metap (version 0.7)

schweder: Schweder and Spjotvoll plot

Description

Produces the plot suggested by Schweder and Spjotvol 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", ...)

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

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

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 Spjotvol 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

Benjamini, Y and Hochberg, Y. On the adaptive control of the false disovery rate in multiple testing with independent statistics. Journal of Educational and Behavioral Statistics, 25: 60--83, 2000.

Schweder, T and Spjotvoll, E. Plots of $P$--values to evaluate many tests simultaneously. Biometrika, 69:493--502, 1982.

Examples

   data(teachexpect)
   schweder(teachexpect)