[R-meta] R-sig-meta-analysis Digest, Vol 35, Issue 7
Tarun Khanna
kh@nn@ @end|ng |rom hert|e-@choo|@org
Tue Apr 21 18:06:25 CEST 2020
Hi Michael,
Sorry. I copied the wrong link. I am using data from this link. Attaching the data as a csv as well. Below is the code and output. http://www.metafor-project.org/doku.php/tips:rma.uni_vs_rma.mv
Perhaps just to be clear - I am trying to bootstrap errors in estimation which uses rma.mv and moderator variables.
##Code
dat <- read_csv("test.csv")
#RE
rma(yi, vi, data=dat)
#CRVE
rma.mv(yi, vi, random = ~ 1 | trial, data=dat)
#Bootstrapping
res <-rma.mv(yi, vi, random = ~ 1 | trial, data=dat, mods = ~ alloc)
boot.func <- function(df, indices) {
sub <- dat[indices,]
res <-rma.mv(yi, vi, random = ~ 1 | trial, data=dat, mods = ~ alloc)
if (is.element("try-error", class(res))) NA else c(coef(res), vcov(res))
}
## Output
Bootstrap Statistics :
original bias std. error
t1* -0.51792376 0 0
t2* -0.44786464 0 0
t3* 0.08899601 0 0
t4* 0.19465035 0 0
t5* -0.19465035 0 0
t6* -0.19465035 0 0
t7* -0.19465035 0 0
t8* 0.26607085 0 0
t9* 0.19465035 0 0
t10* -0.19465035 0 0
t11* 0.19465035 0 0
t12* 0.31363498 0 0
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
index 0 outside bounds
In addition: Warning messages:
1: In sqrt(tv[, 2L]) : NaNs produced
2: In norm.inter(z, (1 + c(conf, -conf))/2) :
extreme order statistics used as endpoints
Tarun Khanna
PhD Researcher
Hertie School
Friedrichstraße 180
10117 Berlin ∙ Germany
khanna using hertie-school.org ∙ www.hertie-school.org<http://www.hertie-school.org/>
________________________________
From: Michael Dewey <lists using dewey.myzen.co.uk>
Sent: 21 April 2020 17:28:43
To: Tarun Khanna; Viechtbauer, Wolfgang (SP); r-sig-meta-analysis using r-project.org
Subject: Re: [R-meta] R-sig-meta-analysis Digest, Vol 35, Issue 7
Dear Tarun
In the example on that page it uses dat.collins1985b but that does not
contain either a variable trial, nor one called alloc. Can you post a
complete minimal reproducible example showing the packages you use and
which data-set you are using?
Michael
On 21/04/2020 15:35, Tarun Khanna wrote:
> Hi Wolfgang,
>
>
> Let me start by just using the example on Metafor help.
>
>
> I used the dataset provided in the example on the Metafor page: http://www.metafor-project.org/doku.php/tips:bootstrapping_with_ma. I was able to replicate the results on the page. Then I added the variable alloc as a moderator variable in the estimation.
