"metafor" package, proportions: single groups wrt to a categorical dependent variable

[Dushanthi Pinnaduwage]

Dear all, I am using R version 2.15.0 and 'metafor' package version 1.6-0. Can this version of the package handle proportions from a  categorical dependent variable for single studies?If so how do I set up my dataframe for the raw data from different studies? Also how do I give inputs, specially xi, mi (or ni) to the function escalc()? Thanks,Dushanthi    
        [[alternative HTML version deleted]]

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[Michael Dewey]

At 01:44 28/07/2012, Dushanthi Pinnaduwage wrote:




>Dear all, I am using R version 2.15.0 and 'metafor' package version
>1.6-0. Can this version of the package handle proportions from
>a  categorical dependent variable for single studies?If so how do I
>set up my dataframe for the raw data from different studies? Also
>how do I give inputs, specially xi, mi (or ni) to the function
>escalc()? Thanks,Dushanthi

You do not give us very much to go on here. When you say your outcome
is proportions do you mean your outcome has more than two values and
you are generating (or have been provided with) several proportions
for each study or do you mean it is a binary variable? If the latter
do you in fact have the numerators and denominators or just the
proportion? It would also help if you showed us the code you have
tried and the error message you got (if any) or told us the
discrepancy between the output you obtained and that which you expected.

>
>         [[alternative HTML version deleted]]

Michael Dewey
[hidden email]
http://www.aghmed.fsnet.co.uk/home.html

______________________________________________
[hidden email] mailing list
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.

[Dushanthi Pinnaduwage]

 Dear Michael, Thanks very much for your quick response. My outcome is not binary. Outcome has more than 2 values (levels) and I have counts for the levels. I have not written a code yet.  I would like to know if escalc() can handle categorical outcome data (more than 2 proportions). If so, how can I input the counts of each level of the categorical outcome to this function. Hope it is little clear now.  Dushanthi   You do not give us very much to go on here. When you say your outcome
>is proportions do you mean your outcome has more than two values and
> you are generating (or have been provided with) several proportions
> for each study or do you mean it is a binary variable? If the latter
> do you in fact have the numerators and denominators or just the
> proportion? It would also help if you showed us the code you have
> tried and the error message you got (if any) or told us the
> discrepancy between the output you obtained and that which you expected.
 > Date: Sat, 28 Jul 2012 14:25:08 +0100

> To: [hidden email]; [hidden email]
> From: [hidden email]
> Subject: Re: [R] "metafor" package, proportions: single groups wrt to a  categorical dependent variable
>
> At 01:44 28/07/2012, Dushanthi Pinnaduwage wrote:
>
>
>
>
> >Dear all, I am using R version 2.15.0 and 'metafor' package version
> >1.6-0. Can this version of the package handle proportions from
> >a  categorical dependent variable for single studies?If so how do I
> >set up my dataframe for the raw data from different studies? Also
> >how do I give inputs, specially xi, mi (or ni) to the function
> >escalc()? Thanks,Dushanthi
>
> You do not give us very much to go on here. When you say your outcome
> is proportions do you mean your outcome has more than two values and
> you are generating (or have been provided with) several proportions
> for each study or do you mean it is a binary variable? If the latter
> do you in fact have the numerators and denominators or just the
> proportion? It would also help if you showed us the code you have
> tried and the error message you got (if any) or told us the
> discrepancy between the output you obtained and that which you expected.
>
> >
> >         [[alternative HTML version deleted]]
>
> Michael Dewey
> [hidden email]
> http://www.aghmed.fsnet.co.uk/home.html
>

     
        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
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 Dewey]

At 15:47 28/07/2012, Dushanthi Pinnaduwage wrote:
>
>Dear Michael,
>
>Thanks very much for your quick response.
>
>My outcome is not binary. Outcome has more than 2 values (levels)
>and I have counts for the levels.
>I have not written a code yet.

