[R-meta] Cooks distance from cluster in multilevel models

[Martineau, Roger]

Dear metafor users,

I downloaded the data set (i.e., p154-dataset.csv) from  Assinka and Wibbelink (2016) available from http://www.tqmp.org/RegularArticles/vol12-3/p154/p154.pdf


3-level model with multiple moderators (Listing 15 in the publication):

> multiplemoderator <- rma.mv(y, v, mods = ~ pyear + typeovert + typecovert,
+                             random =list(~ 1 | effectsizeID, ~ 1 | studyID),
+                             tdist=TRUE, data=dataset)
> summary(multiplemoderator, digits=3)

Multivariate Meta-Analysis Model (k = 100; method: REML)

  logLik  Deviance       AIC       BIC      AICc
 -63.375   126.750   138.750   154.136   139.694

Variance Components:

           estim   sqrt  nlvls  fixed        factor
sigma^2.1  0.085  0.292    100     no  effectsizeID
sigma^2.2  0.149  0.386     17     no       studyID

Test for Residual Heterogeneity:
QE(df = 96) = 609.357, p-val < .001

Test of Moderators (coefficient(s) 2:4):
F(df1 = 3, df2 = 96) = 6.414, p-val < .001

Model Results:

            estimate     se    tval   pval   ci.lb   ci.ub
intrcpt        0.466  0.107   4.346  <.001   0.253   0.678
pyear         -0.038  0.018  -2.077  0.040  -0.074  -0.002
typeovert     -0.204  0.139  -1.473  0.144  -0.479   0.071
typecovert    -0.709  0.191  -3.707  <.001  -1.089  -0.330


>



To plot Cook's Distance values for cluster studyID (17 levels) from model multiple moderator, I did:

> #### Cook's distance ###
> par(mfrow=c(1,1))
> tmp.cook.studyID <- cooks.distance(multiplemoderator,
+                            cluster=dataset$studyID,
+                            progbar=TRUE)
  |=======================================================| 100%
> plot(tmp.cook.studyID, type="o", pch=19)
> which(tmp.cook.studyID > 1)
15
15


>



[cid:image001.jpg at 01D317FF.F01E6720]


> which(tmp.cook.studyID > 0)
1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 17
 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 17


>



Effect sizes are unique among studies. Study 16 is missing despite there are 16 effect sizes in study 16. Any clue for that?

Thanks in advance,

Roger :)

Roger Martineau, mv Ph.D.
Centre de recherche et de développement
sur le bovin laitier et le porc
Agriculture et agroalimentaire Canada/Agriculture and Agri-Food Canada
Téléphone/Telephone: 819-780-7319
Télécopieur/Facsimile: 819-564-5507
2000, Rue Collège / 2000, College Street
Sherbrooke (Québec)  J1M 0C8
Canada
roger.martineau at agr.gc.ca<mailto:roger.martineau at agr.gc.ca>


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