R: Schweder and Spjotvoll plot

schweder {metap} | R Documentation

## 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

### 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.

### 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

### Author(s)

Michael Dewey

### 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)

[Package metap version 0.8 Index]