Well as the name of the key function in metafor (rma.uni) suggests
metafor at present does univariate meta-analysis. If you can reduce
the outcome to a single measure of effect (perhaps using proportional
odds or continuation ratio) then you can enter that with its standard
error using the yi and sei parameters to rma.uni. If the nature of
your outcome does not allow that then you have a multivariate
meta-analysis. In that case you could try mvmeta (available from CRAN)

>
>I would like to know if escalc() can handle categorical outcome data
>(more than 2 proportions). If so, how can I input
>the counts of each level of the categorical outcome to this function.
>
>Hope it is little clear now.
>
>Dushanthi
>
>
>
>You do not give us very much to go on here. When you say your outcome
> >is proportions do you mean your outcome has more than two values and
> > you are generating (or have been provided with) several proportions
> > for each study or do you mean it is a binary variable? If the latter
> > do you in fact have the numerators and denominators or just the
> > proportion? It would also help if you showed us the code you have
> > tried and the error message you got (if any) or told us the
> > discrepancy between the output you obtained and that which you expected.
>
>
>
> > Date: Sat, 28 Jul 2012 14:25:08 +0100
> > To: [hidden email]; [hidden email]
> > From: [hidden email]
> > Subject: Re: [R] "metafor" package, proportions: single groups
> wrt to a categorical dependent variable
> >
> > At 01:44 28/07/2012, Dushanthi Pinnaduwage wrote:
> >
> >
> >
> >
> > >Dear all, I am using R version 2.15.0 and 'metafor' package version
> > >1.6-0. Can this version of the package handle proportions from
> > >a categorical dependent variable for single studies?If so how do I
> > >set up my dataframe for the raw data from different studies? Also
> > >how do I give inputs, specially xi, mi (or ni) to the function
> > >escalc()? Thanks,Dushanthi
> >
> > You do not give us very much to go on here. When you say your outcome
> > is proportions do you mean your outcome has more than two values and
> > you are generating (or have been provided with) several proportions
> > for each study or do you mean it is a binary variable? If the latter
> > do you in fact have the numerators and denominators or just the
> > proportion? It would also help if you showed us the code you have
> > tried and the error message you got (if any) or told us the
> > discrepancy between the output you obtained and that which you expected.
> >
> > >
> > > [[alternative HTML version deleted]]
> >
> > Michael Dewey
> > [hidden email]
> > http://www.aghmed.fsnet.co.uk/home.html
> >

Michael Dewey
[hidden email]
http://www.aghmed.fsnet.co.uk/home.html

______________________________________________
[hidden email] mailing list
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.

[Dushanthi Pinnaduwage]

Thanks very much for the reply Michael.I guess I have to combine some levels to  make categorical variable to a binary variable. Dushanthi  > Date: Sat, 28 Jul 2012 16:38:24 +0100

