schweder: Schweder and Spjotvoll plot

In metap: Meta-Analysis of Significance Values

Schweder and Spjotvoll plot

Description

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

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 \mjseqnp-values
xlab	Label for plot \mjseqnx-axis
ylab	Label for plot \mjseqny-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

Details

After removing invalid \mjseqnp-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 \mjseqnk+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.

Value

A list containing

p	The values of \mjseqnp 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

Author(s)

Michael Dewey

References

\insertRef

becker94metap

\insertRef

benjamini00metap

\insertRef

schweder82metap

Examples

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

metap documentation built on Sept. 11, 2024, 6:53 p.m.