plot.drcte {drcte}

Plotting fitted time-to-event models

Description

plot displays fitted curves and observations in the same plot window, distinguishing between curves by different plot symbols and line types.

Usage

  ## S3 method for class 'drcte'
plot(x, ..., add = FALSE, level = NULL, shading = TRUE,
  type = "all",
  npmle.type = c("interpolation", "midpoint", "right", "left", "none"),
  npmle.points = FALSE, kde.points = TRUE,
  broken = FALSE, bp, bcontrol = NULL, conName = NULL, axes = TRUE,
  gridsize = 100, log = "", xtsty, xttrim = TRUE,
  xt = NULL, xtlab = NULL, xlab, xlim,
  yt = NULL, ytlab = NULL, ylab, ylim,
  cex, cex.axis = 1, col = FALSE, lty, pch,
  legend, legendText, legendPos, cex.legend = 1,
  normal = FALSE, normRef = 1, confidence.level = 0.95)

Arguments

x

an object of class 'drcte'.

...

additional graphical arguments. For instance, use lwd=2 or lwd=3 to increase the width of plot symbols.

add

logical. If TRUE then add to already existing plot.

level

vector of character strings. To plot only the curves specified by their identification number.

shading

For NPMLE, it prints shading on the graphs for the points where the likelihood value is not unique. Defaults to TRUE

type

it has been left for analogy with the plot method for 'drc' objects, but it is neglected in the case of 'drcte' objects.

npmle.type

the NPMLE of the cumulative density function is only specified at the end of each inspection interval, while it is not unique within each interval. This argument specifies how the CDF increases within each interval: possible values are "interpolation" (it is assumed that the CDF increases progressively), "left" (the CDF increases at the beginning of each interval), "right" (the CDF increases at the end of each interval; it is very common in survival analysis) and "midpoint" (the CDF increases in the middle of each interval; it is very common in survival analysis). This argument is neglected with parametric and KDE fits.

npmle.points

If F, with NPMLE fits, plotting the NPMLEs at the end of each interval as symbols is suppressed. Not implemented, yet.

kde.points

If F, with KDE fits, plotting the NPMLE at the end of each interval is suppressed

broken

logical. If TRUE the x axis is broken provided this axis is logarithmic (using functionality in the CRAN package 'plotrix').

bp

numeric value specifying the break point below which the dose is zero (the amount of stretching on the dose axis above zero in order to create the visual illusion of a logarithmic scale including 0). The default is the base-10 value corresponding to the rounded value of the minimum of the log10 values of all positive dose values. This argument is only working for logarithmic dose axes.

bcontrol

a list with components factor, style and width. Controlling the appearance of the break (in case broken is TRUE). The component factor is the distance from the control to the break as a multiple of the value of bp (default is 2). The component style can take the values: gap, slash or zigzag. The component width is the width of the break symbol (default is 0.02).

conName

character string. Name on x axis for dose zero. Default is '"0"'.

axes

logical indicating whether both axes should be drawn on the plot.

gridsize

numeric. Number of points in the grid used for plotting the fitted curves.

log

a character string which contains '"x"' if the x axis is to be logarithmic, '"y"' if the y axis is to be logarithmic and '"xy"' or '"yx"' if both axes are to be logarithmic. The default is "x". The empty string "" yields the original axes.

xtsty

a character string specifying the dose axis style for arrangement of tick marks. By default ("base10") For a logarithmic axis by default only base 10 tick marks are shown ("base10"). Otherwise sensible equidistantly located tick marks are shown ("standard"), relying on axTicks.

xttrim

logical specifying if the number of tick marks should be trimmed in case too many tick marks are initially determined.

xt

a numeric vector containing the positions of the tick marks on the x axis.

xtlab

a vector containing the tick marks on the x axis.

xlab

an optional label for the x axis.

xlim

a numeric vector of length two, containing the lower and upper limit for the x axis.

yt

a numeric vector, containing the positions of the tick marks on the y axis.

ytlab

a vector containing the tick marks on the y axis.

ylab

an optional label for the y axis.

ylim

a numeric vector of length two, containing the lower and upper limit for the y axis.

cex

numeric or numeric vector specifying the size of plotting symbols and text (see par for details).

cex.axis

numeric value specifying the magnification to be used for axis annotation relative to the current setting of cex.

col

either logical or a vector of colours. If TRUE default colours are used. If FALSE (default) no colours are used.

legend

logical. If TRUE a legend is displayed.

legendText

a character string or vector of character strings specifying the legend text (the position of the upper right corner of the legend box).

legendPos

numeric vector of length 2 giving the position of the legend.

cex.legend

numeric specifying the legend text size.

lty

a numeric vector specifying the line types.

pch

a vector of plotting characters or symbols (see points).

normal

logical. If TRUE the plot of the normalized data and fitted curves are shown (for details see Weimer et al. (2012) for details).

normRef

numeric specifying the reference for the normalization (default is 1).

confidence.level

confidence level for error bars. Defaults to 0.95.

Details

The plot method for 'drcte' objects inherits from the plot method for 'drc' objects and adds functionalities for nonparametric time-to-event fits. For parametric time-to-event models, the fitted curve is presented, together with symbols, corresponding to the NPMLE estimator of the cumulative distribution function at the end of each observation interval. For NPMLE fits, the cumulative CDF at the end of each interval is presented and the way that the density increases during the interval is specified through the argument 'npmle.type'. For KDE fits, the cumulative density is presented as a line, while the observed NPMLE of the CDF at the end of each interval can be either presented as symbols or suppressed. For all other information, please consult ?plot.drc. This method does not work for models with environmental covariates.

Value

An invisible data frame with the values used for plotting the fitted curves. The first column contains the dose values, and the following columns (one for each curve) contain the fitted response values.

Author(s)

Andrea Onofri

References

Weimer, M., Jiang, X., Ponta, O., Stanzel, S., Freyberger, A., Kopp-Schneider, A. (2012) The impact of data transformations on concentration-response modeling. Toxicology Letters, 213, 292–298.

Examples

library(drcte)
data(verbascum)
mod <- drmte(nSeeds ~ timeBef + timeAf, fct = NPMLE(),
                 data = verbascum, curveid = Species)
plot(mod)