plot.drc: Plotting fitted curves for a 'drc' or 'mrdrc' object

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 'drc':
plot(x, ..., level = NULL, broken = FALSE, col = FALSE, 
  conLevel, conName, gridsize = 100, legend, legendText, legendPos, legendCex = 1,
  type = c("average", "all", "bars", "none", "obs"), obs, lty, log = "x", xsty = c("base10", "none"), 
  cex, pch, xlab, ylab, xlim, ylim, cex.axis = 1,
  bcontrol = NULL, xt = NULL, xtlab = NULL, yt = NULL, ytlab = NULL,
  add = FALSE, axes = TRUE)

  ## S3 method for class 'mrdrc':
plot(x, ..., pava = FALSE)

Arguments

an object of class 'drc'.

...

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

level

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

broken

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

col

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

conLevel

numeric specifying the dose level 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

conName

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

gridsize

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

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.

legendCex

numeric specifying the legend text size.

type

a character string specifying how to plot the data. There are currently 5 options: "average" (averages and fitted curve(s); default), "none" (only the fitted curve(s)), "obs" (only the data points), "all" (all data points and fitted curve(s))

obs

Outdated argument. Use type.

lty

a numeric vector specifying the line types.

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.

xsty

a character string specifying the dose axis style for arrangement of tick marks. By default ("base10") only base 10 tick marks are shown, unless too few tick marks are available in which case "none" applies (if the range of doses applied is narrow

cex

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

pch

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

xlab

an optional label for the x axis.

ylab

an optional label for the y axis.

xlim

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

ylim

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

cex.axis

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

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 t

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.

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.

add

logical. If TRUE then add to already existing plot.

axes

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

pava

logical. If TRUE the fit is monotoniosed using pool adjacent violators algorithm.

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.

Details

plot.mrdrc takes the same arguments as plot.drc. Suitable labels are automatically provided. The use of xlim allows changing the range of the x axis, extrapolating the fitted dose-response curves. Note that changing the range on the x axis may also entail a change of the range on the y axis. Sometimes it may be useful to extend the upper limit on the y axis (using ylim) in order to fit a legend into the plot. See colors for the available colours. The arguments broken and bcontrol rely on the function link{axis.break} with arguments style and brw in the package plotrix.

Examples

Run this code

## Fitting models to be plotted below
ryegrass.m1 <- drm(rootl~conc, data = ryegrass, fct = LL.4())
ryegrass.m2 <- drm(rootl~conc, data = ryegrass, fct = LL.3())  # lower limit fixed at 0

## Plotting observations and fitted curve for the first model
plot(ryegrass.m1, broken = TRUE) 

## Adding fitted curve for the second model (not much difference)
plot(ryegrass.m2, broken = TRUE, add = TRUE, type = "none", col = 2, lty = 2)

## Finetuning the axis break
plot(ryegrass.m1, broken = TRUE, bcontrol = list(style = "gap"))
plot(ryegrass.m1, broken = TRUE, bcontrol = list(style = "slash"))
plot(ryegrass.m1, broken = TRUE, bcontrol = list(style = "zigzag"))

## Plot without axes
plot(ryegrass.m1, axes = FALSE)

## Fitting model to be plotted below
spinach.m1 <- drm(SLOPE~DOSE, CURVE, data = spinach, fct = LL.4())

## Plot with no colours
plot(spinach.m1, main = "Different line types (default)")

## Plot with default colours
plot(spinach.m1, col = TRUE, main = "Default colours")

## Plot with specified colours
plot(spinach.m1, col = c(2,6,3,23,56), main = "User-specified colours")

## Plot of curves 1 and 2 only
plot(spinach.m1, level = c(1,2), main = "User-specified curves")

## Plot with symbol of different sizes
plot(spinach.m1, cex = c(1,2,3,4,5), main = "User-specified symbil sizes")

## Fitting another model to be plotted below
lettuce.m1 <- drm(weight~conc, data = lettuce, fct = LL.4())

## Using the argument 'conLevel'. Compare the plots!
par(mfrow = c(2, 2))
plot(lettuce.m1, main = "conLevel=1e-2 (default)")  # using the default
plot(lettuce.m1, conLevel = 1e-4, main = "conLevel=1e-4")
plot(lettuce.m1, conLevel = 1e-6, main = "conLevel=1e-6")
plot(lettuce.m1, conLevel = 1e-8, main = "conLevel=1e-8")
par(mfrow = c(1,1))

## User-specified position of legend
S.alba.m1 <- drm(DryMatter~Dose, Herbicide, data = S.alba, fct = LL.4())

plot(S.alba.m1)
plot(S.alba.m1, legendPos = c(0.3, 4.8))