> To: [hidden email]; [hidden email]
> From: [hidden email]
> Subject: RE: [R] "metafor" package, proportions: single groups wrt to a  categorical dependent variable
>
> At 15:47 28/07/2012, Dushanthi Pinnaduwage wrote:
> >
> >Dear Michael,
> >
> >Thanks very much for your quick response.
> >
> >My outcome is not binary. Outcome has more than 2 values (levels)
> >and I have counts for the levels.
> >I have not written a code yet.
>
> Well as the name of the key function in metafor (rma.uni) suggests
> metafor at present does univariate meta-analysis. If you can reduce
> the outcome to a single measure of effect (perhaps using proportional
> odds or continuation ratio) then you can enter that with its standard
> error using the yi and sei parameters to rma.uni. If the nature of
> your outcome does not allow that then you have a multivariate
> meta-analysis. In that case you could try mvmeta (available from CRAN)
>
> >
> >I would like to know if escalc() can handle categorical outcome data
> >(more than 2 proportions). If so, how can I input
> >the counts of each level of the categorical outcome to this function.
> >
> >Hope it is little clear now.
> >
> >Dushanthi
> >
> >
> >
> >You do not give us very much to go on here. When you say your outcome
> > >is proportions do you mean your outcome has more than two values and
> > > you are generating (or have been provided with) several proportions
> > > for each study or do you mean it is a binary variable? If the latter
> > > do you in fact have the numerators and denominators or just the
> > > proportion? It would also help if you showed us the code you have
> > > tried and the error message you got (if any) or told us the
> > > discrepancy between the output you obtained and that which you expected.
> >
> >
> >
> > > Date: Sat, 28 Jul 2012 14:25:08 +0100
> > > To: [hidden email]; [hidden email]
> > > From: [hidden email]
> > > Subject: Re: [R] "metafor" package, proportions: single groups
> > wrt to a categorical dependent variable
> > >
> > > At 01:44 28/07/2012, Dushanthi Pinnaduwage wrote:
> > >
> > >
> > >
> > >
> > > >Dear all, I am using R version 2.15.0 and 'metafor' package version
> > > >1.6-0. Can this version of the package handle proportions from
> > > >a categorical dependent variable for single studies?If so how do I
> > > >set up my dataframe for the raw data from different studies? Also
> > > >how do I give inputs, specially xi, mi (or ni) to the function
> > > >escalc()? Thanks,Dushanthi
> > >
> > > You do not give us very much to go on here. When you say your outcome
> > > is proportions do you mean your outcome has more than two values and
> > > you are generating (or have been provided with) several proportions
> > > for each study or do you mean it is a binary variable? If the latter
> > > do you in fact have the numerators and denominators or just the
> > > proportion? It would also help if you showed us the code you have
> > > tried and the error message you got (if any) or told us the
> > > discrepancy between the output you obtained and that which you expected.
> > >
> > > >
> > > > [[alternative HTML version deleted]]
> > >
> > > Michael Dewey
> > > [hidden email]
> > > http://www.aghmed.fsnet.co.uk/home.html
> > >
>
> Michael Dewey
> [hidden email]
> http://www.aghmed.fsnet.co.uk/home.html
>

     
        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
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 Dewey]

At 01:18 31/07/2012, Dushanthi Pinnaduwage wrote:

>Thanks very much for the reply Michael.
>I guess I have to combine some levels to  make categorical variable
>to a binary variable.

Without knowing more about your outcome variable (you have not even
told us yet whether it is ordered or not) it is a bit hard to offer
more advice. I would regard collapsing categories as a last resort
myself as you lose information.

