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petretta at unina.it

2013-Nov-19 10:29 UTC

[R] metafor escalc(measure="SMCC")

Dear all,

I use R 3.0 for Windows.

I ask how escalc(measure="SMCC") [metafor package] mathematically  
calculate yi and vi when only change score and SD change score are  
provided.

I used the example (repoted below) posted by Qiang Yue at:

http://r.789695.n4.nabble.com/using-metafor-for-meta-analysis-of-before-after-studies-escalc-SMCC-td4667233.html

but it is unclear for me the formula used to derive y1 and v1. I read  
the documentation of metafor package and it is all very well  
described, but I ask if possible for the formula used by  
escalc(measure="SMCC") to mathematically calculate yi and vi.  
Unfortunatel, I have no free access to the paper quoted in metafor  
package.

Beginning example:

fMRS
author year n mean_r sd_r mean_s sd_s r
1 Tom  2006 9  0   0 0.12 0.03    0   0
2 Jack 2012 6  0   0 0.23 0.05    0   0
3 Zhu  2013 8  0   0 0.18 0.05    0   0
>
dat_SMCC=escalc(measure="SMCC",data=fMRS,ni=n,m1i=mean_s,m2i=mean_r,sd1i=sd_s,sd2i=sd_r,ri=r
,append=TRUE)> dat_SMCCauthor year n mean_r sd_r mean_s sd_s r  yi      vi
1 Tom 2006  9  0     0    0.12  0.03  0 3.6108 0.8354
2 Jack 2012 6  0     0    0.23  0.05  0 3.8674 1.4131
3 Zhu 2013  8  0     0    0.18  0.05  0 3.1975 0.7640



Sincerely

-- 
Mario Petretta
Department of Translational Medical Sciences
Naples University Federico II
Italy

Viechtbauer Wolfgang (STAT)

2013-Nov-19 10:48 UTC

head link

[R] metafor escalc(measure="SMCC")

Dear Mario,

You can always just inspect the code:

escalc.default

Best,
Wolfgang

--   
Wolfgang Viechtbauer, Ph.D., Statistician   
Department of Psychiatry and Psychology   
School for Mental Health and Neuroscience   
Faculty of Health, Medicine, and Life Sciences   
Maastricht University, P.O. Box 616 (VIJV1)   
6200 MD Maastricht, The Netherlands   
+31 (43) 388-4170 | http://www.wvbauer.com   
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org]
> On Behalf Of petretta at unina.it
> Sent: Tuesday, November 19, 2013 11:29
> To: r-help at r-project.org
> Subject: [R] metafor escalc(measure="SMCC")
> 
> Dear all,
> 
> I use R 3.0 for Windows.
> 
> I ask how escalc(measure="SMCC") [metafor package] mathematically
> calculate yi and vi when only change score and SD change score are
> provided.
> 
> I used the example (repoted below) posted by Qiang Yue at:
> 
> http://r.789695.n4.nabble.com/using-metafor-for-meta-analysis-of-before-
> after-studies-escalc-SMCC-td4667233.html
> 
> but it is unclear for me the formula used to derive y1 and v1. I read
> the documentation of metafor package and it is all very well
> described, but I ask if possible for the formula used by
> escalc(measure="SMCC") to mathematically calculate yi and vi.
> Unfortunatel, I have no free access to the paper quoted in metafor
> package.
> 
> Beginning example:
> 
> fMRS
> author year n mean_r sd_r mean_s sd_s r
> 1 Tom  2006 9  0   0 0.12 0.03    0   0
> 2 Jack 2012 6  0   0 0.23 0.05    0   0
> 3 Zhu  2013 8  0   0 0.18 0.05    0   0
> 
> >
>
dat_SMCC=escalc(measure="SMCC",data=fMRS,ni=n,m1i=mean_s,m2i=mean_r,sd1i=s
> d_s,sd2i=sd_r,ri=r
> ,append=TRUE)
> > dat_SMCC
> author year n mean_r sd_r mean_s sd_s r  yi      vi
> 1 Tom 2006  9  0     0    0.12  0.03  0 3.6108 0.8354
> 2 Jack 2012 6  0     0    0.23  0.05  0 3.8674 1.4131
> 3 Zhu 2013  8  0     0    0.18  0.05  0 3.1975 0.7640
> 
> 
> 
> Sincerely
> 
> --
> Mario Petretta
> Department of Translational Medical Sciences
> Naples University Federico II
> Italy
> 
> ______________________________________________
> R-help at r-project.org 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.

petretta at unina.it

2013-Nov-21 12:39 UTC

head link

[R] metafor escalc(measure="SMCC")

Many thanks to Wolfgang Viechtbauer for the prompt and clear answer.
However, I'm unable to understand what .cmicalc mathematically does in the
code line:

cmi <- .cmicalc(mi)

I look in the metafor documentation and in R (?.cmical and ??.cmicalc) but
I have no result. Please, can I have further explanation on this point?

