[R-meta] Bubble plot in regresion whith two variables

Thu Nov 7 01:42:42 CET 2019

Hello everyone.
I need to make a bubble plot of a goal of average differences with a covariate. And then add to it the line of adjustment of the model with 2 variables. Is this possible ?
Thank you

Lorenzo Mart�n Lobo MTSAC, FACC, FESC
Especialista Jerarquizado en Cardiolog�a
Jefe de Cardiolog�a Hospital Militar Campo de Mayo
Ex Jefe de Unidad Coronaria Hospital Militar Campo de Mayo
Miembro Titular de la Sociedad Argentina de Cardiolog�a
Fellow American College of Cardiology
Fellow European Society of Cardiology
Miembro del Area de Investigaci�n de la SAC
Ex Director del Consejo de Aterosclerosis y Trombosis de la SAC
Miembro Asesor del Consejo de Aterosclerosis y Trombosis de la SAC
Ex Director del Consejo de Epidemiolog�a y Prevenci�n Cardiovascular de la SAC

Miembro Asesor del Consejo de Epidemiolog�a y Prevenci�n Cardiovascular de la SAC

Instructor de ACLS de la American Heart Association

________________________________
De: R-sig-meta-analysis <r-sig-meta-analysis-bounces using r-project.org> en nombre de r-sig-meta-analysis-request using r-project.org <r-sig-meta-analysis-request using r-project.org>
Enviado: martes, 5 de noviembre de 2019 00:40
Para: r-sig-meta-analysis using r-project.org <r-sig-meta-analysis using r-project.org>
Asunto: R-sig-meta-analysis Digest, Vol 30, Issue 3

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Today's Topics:

   1. Extracting information from model
      (=?utf-8?Q?Tina_Dudenh=C3=B6ffer?=)
   2. Re: Extracting information from model (Wolfgang Viechtbauer)
   3. Re: Extracting information from model
      (=?utf-8?Q?Tina_Dudenh=C3=B6ffer?=)
   4. Replicating robumeta package output by metafor package in R
      (Reza Norouzian)
   5. Re: Nestedness in meta-analysis data using R (metafor or
      metaSEM packages) (James Pustejovsky)

----------------------------------------------------------------------

Message: 1
Date: Mon, 4 Nov 2019 20:46:47 +0100
From: =?utf-8?Q?Tina_Dudenh=C3=B6ffer?= <tina.dudenhoeffer using gmail.com>
To: r-sig-meta-analysis using r-project.org
Subject: [R-meta] Extracting information from model
Message-ID: <69860E3A-4BF6-4E03-AA6B-B90B49D55E0D using gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi all,

I am trying to extract some information from my models such as the Q-Statistic and its p-value or the QE etc.
I found the coef <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fr%2Fstats%2Fcoef.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=e9tpYowfpWJPU0hS3%2BFl76Nh9LhOlN6TOFO13W4V8cs%3D&reserved=0>(summary <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fr%2Fbase%2Fsummary.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=VZph%2ByGI6tq7uz77Vi3hNU33ozippL9kj%2FScgoESe2E%3D&reserved=0>(res)) function but that only lets me extract the estimate, se, zval, pal and ci.lb/ci.ub

Is it possible to extract any other information? The purpose would be to save it in another document, so I don�t have to manually copy/paste everything.

Thanks for your help,

Tina

        [[alternative HTML version deleted]]

------------------------------

Message: 2
Date: Mon, 4 Nov 2019 21:57:28 +0100 (CET)
From: Wolfgang Viechtbauer
        <wolfgang.viechtbauer using maastrichtuniversity.nl>
To: =?ISO-8859-15?Q?Tina_Dudenh=F6ffer?= <tina.dudenhoeffer using gmail.com>
Cc: r-sig-meta-analysis using r-project.org
Subject: Re: [R-meta] Extracting information from model
Message-ID: <alpine.DEB.2.20.1911042152320.5399 using wv-x1>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hi Tina,

Since you have asked some questions about 'metafor' in the past, I assume
this is also what you are asking about now. You can obtain the Q/QE-test
statistic from an object, say 'res', with:

res$QE

and the corresponding p-value with:

res$QEp

More generally, to see what kind of information is stored in such an
object, see:

https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwviechtb.github.io%2Fmetafor%2Freference%2Frma.uni.html%23value&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=VBQHE4XsZfc3u0kKl%2B%2FRIIO1gkGUyR4G5hib3gagiZ4%3D&reserved=0
https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwviechtb.github.io%2Fmetafor%2Freference%2Frma.mv.html%23value&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=1%2FcQ%2BaYHRVwIAT34BIR%2FcAr3nYRY40YSq4AQvCW1M9U%3D&reserved=0

for rma() / rma.uni() and rma.mv(), respectively.

