[R-meta] possible miscalculation of Cook’s distances

Just as a brief follow-up with respect to the calculations: They are
correct. Continuing with your code, Antonina, we can easily manually
compute the Cook's distances here:

cooksd[1:2]

sub <- rma.mv(yi, vi,
              random = ~ 1 | study/experiment,
              data=dat, subset=-1)

(coef(res.ml) - coef(sub))^2 / vcov(res.ml)

sub <- rma.mv(yi, vi,
              random = ~ 1 | study/experiment,
              data=dat, subset=-2)

(coef(res.ml) - coef(sub))^2 / vcov(res.ml)

As you will see, these match up.

With these data, removal of a single row can have a large impact on the
variance components, which can lead to considerable changes in the pooled
estimate.

Best,
Wolfgang

-----Original Message-----
From: R-sig-meta-analysis [mailto:

r-sig-meta-analysis-bounces at r-project.org] On

Behalf Of Reza Norouzian
Sent: Friday, 04 February, 2022 8:01
To: Antonina Dolgorukova
Cc: R meta
Subject: Re: [R-meta] possible miscalculation of Cook?s distances

Dear Antonina,

There was no rationale, I just wanted to indicate that there is no bug
in the function (and save myself a tiny bit of time). The default
reestimate = TRUE is certainly to be preferred given that your model
does include random-effects and, as the documentation correctly
mentions, the influence of each effect estimate on the estimates of
heterogeneity and correlation can only be examined, if you set
reestimate = TRUE.

For instance, if you remove the random-effects from your initial model
(res.ml), then, you'll see that the use of reestimate = TRUE or FALSE
has no effect. In both cases, only the effect estimate associated with
study 1, experiment 1 is influential. Thus, this shows that the use of
reestimate = FALSE in your initial model essentially ignored the
influence of each effect estimate on the estimates of heterogeneity.

In models with complex random-effects structure esp. fit to large
datasets, setting reestimate = TRUE would take a good chunk of time.
In such cases, some (myself included) may be tempted to set reestimate
= FALSE hoping that the approximation will be close enough.

Kind regards,
Reza

res.ml2 <- update.rma(res.ml, random = NULL)

cook_with_reest2 <- cooks.distance.rma.mv(res.ml2)
cook_without_reest2 <- cooks.distance.rma.mv(res.ml2, reestimate = FALSE)

plot(cook_with_reest2,type="b")
plot(cook_without_reest2,type="b")

On Fri, Feb 4, 2022 at 12:19 AM Antonina Dolgorukova
<an.dolgorukova at gmail.com> wrote:

Dear Reza,

Thank you very much for your reply. I do understand that not all

outliers have

to be influential and that not all influential cases have to be outliers.

But

thank you for mentioning this and for the code provided. I did notice you

set the

reestimate = FALSE. This raises two questions, actually. It would be

great if you

help with them.

1) Is there any explanation why cooks.distance.rma.mv(res.ml) and

cooks.distance.rma.mv(res.ml , reestimate = FALSE) give completely

different

results about the experiments 1 and 2 (and very similar for the remaining
experiments)?

According to cooks.distance.rma.mv(res.ml), the Study 1, Experiment 2

is

influential, but

according to  cooks.distance.rma.mv(res.ml , reestimate = FALSE),

Study 1,

Experiment 1 is influential

#the code illustrating my question

dat <- data.frame(study=c(1,1,2,3,3,3), experiment=c(1:6),
                  yi=c( 68, 18, 31,20,10,26),
                  vi=c(60,32, 15, 19, 41, 82))

res.ml <- rma.mv(yi, vi,
                 random = ~ 1 | study/experiment,
                 data=dat,
                 slab = paste("Study ", study,", ", "Experiment ",

experiment,

sep = ""))

cook_with_reest <- cooks.distance.rma.mv(res.ml)
cook_without_reest <- cooks.distance.rma.mv(res.ml, reestimate = FALSE)

plot(1:length(cook_with_reest), cook_with_reest, ylim=c(0,2), type="o",

pch=19,

las=1, xaxt="n",

     xlab="Study and Experiment ID", ylab="Cook's Distance")
points(cook_without_reest, type="o", pch=19, col = "red")
axis(1, 1:length(cook_with_reest), labels=names(cook_with_reest))
abline(h=4/length(cook_with_reest), lty="dotted", lwd=2)
legend("top", pch=19, col=c("black","red"), lty="solid",
       legend=c("reestimate = TRUE","reestimate = FALSE"), bty="n")

2) And could you please explain what is the rationale to set reestimate

=

FALSE? According to the metafor documentation:

"Doing so only yields an approximation to the Cook?s distances that

ignores the

influence of the ith case on the variance/correlation components"

Sincerely,
Antonina

On Fri, Feb 4, 2022 at 3:29 AM Reza Norouzian <rnorouzian at gmail.com>

wrote:

Dear Antonina,

An effect estimate whose standardized deleted residual falls beyond
+/-1.96 doesn't necessarily need to have a cook's distance
(influence), and/or a hat value (if additional moderators are used)
that are likewise extreme.