Sorry for the trouble

Sincerely

Mario Petretta
Department of Translational Medical Sciences
Naples University Federico II
Italy
>Message: 50
Date: Tue, 19 Nov 2013 11:48:33 +0100
From: "Viechtbauer Wolfgang (STAT)"
        <wolfgang.viechtbauer at maastrichtuniversity.nl>
To: "petretta at unina.it" <petretta at unina.it>, "r-help
at r-project.org"
        <r-help at r-project.org>
Subject: Re: [R] metafor escalc(measure="SMCC")
Message-ID:
        <077E31A57DA26E46AB0D493C9966AC730D9925568A at
UM-MAIL4112.unimaas.nl>
Content-Type: text/plain; charset="us-ascii"

Dear Mario,

You can always just inspect the code:

escalc.default

Best,
Wolfgang

--
Wolfgang Viechtbauer, Ph.D., Statistician
Department of Psychiatry and Psychology
School for Mental Health and Neuroscience
Faculty of Health, Medicine, and Life Sciences
Maastricht University, P.O. Box 616 (VIJV1)
6200 MD Maastricht, The Netherlands
+31 (43) 388-4170 | http://www.wvbauer.com
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org]
> On Behalf Of petretta at unina.it
> Sent: Tuesday, November 19, 2013 11:29
> To: r-help at r-project.org
> Subject: [R] metafor escalc(measure="SMCC")
>
> Dear all,
>
> I use R 3.0 for Windows.
>
> I ask how escalc(measure="SMCC") [metafor package] mathematically
> calculate yi and vi when only change score and SD change score are
> provided.
>
> I used the example (repoted below) posted by Qiang Yue at:
>
> http://r.789695.n4.nabble.com/using-metafor-for-meta-analysis-of-before-
> after-studies-escalc-SMCC-td4667233.html
>
> but it is unclear for me the formula used to derive y1 and v1. I read
> the documentation of metafor package and it is all very well
> described, but I ask if possible for the formula used by
> escalc(measure="SMCC") to mathematically calculate yi and vi.
> Unfortunatel, I have no free access to the paper quoted in metafor
> package.
>
> Beginning example:
>
> fMRS
> author year n mean_r sd_r mean_s sd_s r
> 1 Tom  2006 9  0   0 0.12 0.03    0   0
> 2 Jack 2012 6  0   0 0.23 0.05    0   0
> 3 Zhu  2013 8  0   0 0.18 0.05    0   0
>
> >
>
dat_SMCC=escalc(measure="SMCC",data=fMRS,ni=n,m1i=mean_s,m2i=mean_r,sd1i=s
> d_s,sd2i=sd_r,ri=r
> ,append=TRUE)
> > dat_SMCC
> author year n mean_r sd_r mean_s sd_s r  yi      vi
> 1 Tom 2006  9  0     0    0.12  0.03  0 3.6108 0.8354
> 2 Jack 2012 6  0     0    0.23  0.05  0 3.8674 1.4131
> 3 Zhu 2013  8  0     0    0.18  0.05  0 3.1975 0.7640
>
>
>
> Sincerely
>
> --
> Mario Petretta
> Department of Translational Medical Sciences
> Naples University Federico II
> Italy
>

petretta at unina.it

2013-Nov-22 19:08 UTC

head link

[R] metafor escalc(measure="SMCC")

Many thanks to Wolfgang Wiechtbauer for the explanation.

