[R-meta] Extracting values from a list of confint() objects

[Will Hopkins]

Tobias, that dataset appears to be for a single meta, not a set of many (simulated) metas for checking bias and coverage of the fixed effects and tau2. Nevertheless I tried the last few steps on my list of confint objects (adjusted_confint). 

> #get an overview of the list, so that you can see what you need to extract

> str(adjusted_confint)

List of 2500

$ :List of 2

  ..$ fixed : num [1:2, 1:3] 1.5 1.74 1.05 1.1 1.95 ...

  .. ..- attr(*, "dimnames")=List of 2

  .. .. ..$ : chr [1:2] "intrcpt" "mods"

  .. .. ..$ : chr [1:3] "estimate" "ci.lb" "ci.ub"

  ..$ digits: Named num [1:9] 4 4 4 4 4 4 4 4 4

  .. ..- attr(*, "names")= chr [1:9] "est" "se" "test" "pval" ...

  ..- attr(*, "class")= chr "confint.rma"

$ :List of 2

  ..$ fixed : num [1:2, 1:3] 1.665 1.191 1.148 0.563 2.183 ...

  .. ..- attr(*, "dimnames")=List of 2

  .. .. ..$ : chr [1:2] "intrcpt" "mods"

  .. .. ..$ : chr [1:3] "estimate" "ci.lb" "ci.ub"

  ..$ digits: Named num [1:9] 4 4 4 4 4 4 4 4 4

  .. ..- attr(*, "names")= chr [1:9] "est" "se" "test" "pval" ...

  ..- attr(*, "class")= chr "confint.rma"

etc., etc.

I find this hard to understand, but it looks like the stats for tau2 may not be in there.

The next step didn't work:

> #extract tau2 and tau from list

> adjsel <- as.data.frame(adjusted_confint[["random"]])

> adjsel

data frame with 0 columns and 0 rows

 

Nor did the alternative version you suggested:

> adjsel <- as.data.frame(adjusted_confint$random)

> adjsel

data frame with 0 columns and 0 rows

 

However, my adjust_conflim was generated with this line of code within a function:

adjusted_confint <- confint(xxx, level=90, fixed=TRUE, random=TRUE, type="PL")

 

So I made it:

adjusted_confint <- confint(xxx, level=90, fixed=FALSE, tau2=TRUE, type="PL")

 

Now str(adjusted_confint) gave this:

$ :List of 5

  ..$ random : num [1:2, 1:3] 0.909 0.954 0.303 0.55 2.108 ...

  .. ..- attr(*, "dimnames")=List of 2

  .. .. ..$ : chr [1:2] "tau^2" "tau"

  .. .. ..$ : chr [1:3] "estimate" "ci.lb" "ci.ub"

  ..$ digits : Named num [1:9] 4 4 4 4 4 4 4 4 4

  .. ..- attr(*, "names")= chr [1:9] "est" "se" "test" "pval" ...

  ..$ ci.null: logi FALSE

  ..$ lb.sign: chr ""

  ..$ ub.sign: chr ""

  ..- attr(*, "class")= chr "confint.rma"

$ :List of 5

etc., etc.

 

So we're nearly there. I don’t know how to translate the above information into code that will extract the values of tau^2, tau, and their confidence limits. Your previous suggestions,  adjsel <- as.data.frame(adjusted_confint[["random"]]) and adjsel <- as.data.frame(adjusted_confint$random), still gave:

data frame with 0 columns and 0 rows

And my attempts to use sapply() still don't work. I hope you can suggest something else, or point out any silly mistake I might be making.

 

Thanks

 

Will

 

From: R-sig-meta-analysis <r-sig-meta-analysis-bounces using r-project.org> On Behalf Of Tobias Saueressig via R-sig-meta-analysis
Sent: Monday, March 11, 2024 12:42 AM
To: r-sig-meta-analysis using r-project.org
Cc: Tobias Saueressig <t.saueressig using gmx.de>
Subject: Re: [R-meta] Extracting values from a list of confint() objects

 

Dear Will,

 

you can do the following to get the values:

 

install.packages("metafor")

library(metafor)

 

dat <- dat.baskerville2012
dat

 

# fit random-effects model
res <- rma(smd, se^2, data=dat, method="ML", digits=3)
res

 

sel <- selmodel(res, type="beta")
sel

 

#calculate confidence interval for tau2
a <- confint(sel,tau2=TRUE)

 

#get an overview of the list, so that you can see what you need to extract
str(a)

 

#extract tau2 and tau from list
c <- as.data.frame(a[["random"]])
c

 

#you can also use $ to get access
d <- as.data.frame(a$random)
d

 

#now you can export the data e.g. to excel

install.packages("openxlsx")

library(openxlsx)

 

# Export data to an Excel file

write.xlsx(d, "tau2_data.xlsx", rowNames = FALSE)

 

Best Regards,

 

Tobias

  

  

Gesendet: Sonntag, 10. März 2024 um 05:58 Uhr
Von: "Will Hopkins via R-sig-meta-analysis" < <mailto:r-sig-meta-analysis using r-project.org> r-sig-meta-analysis using r-project.org>
An: "'R Special Interest Group for Meta-Analysis'" < <mailto:r-sig-meta-analysis using r-project.org> r-sig-meta-analysis using r-project.org>
Cc: "Will Hopkins" < <mailto:willthekiwi using gmail.com> willthekiwi using gmail.com>
Betreff: [R-meta] Extracting values from a list of confint() objects

With the help of ChatGPT, I have managed to extract values from a list of
rma() objects and values from a list of selmodel() objects derived from the
list of rma() objects. However, I cannot extract values from a list of
confint() objects derived from the selmodel() objects. I hope I am using the
right jargon here. If not, please be gentle, as I am still on the steep part
of the learning curve.



For example, this code (mysteriously) extracts tau2 from meta_results, which
is a list of rma objects:

tau2 <- sapply(meta_results, function(x) x$tau2).



And this code (equally mysteriously) extracts the SE of tau2 from
adjusted_meta, which is a list of selmodel objects derived by applying
selmodel() to meta_results:

seltau2se <- sapply(adjusted_meta, function(x) x$se.tau2).



But I have a list I have called adjusted_confint, which is a list of confint
objects derived by applying confint to the list adjusted_meta. I don't know
how to use sapply on this list to extract the confidence limits for tau2
that are contained within this list. I have "copied blindly" the syntax of
the other sapply statements without success. Basically I don't know what to
put for the x$..., and everything I have tried fails. ChatGPT was not
helpful here. I hope a real maven can help here. Thanks.



Will


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