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<p class="MsoPlainText">Dear metafor users,<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">I am running complex models using <span style="font-size:10.0pt;font-family:"Lucida Console"">
rma.mv function</span> of metafor (<span style="font-size:9.0pt;font-family:"Lucida Console";color:black">metafor_2.0-0;</span><span style="font-size:9.0pt;font-family:"Lucida Console";color:black;mso-fareast-language:EN-CA"> R version 3.4.0</span><span style="font-size:10.0pt;font-family:"Lucida Console";color:black;mso-fareast-language:EN-CA">)</span>
on a large dataset (n = 197 studies) with a 4-level hierarchical structure of data.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console"">#### Model ####<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console"">(tmp.casdiet <- rma.mv(MTPYMean, MTPYSEMtrDP^2, data=tmp.dat.MTPY.new,<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console""> mods = ~<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console""> cMPbal +<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console""> cNELbal +<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console""> cMPsupply.kg +<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console""> factor(CasDiet)*cMPsupply.kg,<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console""> random = ~1|laboratory/experiment/study,<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console""> method = "REML", sparse=TRUE))<o:p></o:p></span></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">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.<o:p></o:p></p>
<p class="MsoPlainText">
<o:p></o:p></p>
<p class="MsoPlainText"> The time spent to execute the task is related to the random statement:<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo1">
<![if !supportLists]><span style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]>random = ~1|<span style="font-size:9.0pt;font-family:"Lucida Console"">laboratory/</span>experiment/study : 14 min 5 sec<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo1">
<![if !supportLists]><span style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]>random = ~1|experiment/study : 8 min 10 sec<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo1">
<![if !supportLists]><span style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]>random = ~1|study: 1 min 12 sec<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Find below more info on variance components and Cook’s distance graphs.
<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">In this model it wouldn’t make much of a difference to run the
<span style="font-size:9.0pt;font-family:"Lucida Console"">cooks.distance.rma.mv</span> function with
<span style="font-size:9.0pt;font-family:"Lucida Console"">random = ~1|study</span> but it is not the correct way to detect influential cases.
<o:p></o:p></p>
<p class="MsoPlainText">
<o:p></o:p></p>
<p class="MsoPlainText">Is there another way to speed up the process ?<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Thanks in advance,<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Roger Martineau <span style="font-family:"Segoe UI Symbol","sans-serif"">
☺<o:p></o:p></span></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">The variance components and the associated Cook’s distance graphs are:<o:p></o:p></p>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-family:"Lucida Console";color:black"><o:p> </o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black">Variance Components: <o:p></o:p></span></pre>
<p class="MsoPlainText"><o:p> </o:p></p>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black"> estim sqrt nlvls fixed<o:p></o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black">sigma^2.1 178.9385 13.3768 21 no<o:p></o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black">sigma^2.2 409.8262 20.2442 47 no<o:p></o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black">sigma^2.3 0.0000 0.0016 69 no<o:p></o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black"> factor<o:p></o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black">sigma^2.1 laboratory<o:p></o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black">sigma^2.2 laboratory/experiment<o:p></o:p></span></pre>
<pre style="line-height:11.25pt;background:white;word-break:break-all"><span style="font-size:9.0pt;font-family:"Lucida Console";color:black">sigma^2.3 laboratory/experiment/study<o:p></o:p></span></pre>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console"">#### Cook's distance ####<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console"">par(mfrow=c(1,1))<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console"">tmp.cook <- cooks.distance.rma.mv(tmp.casdiet, progbar=TRUE)<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console"">plot(tmp.cook, type="o", pch=19)<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size:9.0pt;font-family:"Lucida Console"">which(tmp.cook > 1)<o:p></o:p></span></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText" style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]>random = ~1|<span style="font-size:9.0pt;font-family:"Lucida Console"">laboratory/</span>experiment/study<o:p></o:p></p>
<p class="MsoPlainText"><span style="mso-fareast-language:EN-CA"><img width="536" height="339" id="Image_x0020_1" src="cid:image007.jpg@01D30545.643B8160"></span><o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]>random = ~1|experiment/study<o:p></o:p></p>
<p class="MsoPlainText"><span style="mso-fareast-language:EN-CA"><img width="534" height="349" id="Image_x0020_2" src="cid:image008.jpg@01D30545.643B8160"></span><o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]>random = ~1|study<o:p></o:p></p>
<p class="MsoPlainText"><span style="mso-fareast-language:EN-CA"><img width="526" height="350" id="Image_x0020_3" src="cid:image009.jpg@01D30545.643B8160"></span><o:p></o:p></p>
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