Sincerely

Mario Petretta


Message: 31
  Date: Thu, 21 Nov 2013 19:08:14 +0100
  From: "Viechtbauer Wolfgang (STAT)"
          <wolfgang.viechtbauer at maastrichtuniversity.nl>
  To: "petretta at unina.it" <petretta at unina.it>,
"r-help at r-project.org"
          <r-help at r-project.org>
  Subject: Re: [R] metafor escalc(measure="SMCC")
  Message-ID:
          <077E31A57DA26E46AB0D493C9966AC730D99255ED7 at
UM-MAIL4112.unimaas.nl>
  Content-Type: text/plain; charset="us-ascii"

  .cmicalc is a non-exported function. You can see the code with:

  getAnywhere(.cmicalc)

  Best,
  Wolfgang


[Nascondi Testo quotato]
-----Original Message-----
  From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
  On Behalf Of petretta at unina.it
  Sent: Thursday, November 21, 2013 13:39
  To: r-help at r-project.org
  Subject: [R] metafor escalc(measure="SMCC")

  Many thanks to Wolfgang Viechtbauer for the prompt and clear answer.
  However, I'm unable to understand what .cmicalc mathematically does in the
  code line:

  cmi <- .cmicalc(mi)

  I look in the metafor documentation and in R (?.cmical and ??.cmicalc) but
  I have no result. Please, can I have further explanation on this point?

  Sorry for the trouble

  Sincerely

  Mario Petretta
  Department of Translational Medical Sciences
  Naples University Federico II
  Italy




Message: 50 Date: Tue, 19 Nov 2013 11:48:33 +0100
  From: "Viechtbauer Wolfgang (STAT)"
           <wolfgang.viechtbauer at maastrichtuniversity.nl>
  To: "petretta at unina.it" <petretta at unina.it>,
"r-help at r-project.org"
           <r-help at r-project.org>
  Subject: Re: [R] metafor escalc(measure="SMCC")
  Message-ID:
           <077E31A57DA26E46AB0D493C9966AC730D9925568A at UM-
MAIL4112.unimaas.nl>
  Content-Type: text/plain; charset="us-ascii"

  Dear Mario,

  You can always just inspect the code:

  escalc.default

  Best,
  Wolfgang

  --
  Wolfgang Viechtbauer, Ph.D., Statistician
  Department of Psychiatry and Psychology
  School for Mental Health and Neuroscience
  Faculty of Health, Medicine, and Life Sciences
  Maastricht University, P.O. Box 616 (VIJV1)
  6200 MD Maastricht, The Netherlands
  +31 (43) 388-4170 | http://www.wvbauer.com


-----Original Message-----
  From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
  On Behalf Of petretta at unina.it
  Sent: Tuesday, November 19, 2013 11:29
  To: r-help at r-project.org
  Subject: [R] metafor escalc(measure="SMCC")

  Dear all,

  I use R 3.0 for Windows.

  I ask how escalc(measure="SMCC") [metafor package] mathematically
  calculate yi and vi when only change score and SD change score are
  provided.

  I used the example (repoted below) posted by Qiang Yue at:

http://r.789695.n4.nabble.com/using-metafor-for-meta-analysis-of-before-
  after-studies-escalc-SMCC-td4667233.html

  but it is unclear for me the formula used to derive y1 and v1. I read
  the documentation of metafor package and it is all very well
  described, but I ask if possible for the formula used by
  escalc(measure="SMCC") to mathematically calculate yi and vi.
  Unfortunatel, I have no free access to the paper quoted in metafor
  package.

  Beginning example:

  fMRS
  author year n mean_r sd_r mean_s sd_s r
  1 Tom  2006 9  0   0 0.12 0.03    0   0
  2 Jack 2012 6  0   0 0.23 0.05    0   0
  3 Zhu  2013 8  0   0 0.18 0.05    0   0




dat_SMCC=escalc(measure="SMCC",data=fMRS,ni=n,m1i=mean_s,m2i=mean_r,sd1i=s
d_s,sd2i=sd_r,ri=r
  ,append=TRUE)

dat_SMCC

author year n mean_r sd_r mean_s sd_s r  yi      vi 1 Tom 2006  9  0    
   0    0.12  0.03  0 3.6108 0.8354
  2 Jack 2012 6  0     0    0.23  0.05  0 3.8674 1.4131
  3 Zhu 2013  8  0     0    0.18  0.05  0 3.1975 0.7640



  Sincerely

  --
  Mario Petretta
  Department of Translational Medical Sciences
  Naples University Federico II
  Italy

______________________________________________
R-help at r-project.org 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.


-- 
Mario Petretta
Department of Translational Medical Sciences
Naples University Federico II
Italy

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