panel.bwstrip: Flexible panel.bwplot replacement
In agsemisc: Miscellaneous plotting and utility functions

Description Usage Arguments Details Author(s) See Also Examples

Box plots with added stripplots, densityplots, mean/stderr marker etc.

panel.bwstrip(x, y, groups, subscripts, pch, col, 
      box.ratio = 5, varwidth = FALSE, whiskerpos = 0.1, logbase,
      type="mean,mad,strip,N,grid",
      densityplot=expression(density(X,cut=2)), strip.limit=100, 
      seplines = NULL, N.label = "N=% \n",
      extend = TRUE,
      levels.fos = NULL, ...)

`x`	the data, as in `panel.bwplot`
`y`	the number of the box, as in `panel.bwplot`
`groups`	a factor indicating a partitioning of the data `x`. Relevant for the `pch` and `col` arguments.
`subscripts`	Argument internally used by Lattice to realize the `groups` functionality.
`pch`	A integer vector, character vector or list that indicates the value to be used as pch (plot character) for the stripplot for each level of `groups`. You will need a list if you want to mix plot symbols (indicated by integers) with plot characters (indicated by characters). There is a simpler method to specify any of these cases, namely a single string with entries separated by commas. One-digit numeric entries will evaluate to a plot character, two-digit numeric entries will evaluate to an integer plot symbol. For instance, `"1,w,13,2,02"` will evaluate into `list("1", "w", 13, "2", 2)`. Defaults to all `trellis.par.get("superpose.symbol")$pch`. Note that with `groups=gg` you can often use `pch=levels(gg)`, because Lattice will ignore all but the first character of a string.
`col`	Analogous to pch, but indicating color. Integers indicate color numbers, strings indicate color names, both can be mixed in the comma-separated string format. Defaults to all `trellis.par.get("superpose.symbol")$col`.
`box.ratio`	Like in panel.bwplot, but the different default value withstands the call default of 1 that is imposed by Lattice (as of R 2.2).
`varwidth`	vary box thickness according to number of data values, as in `panel.bwplot`
`whiskerpos`	With large values in the range 1..Inf, `whiskerpos` is equivalent to the `coef` argument to `panel.bwplot` (or really `boxplot.stats`), i.e. each whisker is at the farthest data value that is at most `whiskerpos` times the interquartile range (or box width) away from the box. Only the values 1.5, 2 or 3 are common. In contrast, with small values `w` in the range 0..0.25, the whiskers will indicate the fixed quantiles `w` and `1-w`. This is easier to explain to non-statisticians and often more appropriate for larger samples. So `whiskerpos==0` will produce whiskers at the min and max of the data, the default will indicate the 10-percentile and the 90-percentile, and `whiskerpos==0.25` makes the whiskers disappear.
`logbase`	An argument `logbase=b` indicates that the high-level plot is using a log scale axis to base `b` and hence the data is logarithmic rather than real and needs to be converted back before computing mean, interpolating quantiles etc.
`type`	Declares which boxplot elements to include in the plot. Is either a comma-separated string of element names (as shown in the default) or a vector of such names. The elements have the following meaning: `mean` plots something like –M– indicating the mean and its standard error. `mad` will indicate the stderror of the median (median absolute deviation, as computed by `mad` divided by sqrt(n)) as a line left and right of the median dot. `strip` will produce a stripplot of the individual data points, scattered vertically to make similar values more visible. `density` will add a densityplot and a support line (extending along the range of the data). The plot can be customized via the `densityplot` argument. `N` will indicate the number of datapoints according to the `N.label` argument. `grid` will draw dotted vertical lines aligned with x-axis labels. Elements not mentioned will be left out of the plot. The box and median dot are always included (this is a boxplot, after all), the whiskers can be suppressed by `whiskerpos=0.25`.
`densityplot`	Relevant if `"density"` is mentioned in the `type` argument. Must be an expression describing a call to `density` that concerns the data vector `X` (an uppercase x!), which will be the data for the current boxplot for each evaluation of the expression. If a densityplot appears, the boxplot will not be color-filled.
`strip.limit`	If `T`, will reduce the stripplot to only the outliers, i.e., the values beyond the whiskers. If an integer, will suppress the stripplot entirely if there are more than this many values in the current boxplot.
`seplines`	A vector of vertical positions where horizontal lines will be drawn to separate the boxplots into groups. Position 1.5, 2.5 etc. is above the lowest, second-lowest boxplot etc.
`N.label`	A string such as " number of values underlying the boxplot and the resulting string is printed at the right of the plot iff `N` is mentioned in the `type` argument. Use trailing blanks and newlines to adjust positioning.
`extend`	If TRUE, will print to console some statistics for each sample: the quantiles (0, 0.25, 0.5, 0.75,, 1), mean, quartile ratio (or at least interquartile range) and the number of data points. If `extend` is a function, it will be called with four arguments: data vector x, current y, groups, subscripts.
`levels.fos`	weird stuff, but means the same as in `panel.bwplot`
`...`	all other arguments will be ignored.

