[R-meta] R-sig-meta-analysis Digest, Vol 35, Issue 7

[Michael Dewey]

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/>
> 
> ________________________________
> 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->
>> school.org/>
> 
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-- 
Michael
http://www.dewey.myzen.co.uk/home.html