>
>Dushanthi
>
>
> > Date: Sat, 28 Jul 2012 16:38:24 +0100
> > To: [hidden email]; [hidden email]
> > From: [hidden email]
> > Subject: RE: [R] "metafor" package, proportions: single groups
> wrt to a categorical dependent variable
> >
> > At 15:47 28/07/2012, Dushanthi Pinnaduwage wrote:
> > >
> > >Dear Michael,
> > >
> > >Thanks very much for your quick response.
> > >
> > >My outcome is not binary. Outcome has more than 2 values (levels)
> > >and I have counts for the levels.
> > >I have not written a code yet.
> >
> > Well as the name of the key function in metafor (rma.uni) suggests
> > metafor at present does univariate meta-analysis. If you can reduce
> > the outcome to a single measure of effect (perhaps using proportional
> > odds or continuation ratio) then you can enter that with its standard
> > error using the yi and sei parameters to rma.uni. If the nature of
> > your outcome does not allow that then you have a multivariate
> > meta-analysis. In that case you could try mvmeta (available from CRAN)
> >
> > >
> > >I would like to know if escalc() can handle categorical outcome data
> > >(more than 2 proportions). If so, how can I input
> > >the counts of each level of the categorical outcome to this function.
> > >
> > >Hope it is little clear now.
> > >
> > >Dushanthi
> > >
> > >
> > >
> > >You do not give us very much to go on here. When you say your outcome
> > > >is proportions do you mean your outcome has more than two values and
> > > > you are generating (or have been provided with) several proportions
> > > > for each study or do you mean it is a binary variable? If the latter
> > > > do you in fact have the numerators and denominators or just the
> > > > proportion? It would also help if you showed us the code you have
> > > > tried and the error message you got (if any) or told us the
> > > > discrepancy between the output you obtained and that which
> you expected.
> > >
> > >
> > >
> > > > Date: Sat, 28 Jul 2012 14:25:08 +0100
> > > > To: [hidden email]; [hidden email]
> > > > From: [hidden email]
> > > > Subject: Re: [R] "metafor" package, proportions: single groups
> > > wrt to a categorical dependent variable
> > > >
> > > > At 01:44 28/07/2012, Dushanthi Pinnaduwage wrote:
> > > >
> > > >
> > > >
> > > >
> > > > >Dear all, I am using R version 2.15.0 and 'metafor' package version
> > > > >1.6-0. Can this version of the package handle proportions from
> > > > >a categorical dependent variable for single studies?If so how do I
> > > > >set up my dataframe for the raw data from different studies? Also
> > > > >how do I give inputs, specially xi, mi (or ni) to the function
> > > > >escalc()? Thanks,Dushanthi
> > > >
> > > > You do not give us very much to go on here. When you say your outcome
> > > > is proportions do you mean your outcome has more than two values and
> > > > you are generating (or have been provided with) several proportions
> > > > for each study or do you mean it is a binary variable? If the latter
> > > > do you in fact have the numerators and denominators or just the
> > > > proportion? It would also help if you showed us the code you have
> > > > tried and the error message you got (if any) or told us the
> > > > discrepancy between the output you obtained and that which
> you expected.
> > > >
> > > > >
> > > > > [[alternative HTML version deleted]]
> > > >
> > > > Michael Dewey
> > > > [hidden email]
> > > > http://www.aghmed.fsnet.co.uk/home.html
> > > >
> >
> > Michael Dewey
> > [hidden email]
> > http://www.aghmed.fsnet.co.uk/home.html
> >

Michael Dewey
[hidden email]
http://www.aghmed.fsnet.co.uk/home.html

______________________________________________
[hidden email] mailing list
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.

[Dushanthi Pinnaduwage]

Thanks for the reply.
Goal of my meta analysis is to compare 2 different surgical procedures to fix the same problem.
 
Data (after systematic search) are collected from studies with one or the other procedure applied.
 
There are a couple of outcome variables that measure the effetivenss of the procedures; The same outcome data was extacted from each study.
All outcome variables are categorical with number of levels 4 or 5.  Levels can be combined to make meaningful 2 levels (making binary variables), but prefer not to do this.
 
My analysis plan (say for outcome variable 1):
   
1. Do a metanalysis for all the studies with procedure 1 (say), combining proportions for outcome 1 (estimating the proportions).
2.  Do a metanalysis for all the studies with procedure 2 (say), combining proportions for outcome 1 (estimating the proportions).
3. Finally just discuss the proportion diffenences between the 2 procedures (descriptive) or test the for the proportion difference between the 2 procedures. Hope this will give some insight into the problem.Thank you.Dushanthi
 
 