Best,
Wolfgang

> Hi all,
>
> I am trying to extract some information from my models such as the
> Q-Statistic and its p-value or the QE etc. I found the coef
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fr%2Fstats%2Fcoef.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=e9tpYowfpWJPU0hS3%2BFl76Nh9LhOlN6TOFO13W4V8cs%3D&reserved=0>(summary
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fr%2Fbase%2Fsummary.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=VZph%2ByGI6tq7uz77Vi3hNU33ozippL9kj%2FScgoESe2E%3D&reserved=0>(res)) function but that only lets
> me extract the estimate, se, zval, pal and ci.lb/ci.ub
>
> Is it possible to extract any other information? The purpose would be to
> save it in another document, so I don�t have to manually copy/paste
> everything.
>
> Thanks for your help,
>
> Tina

------------------------------

Message: 3
Date: Mon, 4 Nov 2019 22:07:22 +0100
From: =?utf-8?Q?Tina_Dudenh=C3=B6ffer?= <tina.dudenhoeffer using gmail.com>
To: Wolfgang Viechtbauer
        <wolfgang.viechtbauer using maastrichtuniversity.nl>
Cc: r-sig-meta-analysis using r-project.org
Subject: Re: [R-meta] Extracting information from model
Message-ID: <3808CF0C-F579-4CEE-94ED-1E272228E222 using gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Wolfgang,

I was indeed asking about �metaphor�.

[[elided Hotmail spam]]

Thank you,

Tina

> On Nov 4, 2019, at 9:57 PM, Wolfgang Viechtbauer <wolfgang.viechtbauer using maastrichtuniversity.nl> wrote:
>
> Hi Tina,
>
> Since you have asked some questions about 'metafor' in the past, I assume this is also what you are asking about now. You can obtain the Q/QE-test statistic from an object, say 'res', with:
>
> res$QE
>
> and the corresponding p-value with:
>
> res$QEp
>
> More generally, to see what kind of information is stored in such an object, see:
>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwviechtb.github.io%2Fmetafor%2Freference%2Frma.uni.html%23value&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=VBQHE4XsZfc3u0kKl%2B%2FRIIO1gkGUyR4G5hib3gagiZ4%3D&reserved=0
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwviechtb.github.io%2Fmetafor%2Freference%2Frma.mv.html%23value&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=1%2FcQ%2BaYHRVwIAT34BIR%2FcAr3nYRY40YSq4AQvCW1M9U%3D&reserved=0
>
> for rma() / rma.uni() and rma.mv(), respectively.
>
> Best,
> Wolfgang
>
>> Hi all,
>>
>> I am trying to extract some information from my models such as the Q-Statistic and its p-value or the QE etc. I found the coef <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fr%2Fstats%2Fcoef.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=e9tpYowfpWJPU0hS3%2BFl76Nh9LhOlN6TOFO13W4V8cs%3D&reserved=0>(summary <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fr%2Fbase%2Fsummary.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=VZph%2ByGI6tq7uz77Vi3hNU33ozippL9kj%2FScgoESe2E%3D&reserved=0>(res)) function but that only lets me extract the estimate, se, zval, pal and ci.lb/ci.ub
>>
>> Is it possible to extract any other information? The purpose would be to save it in another document, so I don�t have to manually copy/paste everything.
>>
>> Thanks for your help,
>>
>> Tina

------------------------------

Message: 4
Date: Mon, 4 Nov 2019 15:15:08 -0600
From: Reza Norouzian <rnorouzian using gmail.com>
To: r-sig-meta-analysis using r-project.org
Subject: [R-meta] Replicating robumeta package output by metafor
        package in R
Message-ID:
        <CAKt3tzkg1-8XWfujC-LgcEPTmUMTb0zbRdU7bJcrMW5EKu864g using mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I was wondering if there might be a way to replicate the output from
library robumenta by library metafor in R?

Both package state that they use the same estimation method for robust
variance estimation.