>
>
> ##Code
>
>
> #Bootstrapping
> res <-rma.mv(yi, vi, random = ~ 1 | trial, data=dat, mods = ~ alloc)
>
> boot.func <- function(df, indices) {
> sub <- dat[indices,]
> res <-rma.mv(yi, vi, random = ~ 1 | trial, data=dat, mods = ~ alloc)
> if (is.element("try-error", class(res))) NA else c(coef(res), vcov(res))
> }
>
> library(boot)
>
> set.seed(8781328)
> res.boot <- boot(dat, boot.func, R=10000)
> boot.ci(res.boot, index=1:2) #CI for average effect
> boot.ci(res.boot, index=3:4) #CI for tau2
>
>
> ## Output
>
>
> Bootstrap Statistics :
> original bias std. error
> t1* -0.51792376 0 0
> t2* -0.44786464 0 0
> t3* 0.08899601 0 0
> t4* 0.19465035 0 0
> t5* -0.19465035 0 0
> t6* -0.19465035 0 0
> t7* -0.19465035 0 0
> t8* 0.26607085 0 0
> t9* 0.19465035 0 0
> t10* -0.19465035 0 0
> t11* 0.19465035 0 0
> t12* 0.31363498 0 0
>
>
> Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
> index 0 outside bounds
> In addition: Warning messages:
> 1: In sqrt(tv[, 2L]) : NaNs produced
> 2: In norm.inter(z, (1 + c(conf, -conf))/2) :
> extreme order statistics used as endpoints
>
>
> Best
>
> Tarun
>
>
> Tarun Khanna
>
> PhD Researcher
>
> Hertie School
>
>
> Friedrichstraße 180
>
> 10117 Berlin ∙ Germany
> khanna using hertie-school.org ∙ www.hertie-school.org<http://www.hertie-school.org/<http://www.hertie-school.org<http://www.hertie-school.org/>>
>
> ________________________________
> From: Viechtbauer, Wolfgang (SP) <wolfgang.viechtbauer using maastrichtuniversity.nl>
> Sent: 21 April 2020 15:05:08
> To: Tarun Khanna; r-sig-meta-analysis using r-project.org
> Subject: RE: R-sig-meta-analysis Digest, Vol 35, Issue 7
>
> Yes, one can also use bootstrapping on regression coefficients. Please provide a fully reproducible example that illustrates your attempts.
>
> Best,
> Wolfgang
>
>> -----Original Message-----
>> From: R-sig-meta-analysis [mailto:r-sig-meta-analysis-bounces using r-project.org]
>> On Behalf Of Tarun Khanna
>> Sent: Tuesday, 21 April, 2020 14:35
>> To: r-sig-meta-analysis using r-project.org
>> Subject: Re: [R-meta] R-sig-meta-analysis Digest, Vol 35, Issue 7
>>
>> Dear Wolfgang,
>>
>> I have a follow up question to Crystals'. Does bootstrapping also work with
>> regressions that have moderator variables?
>>
>> I used the link that you provided, http://www.metafor-
>> project.org/doku.php/tips:bootstrapping_with_ma, and ran a regression with
>> "alloc" as a moderator variable and then tried bootstrapping the errors but
>> the std. errrs were calculated as zero. This is the output that i got:
>>
>> Bootstrap Statistics :
>> original bias std. error
>> t1* -0.51792376 0 0
>> t2* -0.44786464 0 0
>> t3* 0.08899601 0 0
>> t4* 0.19465035 0 0
>> t5* -0.19465035 0 0
>> t6* -0.19465035 0 0
>> t7* -0.19465035 0 0
>> t8* 0.26607085 0 0
>> t9* 0.19465035 0 0
>> t10* -0.19465035 0 0
>> t11* 0.19465035 0 0
>> t12* 0.31363498 0 0
>>
>>> boot.ci(res.boot, index=1:2) #CI for average effect
>> Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
>> index 0 outside bounds
>> In addition: Warning messages:
>> 1: In sqrt(tv[, 2L]) : NaNs produced
>> 2: In norm.inter(z, (1 + c(conf, -conf))/2) :
>> extreme order statistics used as endpoints
>>
>> I also tried doing it with my own data set and got the following error:
>>
>> Error in t.star[r, ] <- res[[r]] :
>> number of items to replace is not a multiple of replacement length
>> In addition: There were 50 or more warnings (use warnings() to see the first
>> 50)
>>
>> If bootstrapping does indeed work with moderator variables, what might be
>> wrong?
>>
>> Best
>> Tarun
>>
>> Tarun Khanna
>> PhD Researcher
>> Hertie School
>>
>> Friedrichstraße 180
>> 10117 Berlin ∙ Germany
>> khanna using hertie-school.org ∙ www.hertie-school.org<http://www.hertie-<http://www.hertie-school.org<http://www.hertie-<http://www.hertie-school.org<http://www.hertie-<http://www.hertie-school.org<http://www.hertie->>
>> school.org/>
>
> [[alternative HTML version deleted]]
>
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>
--
Michael
http://www.dewey.myzen.co.uk/home.html
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