> Date: Tue, 31 Jul 2012 17:42:12 +0100
> To: [hidden email]; [hidden email]; [hidden email]
> From: [hidden email]
> Subject: RE: [R] "metafor" package, proportions: single groups wrt to a  categorical dependent variable
>
> At 01:18 31/07/2012, Dushanthi Pinnaduwage wrote:
>
> >Thanks very much for the reply Michael.
> >I guess I have to combine some levels to  make categorical variable
> >to a binary variable.
>
> Without knowing more about your outcome variable (you have not even
> told us yet whether it is ordered or not) it is a bit hard to offer
> more advice. I would regard collapsing categories as a last resort
> myself as you lose information.
>
> >
> >Dushanthi
> >
> >
> > > Date: Sat, 28 Jul 2012 16:38:24 +0100
> > > To: [hidden email]; [hidden email]
> > > From: [hidden email]
> > > Subject: RE: [R] "metafor" package, proportions: single groups
> > wrt to a categorical dependent variable
> > >
> > > At 15:47 28/07/2012, Dushanthi Pinnaduwage wrote:
> > > >
> > > >Dear Michael,
> > > >
> > > >Thanks very much for your quick response.
> > > >
> > > >My outcome is not binary. Outcome has more than 2 values (levels)
> > > >and I have counts for the levels.
> > > >I have not written a code yet.
> > >
> > > Well as the name of the key function in metafor (rma.uni) suggests
> > > metafor at present does univariate meta-analysis. If you can reduce
> > > the outcome to a single measure of effect (perhaps using proportional
> > > odds or continuation ratio) then you can enter that with its standard
> > > error using the yi and sei parameters to rma.uni. If the nature of
> > > your outcome does not allow that then you have a multivariate
> > > meta-analysis. In that case you could try mvmeta (available from CRAN)
> > >
> > > >
> > > >I would like to know if escalc() can handle categorical outcome data
> > > >(more than 2 proportions). If so, how can I input
> > > >the counts of each level of the categorical outcome to this function.
> > > >
> > > >Hope it is little clear now.
> > > >
> > > >Dushanthi
> > > >
> > > >
> > > >
> > > >You do not give us very much to go on here. When you say your outcome
> > > > >is proportions do you mean your outcome has more than two values and
> > > > > you are generating (or have been provided with) several proportions
> > > > > for each study or do you mean it is a binary variable? If the latter
> > > > > do you in fact have the numerators and denominators or just the
> > > > > proportion? It would also help if you showed us the code you have
> > > > > tried and the error message you got (if any) or told us the
> > > > > discrepancy between the output you obtained and that which
> > you expected.
> > > >
> > > >
> > > >
> > > > > Date: Sat, 28 Jul 2012 14:25:08 +0100
> > > > > To: [hidden email]; [hidden email]
> > > > > From: [hidden email]
> > > > > Subject: Re: [R] "metafor" package, proportions: single groups
> > > > wrt to a categorical dependent variable
> > > > >
> > > > > At 01:44 28/07/2012, Dushanthi Pinnaduwage wrote:
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > >Dear all, I am using R version 2.15.0 and 'metafor' package version
> > > > > >1.6-0. Can this version of the package handle proportions from
> > > > > >a categorical dependent variable for single studies?If so how do I
> > > > > >set up my dataframe for the raw data from different studies? Also
> > > > > >how do I give inputs, specially xi, mi (or ni) to the function
> > > > > >escalc()? Thanks,Dushanthi
> > > > >
> > > > > You do not give us very much to go on here. When you say your outcome
> > > > > is proportions do you mean your outcome has more than two values and
> > > > > you are generating (or have been provided with) several proportions
> > > > > for each study or do you mean it is a binary variable? If the latter
> > > > > do you in fact have the numerators and denominators or just the
> > > > > proportion? It would also help if you showed us the code you have
> > > > > tried and the error message you got (if any) or told us the
> > > > > discrepancy between the output you obtained and that which
> > you expected.
> > > > >
> > > > > >
> > > > > > [[alternative HTML version deleted]]
> > > > >
> > > > > Michael Dewey
> > > > > [hidden email]
> > > > > http://www.aghmed.fsnet.co.uk/home.html
> > > > >
> > >
> > > Michael Dewey
> > > [hidden email]
> > > http://www.aghmed.fsnet.co.uk/home.html
> > >
>
> Michael Dewey
> [hidden email]
> http://www.aghmed.fsnet.co.uk/home.html
>

     
        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
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.