A lattice panel function to be used with bwplot. Can draw a boxplot plus stripplot plus densityplot, indicate groups, mark the mean and its stderror, report N, and more. Graphical parameters are controlled by the trellis.par.set parameters box.rectangle, box.umbrella, superpose.symbol (which is non-standard), and reference.line. The horizontal=F option available in panel.bwplot is not supported here.

Lutz Prechelt prechelt@inf.fu-berlin.de

a.resetplotparams, plotf, panel.xy.

# set  grid.prompt(TRUE)  to see each plot separately (click graphics window)
data(iris)
a.resetplotparams()
print(bwplot(Species~Sepal.Length, data=iris, panel=panel.bwstrip))
# A plot including a density plot:
print(bwplot(Species~Sepal.Length, data=iris, panel=panel.bwstrip,
             type="mean,strip,density"))
# A customized plot:
print(bwplot(~Sepal.Length, data=iris, panel=panel.bwstrip, 
             groups=Species, pch=levels(iris$Species), strip.limit=200,
             type="mean,strip,density", 
             densityplot=expression(density(X, cut=1))))
# A conventional-style plot:
print(bwplot(Species~Sepal.Length, data=iris, panel=panel.bwstrip,
             type="mean,strip,grid", strip.limit=TRUE, whiskerpos=1.5,
             densityplot=expression(density(X, cut=1))))
# A plot showing some other features:
print(bwplot(cut(Sepal.Width,4)~Sepal.Length, data=iris, panel=panel.bwstrip,
             groups=Species, varwidth=TRUE, box.ratio=20, 
             which="strip,N", strip.limit=50, pch="1,2,3"))

Loading required package: lattice
1 : 4.3 4.8 5.0 5.2 5.8 mean 5.006 qr 1.083 N 50 
2 : 4.9 5.6 5.9 6.3 7.0 mean 5.936 qr 1.125 N 50 
3 : 4.900 6.225 6.500 6.900 7.900 mean 6.588 qr 1.108 N 50 
1 : 4.3 4.8 5.0 5.2 5.8 mean 5.006 qr 1.083 N 50 
2 : 4.9 5.6 5.9 6.3 7.0 mean 5.936 qr 1.125 N 50 
3 : 4.900 6.225 6.500 6.900 7.900 mean 6.588 qr 1.108 N 50 
1 : 4.3 5.1 5.8 6.4 7.9 mean 5.843 qr 1.255 N 150 
1 : 4.3 4.8 5.0 5.2 5.8 mean 5.006 qr 1.083 N 50 
2 : 4.9 5.6 5.9 6.3 7.0 mean 5.936 qr 1.125 N 50 
3 : 4.900 6.225 6.500 6.900 7.900 mean 6.588 qr 1.108 N 50 
1 : 4.500 5.400 5.650 6.125 7.700 mean 5.721 qr 1.134 N 24 
2 : 4.30 5.60 6.10 6.65 7.70 mean 6.04 qr 1.188 N 83 
3 : 4.6 5.0 5.1 6.0 7.9 mean 5.538 qr 1.2 N 37 
4 : 5.20 5.40 5.45 5.65 5.80 mean 5.5 qr 1.046 N 6