albatros: Albatros plot

In metap: Meta-Analysis of Significance Values

Albatros plot

Description

Produces the albatros plot of Harrison et al\loadmathjax

Usage

albatros(p, n, axes = list(xlimit = NULL, ylimit = NULL,
      lefttext = NULL, righttext = NULL),
   contours = list(type = NULL, contvals = NULL, ltys = NULL, contlabs = NULL),
   plotpars = list(yscale = NULL, pchs = NULL, cols = NULL), ...)
docontours(conttype, xvals, contvals, xtrans, ytrans,
   xlims, ylims, ltys, contlabs)

Arguments

p	A vector of \mjseqnp values
n	A vector of sample sizes
axes	A list containing xlimit a single value, the limit for the x-axis which is used symmetrically ylimit a vector of length 2, limits for the y-axis lefttext character, to label below plot righttext character, to label below plot
contours	A list containing type what effect size to use, a character one of "corr", "or", "smd" contvals a vector, what values to draw the contours at ltys a vector, what line types to use
plotpars	A list containing yscale Scaling for y-axis, See details pchs Symbols to be used cols Colours for points
...	Arguments to be passed through to plot
conttype	Character: one of "smd", "or", "corr"
xvals	A vector of values to evaluate the contour
contvals	The values at which contours are drawn
xtrans	A function for transforming the x-axis
ytrans	A function for transforming the y-axis
xlims	The limits for the x-axis in plotting units
ylims	The limits for the y-axis in plottng units
ltys	A vector of line types for the contours
contlabs	Logical, draw the labels of the contours?

Details

Plots \mjseqnn against \mjseqnp and draws contours of constant effect size. \insertNoCiteharrison17metap

The \mjseqnp value scale on the x-axis is a logarithmic one but folded at the null value so that the extreme values represent small probabilities in each direction. The scale for the y-axis is user selectable. The original scale in the Stata version is \mjeqn(\log_10n)^2log(n, base = 10) ^ 2 which is obtained by setting yscale to "classic" but it is also possible to use \mjeqn\sqrtnsqrt(n) which is the default or \mjseqnn by setting yscale to "n". If the dataset contains extreme values the plot may be uninformative and the xlimit and ylimit parameters my be helpful to clip the plot. If they are not specified the function tries to choose suitable values.

For the contours if the type parameter in contours is NULL (the default) no contours will be plotted. The options available are “smr” (Standardised mean difference) “corr” (Correlation) “or” (Odds ratio).

The contours are labelled unless contlabs is set to FALSE. The function tries to position these so they are not obscured by the contour lines but if that is unsatisfactory then it is best to suppress them and position them manually or use a legend to identify line types.

The pch parameter may either be a single value or a vector of the same length as p. It may contain anything which is legal as input to the parameter of the same name in the graphics library and will be used for the plotted points. The cols parameter works similarly.

The values of lefttext and righttext are used to produce labels under the \mjseqnx-axis and are placed level with the label. By default they are not produced.

The return values from the function may be useful if further annotations are required as they give the axis limits in plotting units.

Value

Returns A list containing

xlims	The limits for the x-axis in plotting units
ylims	The limits for the y-axis in plotting units

Note

The docontours function is for internal use only

Author(s)

Michael Dewey

References

\insertAllCited

See Also

For plotting parameters see par

Examples

data(dat.metap)
validity <- dat.metap$validity
fit.v <- albatros(validity$p, validity$n,
   contours = list(type = "corr", contvals = c(0.25, 0.5, 0.8), ltys = 1:3),
      axes = list(ylimit = c(1,200),  lefttext = "Negative correlation",
         righttext = "Positive correlation"),
   main = "Validity")
#
fit.z <- albatros(dat.metap$zhang$p, dat.metap$zhang$n,
   contours = list(type = "smd", contvals = c(0.25, 0.5, 1), ltys = 1:3),
   plotpars = list(pchs = letters[unclass(dat.metap$zhang$phase)]),
   axes = list(lefttext = "Favours control", righttext = "Favours exercise"),
   main = "Zhang"
   )

metap documentation built on Oct. 9, 2023, 5:10 p.m.