[R-meta] cooks.distance.rma.mv is slow on complex models

Martineau, Roger Roger.Martineau at AGR.GC.CA
Tue Jul 25 18:56:12 CEST 2017

Dear metafor users,

I am running complex models using rma.mv function of metafor (metafor_2.0-0; R version 3.4.0) on a large dataset (n = 197 studies) with a 4-level hierarchical structure of data.

#### Model ####

(tmp.casdiet <- rma.mv(MTPYMean, MTPYSEMtrDP^2, data=tmp.dat.MTPY.new,

                      mods = ~

                        cMPbal +

                        cNELbal +

                        cMPsupply.kg +


                      random = ~1|laboratory/experiment/study,

                      method = "REML", sparse=TRUE))

All metafor functions run well except cooks.distance.rma.mv which is really slowing my work. I have a new computer that should be up to the task.

 The time spent to execute the task  is related to the random statement:

·        random = ~1|laboratory/experiment/study : 14 min 5 sec

·        random = ~1|experiment/study : 8 min 10 sec

·        random = ~1|study: 1 min 12 sec

Find below more info on variance components and Cook’s distance graphs.

In this model it wouldn’t make much of a difference to run the cooks.distance.rma.mv function with random = ~1|study but it is not the correct way to detect influential cases.

Is there another way to speed up the process ?

Thanks in advance,

Roger Martineau ☺

The variance components and the associated Cook’s distance graphs are:

Variance Components:

              estim     sqrt  nlvls  fixed

sigma^2.1  178.9385  13.3768     21     no

sigma^2.2  409.8262  20.2442     47     no

sigma^2.3    0.0000   0.0016     69     no


sigma^2.1                   laboratory

sigma^2.2        laboratory/experiment

sigma^2.3  laboratory/experiment/study

#### Cook's distance ####


tmp.cook <- cooks.distance.rma.mv(tmp.casdiet, progbar=TRUE)

plot(tmp.cook, type="o", pch=19)

which(tmp.cook > 1)

·        random = ~1|laboratory/experiment/study

[cid:image007.jpg at 01D30545.643B8160]

·        random = ~1|experiment/study

[cid:image008.jpg at 01D30545.643B8160]

·        random = ~1|study

[cid:image009.jpg at 01D30545.643B8160]
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