plotSmoothsDevnBoxplots: Produces boxplots for several sets of deviations of the...

In growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

Produces boxplots for several sets of deviations of the smoothed values from a response, possibly along with growth rates.

Description

Calculates and produces, using plotDeviationsBoxes, boxplots of the deviations of the supplied smoothed values from the observed response values for the traits and for combinations of the different smoothing parameters and for subsets of non-smoothing-factor combinations. Which traits are plotted is controlled by trait.types and may include the (responseand the computed traits of the Absolute Growth Rates (AGR) and/or the Relative Growth Rates (RGR). The observed and smoothed values are supplied in long format i.e. with the values for each set of smoothing parameters stacked one under the other in the supplied smooths.frame. Such data can be generated using probeSmooths.

Multiple plots, possibly each having multiple facets, are produced using ggplot2. The layout of these plots is controlled via the arguments plots.by, facet.x and facet.y. The basic principle is that the number of levels combinations of the smoothing-parameter factors Type, TunePar, TuneVal, Tuning (the combination of (TunePar and TuneVal), and Method that are included in plots.by, facet.x and facet.y must be the same as those covered by the combinations of the values incorporated into the smooths.frame input to plotSmoothsDevnBoxplots via the data argument. This ensures that smooths from different parameter sets are not pooled into the same plot. The factors other than the smoothing-parameter factors can be supplied to the plots.by and facet arguments.

Usage

plotSmoothsDevnBoxplots(data, response, response.smoothed = NULL, 
                        individuals = "Snapshot.ID.Tag", times = "DAP", 
                        trait.types = c("response", "AGR", "RGR"), 
                        which.plots =  "absolute.boxplots", 
                        x.title = NULL, y.titles = NULL, 
                        devnboxes.plot.args = 
                          args4devnboxes_plot(plots.by = NULL, 
                                              facet.x = ".", facet.y = "."),
                        printPlot = TRUE, ...)

Arguments

data	A smooths.frame, such as is produced by probeSmooths and that contains the data resulting from smoothing a response over time for a set of individuals, the data being arranged in long format both with respect to the times and the smoothing-parameter values used in the smoothing. That is, each response occupies a single column. The unsmoothed response and the response.smoothed are to be plotted for different sets of values for the smoothing parameters. The smooths.frame must include the columns Type, TunePar, TuneVal, Tuning and Method, and the columns nominated using the arguments individuals, times, plots.by, facet.x, facet.y, response, response.smoothed, and, if requested, the AGR and the RGR of the response and response.smoothed. The names of the growth rates should be formed from response and response.smoothed by adding .AGR and .RGR to both of them.
response	A character specifying the response variable for which the observed values are supplied.
response.smoothed	A character specifying the name of the column containing the values of the smoothed response variable, corresponding to response and obtained for the combinations of smoothing.methods and df, usually using smoothing splines. If response.smoothed is NULL, then response.smoothed is set to the response to which is added the prefix s.
times	A character giving the name of the column in data containing the times at which the data was collected, either as a numeric, factor, or character. It will be used to provide the values to be plotted on the x-axis. If a factor or character, the values should be numerics stored as characters.
individuals	A character giving the name of the factor that defines the subsets of the data for which each subset corresponds to the response values for an individual (e.g. plant, pot, cart, plot or unit).
trait.types	A character giving the trait.types that are to be plotted. If all, each of response, AGR and RGR is plotted.
which.plots	A logical indicating which plots are to be produced. The options are either none or absolute.deviations and/or relative.deviations. Boxplots of the absolute deviations are specified by absolute.boxplots, the absolute deviations being the values of a trait minus their smoothed values (observed - smoothed). Boxplots of the relative deviations are specified by relative.boxplots, the relative deviations being the absolute deviations divided by the smoothed values of the trait.
x.title	Title for the x-axis, used for all plots. If NULL then set to times.
y.titles	A character giving the titles for the y-axis, one for each trait specified by trait.types and used for all plots. If NULL, then set to the traits derived for response from trait.types.
devnboxes.plot.args	A named list that is most easily generated using args4devnboxes_plot, it documenting the options available for varying the boxplots. Note that if args4devnboxes_plot is to be called to change from the default settings given in the default probeSmooths call and some of those settings are to be retained, then the arguments whose settings are to be retained must also be included in the call to args4devnboxes_plot; be aware that if you call args4devnboxes_plot, then the defaults for this call are those for args4devnboxes_plot, NOT the call to args4devnboxes_plot shown as the default for probeSmooths.
printPlot	A logical indicating whether or not to print any plots.
...	allows passing of arguments to plotProfiles.

Value

A multilevel list that contains the ggplot objects for the plots produced. The first-level list has a component for each trait.types and each of these is a second-level list with contains the deviations boxplots for a response. Each plot is in an object of class ggplot, which can be plotted using print.

Author(s)

Chris Brien

See Also

traitSmooth, probeSmooths, args4profile_plot, plotDeviationsBoxes, plotSmoothsMedianDevns, ggplot.

Examples

data(exampleData)
traits <- probeSmooths(data = longi.dat, 
                       response = "PSA", response.smoothed = "sPSA", 
                       times = "DAP", 
                       #only df is changed from the probeSmooth default
                       smoothing.args = 
                         args4smoothing(smoothing.methods = "direct", 
                                        spline.types = "NCSS", 
                                        df = c(4,7), lambdas = NULL), 
                       which.plots = "none")
plotSmoothsDevnBoxplots(data = traits, 
                        response = "PSA", response.smoothed = "sPSA", 
                        times = "DAP", x.title = "DAP",
                        #only facet.x is changed from the probeSmooth default
                        devnboxes.plot.args = 
                          args4devnboxes_plot(plots.by = NULL, 
                                              facet.x = "Tuning", facet.y = "."))

growthPheno documentation built on Oct. 24, 2023, 5:08 p.m.