[R-meta] escalc() function and weights

[Prof. Mario Petretta]

Dear All,

in a previous post (see below) it was pointed out by Wolfgang Viechtbauer
that the use of weight in the escalc () function is deprecated.

Please, it is possible to clarify:

1) Why is the use of weight in the escalc () function is now deprecated?

2) What is the correct code to use for the example of the tutorial on the
"Metafor" package and the "escalc" function using the "long" bcg data
obtained with the reshape2 function, as shown in the previous post ?

Thank you for your time

Mario Petretta

 

 

Mario Petretta

Professor of Internal Medicine

Department of Translational Medical Science

University of Naples Federico II

Naples - Italy

 

 
<https://www.mail-archive.com/search?l=r-help@r-project.org&q=subject:%22Re%
5C%3A+%5C%5BR%5C%5D+Error+message+in+meta%5C-analysis+package+Metafor%5C-wei
ghts+%3D%5C%22%5C%22%22&o=newest> Re: [R] Error message in meta-analysis
package Metafor-weights =""

 
<https://www.mail-archive.com/search?l=r-help@r-project.org&q=from:%22Viecht
bauer%2C+Wolfgang+%5C%28SP%5C%29%22> Viechtbauer, Wolfgang (SP)
<https://www.mail-archive.com/search?l=r-help@r-project.org&q=date:20200616>
Tue, 16 Jun 2020 09:51:21 -0700

Dear Amoatwi,

 

This way of using the escalc() function has been deprecated. It might be
added 

back once there is actually any benefit from having this functionality, but
for 

years it just meant that I had to maintain two different ways of doing the 

exact same thing without any additional benefits.

 

Best,

Wolfgang

 

-- 

Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and    

Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD    

Maastricht, The Netherlands | +31 (43) 388-4170 |  <http://www.wvbauer.com/>
http://www.wvbauer.com    

 

>-----Original Message-----

>From: R-help [ <mailto:r-help-boun... using r-project.org>
mailto:r-help-boun... using r-project.org] On Behalf Of K Amoatwi

>Sent: Tuesday, 16 June, 2020 4:50

>To: r-help using r-project.org

>Subject: [R] Error message in meta-analysis package Metafor-weights =""

> 

>Dear All,

>I am using the example from one of the tutorial about "Metafor" package and

>"escalc" function, to learn how this package can be applied to do

>meta-analysi; the code and the data is directly from the tutorials but

>"weights=freq" option in the escalc function is given me error message

>This is the code below:

> 

>library(metafor) # Load package

>#####DATASET 1: BCG Vaccine Trials

>data(dat.bcg) # BCG meta-analytic dataset

> 

>##Formula based Specification

>##That is, what if I have multiple rows per study, corresponding to

>difference treatment groups?

> 

>library(reshape2) # Load package for data reshaping

> 

>bcg.long <- melt(dat.bcg[, c("trial", "tpos", "tneg", "cpos", "cneg")], id

>= "trial")

>bcg.long$pos <- ifelse(bcg.long$var == "tpos" | bcg.long$var == "cpos", 1,

>0)

>bcg.long$group <- ifelse(bcg.long$var == "tpos" | bcg.long$var == "tneg",

>1, 0)

> 

>##sample of the data, the first 6 rows

>head(bcg.long)

>  trial variable value pos group

>1     1     tpos     4     1     1

>2     2     tpos     6     1     1

>3     3     tpos     3     1     1

>4     4     tpos    62    1     1

>5     5     tpos    33    1     1

>6     6     tpos   180   1     1

> 

>##Now applying the " escalc " function

> 

>escalc(factor(pos)~factor(group)| factor(trial),weights = value,data =

>bcg.long, measure = "OR")

> 

>##Then I got this error message

>Error in escalc(factor(pos) ~ factor(group) | factor(trial), weights =

>value,  :

>  object 'value' not found

> 

>I used the same data with different example from another author and got a

>similar error message

>Second code with the same data but different coding

>Sample data

> 

>with the first 6 rows of the rearranged data shown below. (T=treatment,

>C=Control group, Out=outcome whether positive or negative, and then

>frequency)

>    study grp out freq

>1        1    T    +      4

>2        1    T    -    119

>3        1    C   +      11

>4        1    C   -     128

>5        2    T   +        6

>6        2    T   -      300

> 

>>escalc(out ~ grp | study, weights = freq, data = dat.fm, measure = "OR")

> 

>Error in escalc(out ~ grp | study, weights = freq, data = dat.fm, measure =

>"OR") :

>  object 'freq' not found

> 

>I am not sure what I am doing wrong since both authors were able to get

>their results while I am getting error messages.

> 

>Any help will be very much appreciated

> 

>Amoatwi

 

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