations of the observed values from the sm...
Plots the position of a time within an interval against the interval f...
Produces profile plots of longitudinal data for a set of individuals
Plots several sets of smoothed values for a response, possibly along w...
Produces boxplots for several sets of deviations of the smoothed value...
Calculates and plots the medians of the deviations from the observed v...
Prepares raw imaging data for further processing
For a response in a data.frame in long format, computes and compares...
Selects a subset of variables stored in a data.frame using Principal V...
Selects a subset of variables using Principal Variable Analysis (PVA) ...
Selects a subset of variables using Principal Variable Analysis (PVA)
Computes a measure of how correlated each variable in a set is with th...
Computes a measure of how correlated each variable in a set is with th...
Computes a measure of how correlated each variable in a set is with th...
Description of a smooths.frame object
Fit a spline to smooth the relationship between a response and an `x...
Extract features, that are single-valued for each individual, from tra...
Obtain smooths for a trait by fitting spline functions and, having com...
Creates a data.frame formed by applying, for each response, a binary o...
Checks that an object is a valid smooths.frame.
Calculates the Water Use Index (WUI)
Assists in the plotting and functional smoothing of traits measured over time and the extraction of features from these traits, implementing the SET (Smoothing and Extraction of Traits) method described in Brien et al. (2020) Plant Methods, 16. Smoothing of growth trends for individual plants using natural cubic smoothing splines or P-splines is available for removing transient effects and segmented smoothing is available to deal with discontinuities in growth trends. There are graphical tools for assessing the adequacy of trait smoothing, both when using this and other packages, such as those that fit nonlinear growth models. A range of per-unit (plant, pot, plot) growth traits or features can be extracted from the data, including single time points, interval growth rates and other growth statistics, such as maximum growth or days to maximum growth. The package also has tools adapted to inputting data from high-throughput phenotyping facilities, such from a Lemna-Tec Scananalyzer 3D (see <https://www.youtube.com/watch?v=MRAF_mAEa7E/> for more information). The package 'growthPheno' can also be installed from <http://chris.brien.name/rpackages/>.