plot.drc: Plotting fitted curves for a 'drc' 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, grid = 100, legend, legendText, legendPos, legendCex = 1,
  type = "average", obs, lty, log = "x", cex, pch, xlab, ylab, xlim, ylim,
  bcontrol = NULL, xt = NULL, xtlab = NULL, yt = NULL, ytlab = NULL,
  add = FALSE, axes = TRUE)

Arguments

an object of class 'drc'. For instance, lwd=2 or lwd=3 increase the width of plot symbols.

...

additional arguments.

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. Dose level below which the dose is zero (the amount of stretching on the x-axis above zero). Default is 1e-2.

conName

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

grid

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 the originals observations should be plotted. 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

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Outdated argument.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.

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.

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.

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

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
model1 <- multdrc(rootl~conc, data = ryegrass)
model2 <- multdrc(rootl~conc, data = ryegrass, fct=l3())  # lower limit fixed at 0

## Plotting observations and fitted curve for 'model1'
plot(model1) 

## Adding fitted curve for 'model2'
plot(model2, add = TRUE, type = "none", 
col = 2, lty = 2)

## Fitting model to be plotted below
model3 <- multdrc(SLOPE~DOSE, CURVE, data=spinach)

## Plot with no colours
plot(model3, main="Different line types (default)")

## Plot with default colours
plot(model3, col=TRUE, main="Default colours")

## Plot with specified colours
plot(model3, col=c(2,6,3,23,56), main="User-specified colours")

## Plot of curves 1 and 2 only
plot(model3, level=c(1,2), main="User-specified curves")

## Plot with symbol of different sizes
plot(model3, cex=c(1,2,3,4,5), main="User-specified curves")

## Fitting another model to be plotted below
model4 <- multdrc(weight~conc, data=lettuce)

## Using the argument 'conLevel'. Compare the plots!
par(mfrow=c(2, 2))
plot(model4, main="conLevel=1e-2 (default)")  # using the default
plot(model4, conLevel=1e-4, main="conLevel=1e-4")
plot(model4, conLevel=1e-6, main="conLevel=1e-6")
plot(model4, conLevel=1e-8, main="conLevel=1e-8")
par(mfrow=c(1,1))

## Using the argument 'broken'
plot(model1, conLevel = 0.1, broken = TRUE)
plot(model1, conLevel = 0.1, broken = TRUE, 
bcontrol=list(style="zigzag"))

## Plot without axes
plot(model1, axes = FALSE)

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

plot(m1)
plot(m1, legendPos = c(0.3, 4.8))