R help - Aug 2011 - Change color in forest.rma (metafor)

My script is the following:

library(metafor)

yi<-c(-0.1, 0.2, 0.3, 0.4)
sei<-c(0.4, 0.2, 0.6, 0.1)
vi<-sei^2
studi<-c("A", "B", "C", "D")
eventi.c<-c(10, 5, 7, 6)
n.c<-c(11, 34, 25, 20)
eventi.a<-c(2, 7, 6, 5)
n.a<-c(11, 35, 25, 15)
dfs<-rma(yi, vi, method="DL")
dfs

windows(height=6, width=10, pointsize=10)
windowsFonts(B=windowsFont("Bookman Old Style"))

forest.rma(dfs, slab=studi, xlim=c(-15, 10), ilab=cbind(eventi.c, n.c,
eventi.a, n.a), ilab.xpos=c(-9.5, -8, -6, -4.5), cex=1.2, at=c(-2, -1, 0, 1,
2), family="B", xlab="Hazard Ratio (log scale)",
mlab="Random Effects
Model", efac=5, col="red", border="red")
text(-10, -1.3, paste("Heterogeneity: I-squared=",
paste(paste(round(dfs$I2,
2), "%", sep=""), paste("p", round(dfs$QEp, 4),
sep="="), sep=", "),
sep=""), font=4, cex=1.2, family="B")

op<-par(cex=1.2, font=2, family="B", oma=c(0.5, 0.5, 0.5, 0.5),
mar=c(0.5,
0.5, 0.5, 0.5))
text(x=c(-9.5, -8, -6, -4.5), 6, c("Events", "N",
"Events", "N"), cex=1.2 )
text(c(-8.7, -5.5, 8), 6.5, c("S", "A", "Log"))
text(-15, 6, "Trials", pos=4)
text(10, 6, "Hazard Ratio [95% CI]", pos=2)
par(op)

Even if I have specified "col="red",
border="red"", color of squares and
diamond rests black! Why?

Thanks,
Paola


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Am 24.08.2011 07:50, schrieb Paola Tellaroli:
> My script is the following:
> 
> library(metafor)
> 
> yi<-c(-0.1, 0.2, 0.3, 0.4)
> sei<-c(0.4, 0.2, 0.6, 0.1)
> vi<-sei^2
> studi<-c("A", "B", "C", "D")
> eventi.c<-c(10, 5, 7, 6)
> n.c<-c(11, 34, 25, 20)
> eventi.a<-c(2, 7, 6, 5)
> n.a<-c(11, 35, 25, 15)
> dfs<-rma(yi, vi, method="DL")
> dfs
> 
> windows(height=6, width=10, pointsize=10)
> windowsFonts(B=windowsFont("Bookman Old Style"))
> 
> forest.rma(dfs, slab=studi, xlim=c(-15, 10), ilab=cbind(eventi.c, n.c,
> eventi.a, n.a), ilab.xpos=c(-9.5, -8, -6, -4.5), cex=1.2, at=c(-2, -1, 0,
1,
> 2), family="B", xlab="Hazard Ratio (log scale)",
mlab="Random Effects
> Model", efac=5, col="red", border="red")
> text(-10, -1.3, paste("Heterogeneity: I-squared=",
paste(paste(round(dfs$I2,
> 2), "%", sep=""), paste("p", round(dfs$QEp,
4), sep="="), sep=", "),
> sep=""), font=4, cex=1.2, family="B")
> 
> op<-par(cex=1.2, font=2, family="B", oma=c(0.5, 0.5, 0.5,
0.5), mar=c(0.5,
> 0.5, 0.5, 0.5))
> text(x=c(-9.5, -8, -6, -4.5), 6, c("Events", "N",
"Events", "N"), cex=1.2 )
> text(c(-8.7, -5.5, 8), 6.5, c("S", "A",
"Log"))
> text(-15, 6, "Trials", pos=4)
> text(10, 6, "Hazard Ratio [95% CI]", pos=2)
> par(op)
> 
> Even if I have specified "col="red",
border="red"", color of squares and
> diamond rests black! Why?
As far as I know, "col" and "border" do only affect the
fitted values
("diamonds"), i.e. the FEM/REM estimators (see ?forest.rma: "col:
character string specifying the name of a color to use for _the fitted_
values (?"darkgray"? by default).")

Furthermore, I had a quick look at the source code and it might be a
bug. If I replace in line 2770 the line

cex * efac), col = "black", ...)

with

cex * efac), col = col, ...)

you can at least specify your own colour. Changing the border color
seems a bit more tricky...

However, Wolfgang Viechbauer (the package author) is always a very
responsive and helpful person and I suggest you better wait for his answer.

Bernd