schweder: Schweder and Spjotvoll plot

Description

Produces the plot suggested by Schweder and Spjotvoll to display a collection of p-values and also optionally draws the lowest slope line suggested by Benjamini and Hochberg

Usage

schweder(p, xlab = "Rank of p", ylab = "p", drawline = NULL,
   bh.lwd = 1, bh.lty = "solid", bh.col = "black",
   ls.control = list(frac = NULL),
   ls.lwd = 1, ls.lty = "dotted", ls.col = "black",
   ab.control = list(a = NULL, b = NULL),
   ab.lwd = 1, ab.lty = "dashed", ab.col = "black", ...)

Value

A list containing

p: The values of p plotted
bh.params: A list containing at least items a and b the intercept and slope of the line drawn. This is only included if the lowest slope line was drawn
ls.params: A list containing at least items a and b the intercept and slope of the line drawn. This is only included if the least squares line was drawn
ab.params: A list containing at least items a and b the intercept and slope of the line drawn. This is only included if the user specified line was drawn

Arguments

p: A vector of p-values
xlab: Label for plot x-axis
ylab: Label for plot y-axis
drawline: Which line, if any, to draw. See Details
bh.lwd: Width of the lowest slope line
bh.lty: Line type of the lowest slope line
bh.col: Colour of the lowest slope line
ls.control: A list containing a named element frac. See Details
ls.lwd: Width of the least squares line
ls.lty: Line type of the least squares line
ls.col: Colour of the least squares line
ab.control: A list containing two elements a and b. See Details
ab.lwd: Width of the specified line
ab.lty: Line type of the specified line
ab.col: Colour of the specified line
...: Further parameters to be passed through to plot

Author

Michael Dewey

Details

After removing invalid p-values plots them. Any graphics parameters passed in ... affect this part of the plot only. Note that the axes are chosen according to the scheme of Banjamini and Hochberg, Schweder and Spjotvoll used a different system.

By setting drawline appropriately up to three lines may be drawn.

If drawline includes the string "bh" the lowest slope line of Benjaimin and Hochberg is drawn. No further parameters are needed here but the characteristics of the line may be set: width, line type, and colour.

If drawline includes the string "ls" a least squares line is drawn passing through the point k+1, 1. The parameter frac specified what fraction of the values be used for this and may need experimentation to obtain a suitable line. The characteristics of the line may be set: width, line type, and colour.

If drawline includes the string "ab" a user specified line is drawn. The parameters a and b specify the intercept and slope. The characteristics of the line may be set: width, line type, and colour.

References

becker94metap

benjamini00metap

schweder82metap

Examples

Run this code

   data(dat.metap)
   teachexpect <- dat.metap$teachexpect
   schweder(teachexpect)

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