As a general proposition, it may be methodologically more reasonable
to simultaneously consult all these indices to flag an extreme effect
estimate.

That said, in your case, it does seem that the estimate from study 1,
experiment 1 has a large standardized deleted residual as well as a
large Cook's distance relative to that of other effect estimates. So,
I don't think there is any bug in any of the metafor functions you
used.

Below is a bit of code to catch that outlying effect estimate.

Kind regards,
Reza

dat <- data.frame(study=c(1,1,2,3,3,3), experiment=c(1:6),
                  yi=c( 68, 18, 31,20,10,26),
                  vi=c(60,32, 15, 19, 41, 82))

res.ml <- rma.mv(yi, vi,
                 random = ~ 1 | study/experiment,
                 data=dat,
                 slab = paste("Study ", study,", ", "Experiment ",
                              experiment, sep = ""))

dat <- transform(dat, obs = res.ml$slab)

outlier_limit <- qnorm(.975)

cook <- cooks.distance.rma.mv(res.ml,
                              reestimate = FALSE)

st_del_res_z <- rstudent.rma.mv(res.ml,
                                reestimate = FALSE)$z

cook_limit <- max(mean(range(cook)), boxplot.stats(cook, coef =

1.5)$stats[5])

i <- abs(st_del_res_z) > outlier_limit
k <- cook > cook_limit
oo <- which(i & k)

LL <- names(oo)

removed <- subset(dat, obs %in% LL)
new_dat <- subset(dat, !obs %in% LL)

On Thu, Feb 3, 2022 at 3:36 PM Antonina Dolgorukova
<an.dolgorukova at gmail.com> wrote:

Dear Dr. Viechtbauer and all,

I have a multilevel data structure (experiments nested within

studies) are

use rma.mv to calculate an overall effect estimate. The next step

requires

sensitivity analysis on the experiment-level data. For detecting

outliers

I've used standardized (deleted) residuals and for detecting

influential

experiments I've used Cook?s distance. However, the last test

provides

contradictory results.

The forest plot indicates that the 1st experiment may be an outlier,

and

standardized (deleted) residuals confirm this. But according to

Cook?s

distance plot, the 2nd experiment is influential. It seems that

there may

be a miscalculation of Cook?s distance since I can easily reproduce

this

issue (in one study one of the experiments have to provide a much

larger ES

than the other) also if use the model with random = ~ 1 |

experiment, the

1st experiment is influential, not the second.

Could you please clarify is this a bug or a feature of the

cooks.distance()

function? Maybe it does not work properly with rma.mv objects?

  ## Reproducible Example

# data frame
  dat <- data.frame(study=c(1,1,2,3,3,3), experiment=c(1:6),
                    yi=c( 68, 18, 31,20,10,26),
                    vi=c(60,32, 15, 19, 41, 82))

# multilevel model
res.ml <- rma.mv(yi, vi,
                 random = ~ 1 | study/experiment,
                 data=dat,
                 slab = paste("Study ", study,", ", "Experiment ",
experiment, sep = ""))

# forest plot examination  indicates that the 1st experiment may be

an

outlier
forest(res.ml,
       header = "Study and Experiment ID")

# standardized (deleted) residuals confirm this
rst <- rstudent(res.ml)
plot(NA, NA, xlim=c(1, res.ml$k), ylim=c(-3,5),
     xlab="Study and Experiment ID", ylab="Standardized (Deleted)

Residual",

     xaxt="n", las=1)
axis(side=1, at=1:res.ml$k, labels=rst$slab)
abline(h=c(-1.96,1.96), lty="dotted")
abline(h=0)
points(1:res.ml$k, rst$z, type="o", pch=19)

# according to Cook?s distance plot, the 2nd experiment is

influential

cooksd <- cooks.distance(res.ml)
plot(1:length(cooksd), cooksd, ylim=c(0,2), type="o", pch=19, las=1,
xaxt="n",
     xlab="Experiment ID", ylab="Cook's Distance")
axis(1, 1:length(cooksd), labels=names(cooksd))
abline(h=4/length(cooksd), lty="dotted", lwd=2)

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
[1] metafor_3.1-43 metadat_1.0-0  Matrix_1.3-4

--
Antonina Dolgorukova, M.D.
Pavlov First Saint Petersburg State Medical University
Lev Tolstoy str., 6-8, 197022
Saint Petersburg, Russia