Kernel: R (R-Project)
RStan in CoCalc (Kernel: "R-Project")
https://mc-stan.org/users/interfaces/rstan
Going through https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started with slight changes for CoCalc.
Be aware, that the initial compilation takes about 2.5 gb of RAM!
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Trying to compile a simple C file
Running /usr/lib/R/bin/R CMD SHLIB foo.c
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c foo.c -o foo.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o foo.so foo.o -L/usr/lib/R/lib -lR
TRUE
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'2.18.2'
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Loading required package: rstan
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.18.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
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SAMPLING FOR MODEL '77851864eaef144f4a34884224755b9c' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds.
Chain 1: Adjust your expectations accordingly!
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SAMPLING FOR MODEL '77851864eaef144f4a34884224755b9c' NOW (CHAIN 2).
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Chain 2: Gradient evaluation took 9e-06 seconds
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SAMPLING FOR MODEL '77851864eaef144f4a34884224755b9c' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 8e-06 seconds
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SAMPLING FOR MODEL '77851864eaef144f4a34884224755b9c' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 7e-06 seconds
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Warning message:
“There were 3 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup”Warning message:
“Examine the pairs() plot to diagnose sampling problems
”
In [15]:
Inference for Stan model: 77851864eaef144f4a34884224755b9c.
4 chains, each with iter=2000; warmup=1000; thin=1;
post-warmup draws per chain=1000, total post-warmup draws=4000.
mean se_mean sd 2.5% 25% 50% 75% 97.5% n_eff Rhat
mu 7.86 0.12 5.11 -2.45 4.61 7.90 11.15 17.70 1857 1
tau 6.54 0.13 5.38 0.29 2.44 5.31 9.20 20.25 1599 1
eta[1] 0.40 0.01 0.95 -1.51 -0.24 0.43 1.05 2.18 4156 1
eta[2] 0.01 0.01 0.86 -1.69 -0.57 0.00 0.59 1.77 4138 1
eta[3] -0.21 0.01 0.92 -2.05 -0.82 -0.21 0.40 1.62 5337 1
eta[4] -0.01 0.01 0.90 -1.78 -0.59 0.00 0.56 1.78 4212 1
eta[5] -0.35 0.01 0.88 -2.07 -0.94 -0.35 0.23 1.41 4105 1
eta[6] -0.20 0.01 0.87 -1.84 -0.78 -0.21 0.37 1.58 4185 1
eta[7] 0.33 0.01 0.87 -1.46 -0.22 0.34 0.92 2.00 4145 1
eta[8] 0.06 0.01 0.92 -1.79 -0.56 0.07 0.69 1.81 4672 1
theta[1] 11.53 0.15 8.29 -2.12 6.08 10.50 15.77 31.26 3107 1
theta[2] 7.91 0.09 6.24 -4.38 4.03 7.78 11.76 20.43 4724 1
theta[3] 6.14 0.12 7.77 -11.13 2.17 6.57 10.92 20.15 3935 1
theta[4] 7.68 0.09 6.57 -5.30 3.71 7.67 11.84 20.92 5068 1
theta[5] 5.18 0.10 6.48 -8.82 1.20 5.63 9.52 16.46 3825 1
theta[6] 6.16 0.10 6.54 -7.89 2.27 6.53 10.52 18.08 4642 1
theta[7] 10.59 0.11 6.74 -1.56 6.09 9.93 14.54 25.98 3714 1
theta[8] 8.37 0.13 7.94 -7.34 3.71 8.28 12.72 25.05 3846 1
lp__ -39.49 0.08 2.61 -45.37 -41.08 -39.26 -37.61 -35.10 1208 1
Samples were drawn using NUTS(diag_e) at Thu Jan 10 17:15:29 2019.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
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'pars' not specified. Showing first 10 parameters by default.
