I'm running a script that performs automated backwards selection on glmer models. The script runs sequential drop1() commands, automatically removing the predictor with the highest p-value after each step.
It's very time-consuming so I want to leave it to run overnight, but R stops running when I leave the computer. I'm running R 3.1.1 in Snow Leopard. I have already set the System Preferences to prevent the computer from sleeping, and I am also preventing sleep by running 'pmset noidle' in Terminal. Despite all this, when I leave my script to run, it silently pauses about 45 minutes after my last activity (in any application), and silently resumes when I start using the computer again in the morning. I can tell approximately when the script is active because it periodically prints timestamps.
Mar 28, 2017 Keep your Mac from going to sleep automatically. Select “Prevent computer from sleeping automatically when the display is off” in the Power Adapter pane. Put hard disks to sleep. Select the “Put hard disks to sleep when possible” option in the Battery or Power Adapter pane. If you're tired of Windows dimming the screen or going to sleep without permission, try this. You're watching a video or running a slide deck, when suddenly the screen dims.
I've pasted an example fragment of the output at the bottom of this post (mostly so folks can see the timestamps). I recognize that I'm getting some warnings related to the model fitting, but I'm pretty sure these are not causing the 7.5-hour delay!
Has this happened to anyone else? Any suggestions for how to keep my script running while I'm away from the computer? I'm new to the site, so please let me know what additional info I can provide. [1] 'Wed Feb 25 21:' Single term deletions Model: Pref ~ Nut * Subfamily + Nut * Sex + Subfamily * Sex + DrinkDur + TrialTime + holdDur + FeedOrder + (1 SpCode/Indiv) Df AIC LRT Pr(Chi) 809.07 DrinkDur 1 810.77 3.703 0.05433.
TrialTime 1 807.06 -0.011 1.00000 holdDur 1 807.37 0.306 0.58036 FeedOrder 1 810.24 3.172 0.07490. Nut:Subfamily 32 820.47 75.404 2.315e-05 *** Nut:Sex 4 843.44 42.375 1.395e-08 *** Subfamily:Sex 8 809.06 15.995 0.04245 * --- Signif. Codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 [1] 'Now dropping TrialTime' [1] 'Wed Feb 25 22:' Single term deletions Model: Pref ~ Nut + Subfamily + Sex + DrinkDur + holdDur + FeedOrder + (1 SpCode/Indiv) + Nut:Subfamily + Nut:Sex + Subfamily:Sex Df AIC LRT Pr(Chi) 807.06 DrinkDur 1 808.72 3.665 0.05556. HoldDur 1 805.33 0.276 0.59950 FeedOrder 1 808.19 3.134 0.07667.
Nut:Subfamily 32 818.18 75.125 2.523e-05 *** Nut:Sex 4 841.42 42.360 1.405e-08 *** Subfamily:Sex 8 807.18 16.125 0.04062 * --- Signif. Codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 [1] 'Now dropping holdDur' [1] 'Thu Feb 26 00:' Single term deletions Model: Pref ~ Nut + Subfamily + Sex + DrinkDur + FeedOrder + (1 SpCode/Indiv) + Nut:Subfamily + Nut:Sex + Subfamily:Sex Df AIC LRT Pr(Chi) 805.33 DrinkDur 1 806.85 3.519 0.06066. FeedOrder 1 806.47 3.134 0.07667. Nut:Subfamily 32 816.48 75.144 2.508e-05 *** Nut:Sex 4 839.69 42.357 1.407e-08 *** Subfamily:Sex 8 805.55 16.220 0.03934 * --- Signif. Codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 [1] 'Now dropping FeedOrder' [1] 'Thu Feb 26 08:' There were 50 or more warnings (use warnings() to see the first 50) Single term deletions Model: Pref ~ Nut + Subfamily + Sex + DrinkDur + (1 SpCode/Indiv) + Nut:Subfamily + Nut:Sex + Subfamily:Sex Df AIC LRT Pr(Chi) 806.47 DrinkDur 1 808.10 3.636 0.05655. Nut:Subfamily 32 819.11 76.647 1.574e-05 *** Nut:Sex 4 840.14 41.678 1.945e-08 *** Subfamily:Sex 8 806.69 16.222 0.03931 * --- Signif. Codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 [1] 'Now dropping DrinkDur' [1] 'Thu Feb 26 09:' Single term deletions Model: Pref ~ Nut + Subfamily + Sex + (1 SpCode/Indiv) + Nut:Subfamily + Nut:Sex + Subfamily:Sex Df AIC LRT Pr(Chi) 808.10 Nut:Subfamily 32 821.02 76.918 1.446e-05 *** Nut:Sex 4 842.05 41.944 1.713e-08 *** Subfamily:Sex 8 807.25 15.147 0.05635.