qqnorm.rma.uni {metafor} | R Documentation |
Function to create normal QQ plots for objects of class "rma.uni"
, "rma.mh"
, and "rma.peto"
.
## 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, ...) ## S3 method for class 'rma.mh': qqnorm(y, type="rstandard", pch=19, ...) ## S3 method for class 'rma.peto': qqnorm(y, type="rstandard", pch=19, ...)
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. |
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.
Wolfgang Viechtbauer; wvb@www.wvbauer.com; http://www.wvbauer.com/
Cook, R. D. & Weisberg, S. (1982) Residuals and influence in regression. London: Chapman and Hall.
### load BCG vaccine data data(dat.bcg) ### meta-analysis of the log risk ratios 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=ablat, measure="RR", data=dat.bcg, method="REML") qqnorm(res)