ci_level: 0.8 (80% intervals)
outer_level: 0.95 (95% intervals)
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- 5.39618350392046
- 0.686046105579853
- 12.2207867201285
- -0.178791454000923
- 11.0161502498223
- 5.34968907655748
- 6.93197826928302
- 5.68811738463849
- 10.7213844859233
- 1.68269235068929
In [19]:
mu | tau | eta[1] | eta[2] | eta[3] | eta[4] | eta[5] | eta[6] | eta[7] | eta[8] |
---|---|---|---|---|---|---|---|---|---|
5.3961835 | 2.3685829 | -0.5567546 | 0.56348542 | 2.01522095 | 0.169342623 | 0.50181571 | -0.208145098 | -1.1217359 | 1.91946027 |
0.6860461 | 4.1367774 | -1.0802441 | 0.42963362 | 1.99876081 | 0.887993281 | 1.20276288 | -0.240802263 | -0.9450431 | 2.28220115 |
12.2207867 | 0.5989557 | -1.3517758 | -1.50313373 | -1.26931261 | 0.090716307 | -0.95829548 | 0.395428980 | -0.1213342 | -1.29870404 |
-0.1787915 | 1.2749352 | -0.3583841 | -0.59696618 | 0.99716760 | -0.890219718 | -0.92933774 | -1.007676229 | -0.7057188 | 0.57632729 |
11.0161502 | 1.7843548 | -0.2232293 | 0.04109137 | 0.45007966 | -0.438513460 | -1.30454790 | -1.048199309 | -0.4806426 | -0.64408486 |
5.3496891 | 4.6905826 | -0.9736077 | 0.54301954 | 0.86772042 | 0.500115637 | -0.45801685 | -1.452564628 | 2.3787168 | 0.17005574 |
6.9319783 | 5.3027711 | 1.3647102 | 0.08618644 | -2.15494141 | -1.745484748 | 0.68330836 | 0.570792391 | -0.3023055 | 0.43175128 |
5.6881174 | 1.6164703 | -1.8529150 | 0.21515663 | 0.91532076 | 0.189292082 | -0.14087814 | -0.067037906 | -0.1208038 | 0.62964552 |
10.7213845 | 8.9996004 | -1.9365577 | 0.13085916 | 1.77016072 | -0.003299785 | -0.86071803 | 0.473711690 | 0.2658253 | 1.45396565 |
1.6826924 | 0.1691010 | 1.1240211 | 0.39374889 | 0.42215091 | -0.482868850 | -1.04063432 | 0.049669334 | -1.4084845 | 0.45945727 |
14.7804757 | 3.8119272 | -0.6679941 | -0.05020627 | -0.13868226 | 1.116695069 | 0.01027008 | -0.685884853 | 0.6550268 | 0.23060747 |
10.1087903 | 2.4634371 | -2.5762966 | -0.68724688 | -1.86960612 | -0.279329749 | -1.26457829 | -2.805158102 | 0.1750718 | -0.09148728 |
24.0811459 | 1.8356451 | -2.9145325 | 1.11611710 | -0.94643350 | 0.319774308 | 1.34581207 | 0.165335433 | -0.2260273 | 1.09373800 |
-7.4851807 | 6.6397290 | 3.3438356 | -1.06011093 | 0.87519429 | 0.473639239 | -1.70560951 | -0.529120226 | 0.4812363 | -1.04239608 |
-0.3013699 | 13.9068516 | 2.3604325 | 0.85464726 | -0.22416280 | 0.651395582 | -0.30136386 | 0.343451168 | 2.0920786 | 0.78442915 |
11.4391144 | 11.6837877 | -1.3756533 | -0.70986594 | -0.54579781 | -0.644570508 | -0.48813750 | 0.009779451 | -0.1877553 | 0.52216926 |
13.4169475 | 14.3643945 | 1.8847251 | -0.18508920 | 0.17401990 | 0.182930297 | -1.17503408 | -1.308482204 | 0.7070368 | -0.13166273 |
8.7048968 | 6.7834231 | 0.4628655 | -0.08120005 | -0.21238590 | 0.162767090 | -0.95412743 | -0.427018160 | -1.0112350 | -1.44880478 |
