R help - Apr 2015 - Trim and fill procedure

Hi all,

I have a question concerning the trim and fill procedure in metafor. In STATA it
is possible to obtain the values of the added estimated effect sizes. I was
wondering if this is also possible in R and if so, how I can obtain the new data
with the added values.
I would really appreciate your response. 


 		 	   		  
	[[alternative HTML version deleted]]

Hello Carlijn

Well the documentation for trimfill says they are added.

library(metafor)
example(trimfill)

This now leaves you with
res
res.tf

By looking at these and seeing which vectors have grown you should be 
able to extract the yi and vi which you want.

Wolfgang will doubtless be on the list soon to tell us there is a neater 
way of doing this.

On 04/04/2015 21:27, Carlijn Wibbelink wrote:
> Hi all,
>
> I have a question concerning the trim and fill procedure in metafor. In
STATA it is possible to obtain the values of the added estimated effect sizes. I
was wondering if this is also possible in R and if so, how I can obtain the new
data with the added values.
> I would really appreciate your response.
>
>
>   		 	   		
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Michael
http://www.dewey.myzen.co.uk/home.html

Yes, a comparison of the two objects would tell you what's been added.

An object returned by the trimfill() function also has a vector added to it,
named 'fill', which indicates whether the data (which are stored in the
vector 'yi') are observed or augmented values. So, for example:

library(metafor)

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

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

### trim and fill analysis
tmp <- trimfill(res)

### show log relative risks and dummy variable to indicate augmented values
data.frame(tmp$yi, tmp$fill)

### that's in fact how the funnel() function knows how to draw the points
when you do:
funnel(tmp)

Best,
Wolfgang
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Michael
> Dewey
> Sent: Monday, April 06, 2015 14:55
> To: Carlijn Wibbelink; r-help at r-project.org
> Subject: Re: [R] Trim and fill procedure
> 
> Hello Carlijn
> 
> Well the documentation for trimfill says they are added.
> 
> library(metafor)
> example(trimfill)
> 
> This now leaves you with
> res
> res.tf
> 
> By looking at these and seeing which vectors have grown you should be
> able to extract the yi and vi which you want.
> 
> Wolfgang will doubtless be on the list soon to tell us there is a neater
> way of doing this.
> 
> On 04/04/2015 21:27, Carlijn Wibbelink wrote:
> > Hi all,
> >
> > I have a question concerning the trim and fill procedure in metafor.
In
> STATA it is possible to obtain the values of the added estimated effect
> sizes. I was wondering if this is also possible in R and if so, how I can
> obtain the new data with the added values.
> > I would really appreciate your response.
> >
> > 	[[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> > and provide commented, minimal, self-contained, reproducible code.