*Here is reproducible data and the code I tried with no success:*

d <- read.csv("https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2Fizeh%2Fm%2Fmaster%2Fe.csv&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227595381&sdata=zBlZqYWNu5qsv2A70bKD99Mu4a1gRtqQiGcb05pHLKc%3D&reserved=0",
h = T) # DATA

library(robumeta)
robu(y~factor(time), data = d, studynum = study.name, var = SD^2, small = F)

library(metafor)
robust(rma(y~factor(time), sei = SD, data = d), cluster = d$id, adjust = F)

        [[alternative HTML version deleted]]

------------------------------

Message: 5
Date: Mon, 4 Nov 2019 21:40:11 -0600
From: James Pustejovsky <jepusto using gmail.com>
To: Reza Norouzian <rnorouzian using gmail.com>
Cc: R meta <r-sig-meta-analysis using r-project.org>
Subject: Re: [R-meta] Nestedness in meta-analysis data using R
        (metafor or metaSEM packages)
Message-ID:
        <CAFUVuJxViwL_eqpFm_231=5FjXELt4BhuMUfgk+g7kb0ZEBJBg using mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Reza,

Here is a recent article provides a review of the main analytic approaches
available for the data structure that you've described:

   - Moeyaert, M., Ugille, M., Natasha Beretvas, S., Ferron, J., Bunuan,
   R., & Van den Noortgate, W. (2017). Methods for dealing with multiple
   outcomes in meta-analysis: a comparison between averaging effect sizes,
   robust variance estimation and multilevel meta-analysis. *International
   Journal of Social Research Methodology*, *20*(6), 559-572.

The question has come up periodically on the mailing list too, so you might
find past posts helpful. A few to get you started:

   -
   https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fr-sig-meta-analysis%2F2017-September%2F000197.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227605391&sdata=Y0tLP8epuMDW397gfbNB7m6QNN0qlRpeNz8RLEyP1CA%3D&reserved=0

   -
   https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fr-sig-meta-analysis%2F2017-August%2F000094.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227605391&sdata=%2BMq%2BOCqrudgMsZHMtAKhMHaAL0OfmXlM%2Fx%2BqSjSkJGM%3D&reserved=0

   -
   https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fr-sig-meta-analysis%2F2019-March%2F001479.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227605391&sdata=Gnlm9MdUgrZttLHpncBNYdBDcXhDubRo0PLNDxyxxj0%3D&reserved=0

   -
   https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fr-sig-meta-analysis%2F2018-October%2F001153.html&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227605391&sdata=ex%2Bllc4hRt20jXxEYEZLnx7mDdVeMhuuGAMv6p8Wnlg%3D&reserved=0

James

On Sun, Nov 3, 2019 at 7:36 PM Reza Norouzian <rnorouzian using gmail.com> wrote:

> Hi,
>
> I have 51 studies. These studies have produced 257 effect sizes (denoted
> y).
> In each study, each effect size is obtained some time (categorized as 1, 2,
> 3, 4) after a treatment. Also, in15 of the studies, some effect sizes have
> been reported on up to 4 correlated outcomes.
>
> What reasonable model using the library(metafor) [e.g., via rma.mv] or
> library(metaSEM) [e.g., via meta3] can capture the structure of my data
> described above?
>
> For concreteness, I'm providing demo data below.
>
> d <- read.csv("https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2Fizeh%2Fm%2Fmaster%2Fe.csv&data=02%7C01%7C%7C53bfaddbf2074bc7a94508d761a1e2b2%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637085220227605391&sdata=uHuhgIpAOywCxhjKIu%2BQWGjFO9%2BLy94xyX0P%2FBE2vd4%3D&reserved=0",
> h = T) # DATA
> # First 6 lines of DATA:
>
>           study.name            y        SD id outcome time 1
> Al.Ahm_Al.Jar  0.533733731 0.4286817  1       1    1          2
> Al.Ahm_Al.Jar  0.296116599 0.4132781  1       1    4          3
> Al.Ahm_Al.Jar -0.155386371 0.4267881  1       1    1          4
> Al.Ahm_Al.Jar  0.131015334 0.4384274  1       1    4          5
>     Al_Ajmi  3.444226818 0.2182068  2       1    1          6
>   Al_Ajmi  4.376457433 0.2090771  2       1    2
>
>         [[alternative HTML version deleted]]
>
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End of R-sig-meta-analysis Digest, Vol 30, Issue 3
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