6.6540698 | 4.9487404 | 1.3854939 | 0.96121890 | -0.26556847 | 0.195825372 | 0.49529749 | 0.328893927 | 1.0500572 | 1.55579236 |
-2.5387590 | 16.4575783 | 0.3717619 | 0.50999642 | 0.96570505 | -0.157000076 | 0.47046243 | -0.050642907 | 1.3414407 | 1.46431963 |
-2.5387590 | 16.4575783 | 0.3717619 | 0.50999642 | 0.96570505 | -0.157000076 | 0.47046243 | -0.050642907 | 1.3414407 | 1.46431963 |
16.3980514 | 13.5989202 | 1.4541320 | -0.39967342 | -1.20405390 | 0.098571305 | -1.23094236 | -0.824934046 | -0.1621034 | -1.10090304 |
14.4847117 | 13.7989773 | 0.2092602 | 0.12059297 | -1.49481657 | -0.689796320 | -0.37982431 | -0.958498537 | -0.3457315 | -0.13843692 |
12.3469263 | 2.0297331 | 0.4319855 | -1.19744527 | 0.24561412 | -0.072166641 | -1.15542862 | 0.548836712 | 0.6966082 | 0.01814399 |
12.4287394 | 0.9902857 | 1.1037543 | -1.27847109 | -0.43530026 | 0.494160859 | 0.26845793 | 0.157840373 | 0.6658382 | 0.60015112 |
10.6641490 | 2.5483680 | -0.7839886 | -0.77121420 | -1.35230236 | 0.549695398 | -0.04613958 | -1.733963274 | 0.2421487 | 0.28274715 |
10.6199698 | 0.2835570 | -0.2917623 | 0.19324122 | -0.46244387 | 0.782276174 | 0.25997656 | -0.539997086 | 0.4743405 | -0.29992826 |
8.8833887 | 0.5482013 | -0.1314144 | -0.48854279 | -0.34184416 | -0.112882179 | 1.03627536 | 0.698999798 | 1.2983051 | -0.47556639 |
3.3082875 | 1.5641125 | 0.4397713 | -0.21005412 | 0.99517117 | -1.022978212 | -0.55439391 | 1.317178312 | -0.1755756 | -0.26944904 |
7.6743617 | 7.6847889 | 0.6286669 | -0.77196167 | 0.06247897 | -1.503346589 | -0.66778958 | 0.600880524 | 1.4895017 | 0.61987915 |
⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
9.886547 | 8.7464343 | 1.8607923 | -0.155244942 | -1.92769611 | -1.1736117 | -1.05415111 | 0.86365921 | -0.78806516 | 0.36300414 |
11.364010 | 4.7500489 | -1.1666333 | 0.007529395 | -0.61787671 | -1.4561706 | -1.60222744 | -0.10814093 | -0.85543032 | 0.83673123 |
12.922030 | 2.4673147 | -0.8138930 | -0.638404194 | -1.16309929 | -1.3853016 | -2.07147697 | -0.11207489 | -0.99742529 | 0.98280938 |
9.004027 | 3.4505590 | -0.5446533 | 0.185183857 | 0.19112569 | -2.2194860 | -0.16581317 | 1.00831837 | -0.60580365 | 1.42806526 |
8.532313 | 3.6696136 | -1.2224762 | -0.485543666 | -1.25071786 | -1.1871044 | 0.06247177 | 0.94131544 | 0.10498538 | 0.77952432 |
9.308727 | 4.3011331 | 0.7358349 | -0.431700486 | 0.32954572 | -0.2472215 | -1.04841285 | -0.64676165 | -1.22708457 | -0.33212684 |
15.159718 | 2.7690557 | 1.0476665 | -0.264712384 | -0.50345320 | -1.4397583 | -1.53447871 | -0.82564645 | 1.45288789 | 0.07194064 |
14.807279 | 5.5387126 | 0.2781911 | -0.232648400 | -1.20349057 | -1.2788765 | -2.20007530 | -0.74980024 | 1.75414821 | -0.21797300 |
14.354266 | 1.4427400 | 0.4608208 | -0.698071530 | 0.05452116 | 0.4823497 | 0.13507947 | -0.36418955 | -2.02677862 | -0.07404370 |
