Creates a list of the values for the options of profile plots for comparing smooths
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.
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.
Creates a list of the values for the options of profile plots for comparing smooths
Creates a list of the values for the smoothing parameters to be passed to a smoothing function
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.
Forms a smooths.frame from a data.frame, ensuring that the correct
columns are present.
Creates a list of the values for the options of median deviations plots for smooths
Calculates, water use traits (WU, WUR, WUI) over a specified time interval
for each individual in a data.frame in long format.
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.
Deprecated Functions in the Package growthPheno
Calculates the cumulative sum, ignoring the first element if exclude.1st is TRUE
A small data set to use in function examples
Forms a subset of responses in data that contains their values for the nominated times
Fits a spline to a response in a data.frame, and growth rates can be
computed using derivatives
Adds the factors and covariates for a blocked, split-unit design
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.
Calculates a single value that is a function of an individual's values for a response.
Replaces the values in a vector with the result of applying an operation to it
and a lagged value
Calculates for a set of times, the time intervals after an origin time and the position of each within a time interval
Imports an Excel imaging file and allows some renaming of variables
Calculates the growth rates for a specified time interval by taking weighted averages of growth rates for times within the interval
tools:::Rd_package_title("growthPheno")
Selects a set variables to be retained in a data frame of longitudinal data
Calculates the growth rates for a specified time interval
Selects a subset of variables using Principal Variable Analysis (PVA), based on the observed values within a specified time interval
Calculates a single value that is a function of an individual's values for a response over a specified time interval
Identifies anomalous individuals and produces profile plots without them and with just them
Calculates water use indices (WUI) over a specified time interval to a
data.frame
Tests whether an object is of class smooths.frame
Calculates and plots the median of the deviations of the smoothed values from the observed values.
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.
Produces profile plots of longitudinal data for a set of individuals
Produces profile plots of longitudinal data for a set of individuals
Plots the position of a time within an interval against the interval for each cart
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.
Calculates and plots correlation matrices for a set of responses
Prepares raw imaging data for further processing
Produces boxplots of the deviations of the observed values from the smoothed values over values of x.
Produces boxplots for several sets of deviations of the smoothed values from a response, possibly along with growth rates.
Computes a measure of how correlated each variable in a set is with the other variable,
conditional on a nominated subset of them
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
Fit a spline to smooth the relationship between a response and an x in a data.frame,
optionally computing growth rates using derivatives.
Computes a measure of how correlated each variable in a set is with the other variable,
conditional on a nominated subset of them
Calculates a single value that is a function of an individual's values for a response
Computes a measure of how correlated each variable in a set is with the other variable,
conditional on a nominated subset of them
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
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.
Description of a smooths.frame object
Adds, to a data.frame, the growth rates for individuals calculated
continuously over time by differencing response values.
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.
Checks that an object is a valid smooths.frame.
Longitudinal data for an experiment to investigate tomato response to mycorrhizal fungi and zinc
Extract features, that are single-valued for each individual, from traits observed over time.
Creates a data.frame formed by applying, for each response, a binary operation
to the paired values of two different treatments
Selects a subset of variables using Principal Variable Analysis (PVA) based on a correlation matrix
Calculates the Water Use Index (WUI)
Creates a list of the values for the options of profile plots for the chosen smooth
Data for an experiment to investigate a rice germplasm panel
Prepped data from an experiment to investigate a rice germplasm panel.
Calculates growth rates (AGR, PGR, RGRdiff) between pairs of values in a vector
Selects a subset of variables stored in a data.frame using Principal Variable Analysis (PVA)
Tests if any values in a vector are anomalous in being outside specified limits
Selects a subset of variables using Principal Variable Analysis (PVA)
Creates a list of the values for the smoothing parameters for
which a smooth is to be extracted