metafor (version 1.4-0)

qqnorm.rma.uni: Normal QQ Plot for rma Objects

Description

Function to create normal QQ plots for objects of class "rma.uni", "rma.mh", and "rma.peto".

Usage

## S3 method for class 'rma.uni':
qqnorm(y, type="rstandard", pch=19, envelope=TRUE, level=y$level, 
       bonferroni=FALSE, reps=1000, smooth=TRUE, bass=0, \dots)
## S3 method for class 'rma.mh':
qqnorm(y, type="rstandard", pch=19, \dots)
## S3 method for class 'rma.peto':
qqnorm(y, type="rstandard", pch=19, \dots)

Arguments

y

an object of class "rma.uni", "rma.mh", or "rma.peto".

type

either "rstandard" (default) or "rstudent" indicating whether the usual or deleted residuals should be used in creating the plot. See Details.

pch

plotting symbol to use for the observed effect sizes or outcomes. By default, a solid circle is used. See points for other options.

envelope

logical indicating whether a pseudo confidence envelope should be simulated and added to the plot (default is TRUE)). Only for objects of class "rma.uni". See Details.

level

numerical value between 0 and 100 specifying the level of the pseudo confidence envelope (the default is to take the value from the object).

bonferroni

logical indicating whether the bounds of the envelope should be Bonferroni corrected.

reps

numerical value indicating the number of iterations to use for simulating the pseudo confidence envelope (default is 1000).

smooth

logical indicating whether the results from the simulation should be smoothed (default is TRUE).

bass

numerical value that controls the degree of smoothing (default is 0).

...

other arguments.

Details

The plot shows the theoretical quantiles of a normal distribution on the horizontal axis against the observed quantiles for either the standardized residuals (type="rstandard", the default) or the externally standardized residuals (type="rstudent") on the vertical axis. For reference, a line is added to the plot with slope of 1, going through the (0,0) point. For objects of class "rma.uni", it is also possible to add a pseudo confidence envelope to the plot. The envelope is created based on the quantiles of sets of pseudo residuals simulated from the given model (for details, see Cook & Weisberg, 1982). The number of sets simulated can be controlled with the reps argument. When smooth=TRUE, the simulated bounds are smoothed with Friedman's SuperSmoother (see supsmu). The bass argument can be set to a number between 0 and 10, with higher numbers indicating increasing smoothness. If bonferroni=TRUE, the envelope bounds are Bonferroni corrected, so that the envelope can be regarded as a confidence region for all $k$ residuals simultaneously. The default however is bonferroni=FALSE, which makes the plot more sensitive to deviations from normality.

References

Cook, R. D. & Weisberg, S. (1982). Residuals and influence in regression. London: Chapman and Hall. Viechtbauer, W. (2010). Conducting meta-analyses in R with the metafor package. Journal of Statistical Software, 36(3), 1--48. http://www.jstatsoft.org/v36/i03/.

See Also

rma.uni, rma.mh, rma.peto

Examples

### load BCG vaccine data
data(dat.bcg)

### meta-analysis of the log relative risks using a random-effects model
res <- rma(ai=tpos, bi=tneg, ci=cpos, di=cneg, 
           data=dat.bcg, measure="RR", method="REML")
qqnorm(res)

### mixed-effects model with absolute latitude as a moderator
res <- rma(ai=tpos, bi=tneg, ci=cpos, di=cneg, mods=cbind(ablat), 
           measure="RR", data=dat.bcg, method="REML")
qqnorm(res)