8.731571 | 1.8346451 | 0.3800160 | -0.581235586 | -0.32387452 | 1.1167866 | 0.58360983 | -1.26223659 | -1.85069180 | -0.23949578 |
8.141408 | 13.5718821 | 0.9911613 | 0.479031309 | -0.13500755 | 0.3051145 | -1.19999842 | 0.33299510 | 2.28823572 | -0.68887381 |
5.223351 | 9.4409972 | 1.1392715 | 0.638647869 | -0.76410606 | 0.1237237 | -0.90769248 | -0.13822845 | 1.41619995 | -0.74254328 |
4.175857 | 9.7919858 | 1.6459312 | -0.225571376 | 1.23100186 | 0.7472079 | 0.46678288 | -0.61453897 | -0.04342235 | 0.19795917 |
13.516229 | 2.4123927 | -0.5653916 | -0.506821106 | -0.86345996 | -1.4461655 | -0.37638387 | 0.25572666 | 0.27263606 | 0.12147005 |
8.195783 | 0.4985395 | -0.1596514 | -0.227068158 | -2.20298982 | -1.5556816 | -0.50401496 | -0.82348689 | -1.69214290 | 1.67993505 |
5.724590 | 0.5074447 | 0.1463413 | 0.777902171 | -0.88910865 | -0.5522545 | -0.03084518 | 0.25136057 | -0.54789818 | 2.38617182 |
7.189569 | 12.4709405 | -0.2319947 | 0.997506062 | 0.11218081 | -1.4477460 | -0.84611043 | -0.04976682 | 0.60869760 | -0.30506043 |
11.821388 | 5.0489694 | 1.5068324 | -1.589650827 | -0.85868506 | 1.7814902 | -0.22197141 | -0.67997223 | -0.01054010 | 0.72218861 |
6.991630 | 6.1293814 | -0.1149275 | -0.620351195 | -0.78686414 | -1.5704500 | -0.77792137 | 0.99757089 | 0.92422567 | -0.90226504 |
8.394466 | 1.9009057 | 0.2836753 | 1.113406309 | 0.63902720 | 1.5701933 | 0.35866455 | -1.35776173 | -0.36234836 | -0.04246596 |
8.227097 | 13.8285292 | -0.1128386 | -0.864252583 | -1.04510557 | -1.2310453 | -0.32135086 | -0.18709069 | 0.45175475 | -1.08077260 |
4.756219 | 4.8510982 | 1.0809501 | 1.075581321 | 0.47707824 | 1.5348927 | -0.59170947 | -0.44832337 | 0.60559299 | 1.37185410 |
9.125994 | 4.6916668 | 0.7902582 | -0.360020171 | -1.13269192 | -0.9154454 | -0.19690435 | -0.42695352 | 1.23209184 | 0.68186416 |
10.401728 | 8.5582942 | 0.9907257 | 0.316102757 | -1.12876402 | 0.4033975 | -0.64321177 | -0.50959635 | -0.44911528 | -0.39420160 |
11.755744 | 19.4218130 | -0.2288889 | -0.470286217 | -0.53298429 | 0.2498006 | -1.07497742 | -0.05123380 | 0.52598584 | 0.75638694 |
8.386704 | 24.7611511 | 1.2541720 | 0.265327917 | 0.03457989 | -0.4722916 | 0.19660066 | -0.45530531 | 0.35719173 | -0.63764690 |
5.201969 | 5.9500500 | 0.7144015 | -0.497214555 | -0.56814769 | 0.3120196 | -1.06307262 | 0.06060043 | 0.18038785 | -1.69056192 |
11.117786 | 6.2049786 | 0.5332541 | 0.610885496 | -0.25031408 | 0.0660660 | 0.11059952 | -0.89447537 | 0.68927347 | 1.31855236 |
7.675931 | 17.1808587 | 0.5752803 | -0.043668107 | -0.20804228 | -0.3081718 | -0.81270383 | 0.24382377 | -0.15226967 | -1.74742574 |
9.331831 | 7.7080905 | 0.9305285 | -0.810825690 | -1.19654748 | 0.2710335 | -0.11800252 | -0.94605939 | 0.96818966 | 0.87161380 |
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