RCall_tryStan_2.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "hide_input": false
   },
   "outputs": [],
   "source": [
    "using PyCall,RCall;\n",
    "R\"\"\"\n",
    ".libPaths(c(\"/mnt/juliabox/R_library\", .libPaths()))\n",
    "print(.libPaths())\n",
    "print(sessionInfo())\n",
    "\"\"\";"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Code in Chapter 9\\shell.jl:\n",
    "   cmd = `echo Julia is smart`\n",
    "typeof(cmd) #> Cmd \n",
    "    run(cmd) # returns Julia is smart\n",
    "    run(`date`) #> Sun Oct 12 09:44:50 GMT 2014\n",
    "cmd = `cat file1.txt`\n",
    "run(cmd) ..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run(cmd)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run(`date`) \n",
    "#run(`man quota`)\n",
    "run(`ls -la`)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run(`echo hello`)\n",
    "run(`du -sh `)\n",
    "#run(`du ./`)\n",
    "run(`man du `)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ENV[\"HOME\"]\n",
    "#outfile = ENV[\"HOME\"]*\"/run_rstan.R\"\n",
    "outfile = ENV[\"HOME\"]*\"/tutorials\"\n",
    "run(`du -sh $outfile`)\n",
    "#mypath = \"show_a_path\"\n",
    "run(`set mypath = \"show_a_path\"`)\n",
    "run(`echo $mypath`)\n",
    "run(`quota -vs`)\n",
    "#run(`ls` |> \"out.log\")\n",
    "#run(\"out.log\" |> `cat`)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run(`cp run_rstan.R  mytempfile`)\n",
    "run(pipeline(`cat mytempfile`))\n",
    "run(pipeline(`tail -n5`))\n",
    "#run(pipeline(`cat mytempfile`, `tail -n5`))\n",
    "\n",
    "#see https://docs.julialang.org/en/v0.7/manual/running-external-programs/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "R\"\"\"\n",
    "1+1.2\n",
    "source(\"/mnt/juliabox/run_rstan.R\")\n",
    "\"\"\";"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"/mnt/juliabox/R_library\"       \"/usr/local/lib/R/site-library\"\n",
      "[3] \"/usr/lib/R/site-library\"       \"/usr/lib/R/library\"           \n",
      "R version 3.4.4 (2018-03-15)\n",
      "Platform: x86_64-pc-linux-gnu (64-bit)\n",
      "Running under: Ubuntu 16.04.5 LTS\n",
      "\n",
      "Matrix products: default\n",
      "BLAS: /usr/lib/libblas/libblas.so.3.6.0\n",
      "LAPACK: /usr/lib/lapack/liblapack.so.3.6.0\n",
      "\n",
      "locale:\n",
      "[1] C\n",
      "\n",
      "attached base packages:\n",
      "[1] stats     graphics  grDevices utils     datasets  methods   base     \n",
      "\n",
      "loaded via a namespace (and not attached):\n",
      "[1] compiler_3.4.4\n",
      "\n",
      "SAMPLING FOR MODEL 'simu_GP' NOW (CHAIN 1).\n",
      "Chain 1: Iteration: 1 / 1 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0 seconds (Warm-up)\n",
      "Chain 1:                3.1e-05 seconds (Sampling)\n",
      "Chain 1:                3.1e-05 seconds (Total)\n",
      "Chain 1: \n",
      " [1] \"G_total\"     \"M\"           \"N\"           \"Z\"           \"a\"          \n",
      " [6] \"alpha_T\"     \"avec\"        \"g\"           \"integrity\"   \"mod_OLS\"    \n",
      "[11] \"r\"           \"rho_T\"       \"sd_r\"        \"sigma_T\"     \"sim_GP_data\"\n",
      "[16] \"simu_fit\"    \"t_total\"    \n",
      "DIAGNOSTIC(S) FROM PARSER:\n",
      "Info (non-fatal): Comments beginning with # are deprecated.  Please use // in place of # for line comments.\n",
      "\n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.000229 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.29 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: WARNING: No variance estimation is\n",
      "Chain 1:          performed for num_warmup < 20\n",
      "Chain 1: \n",
      "Chain 1: Iteration: 1 / 10 [ 10%]  (Warmup)\n",
      "Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)\n",
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      "Chain 1: Iteration: 9 / 10 [ 90%]  (Sampling)\n",
      "Chain 1: Iteration: 10 / 10 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.00262 seconds (Warm-up)\n",
      "Chain 1:                0.008528 seconds (Sampling)\n",
      "Chain 1:                0.011148 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.000164 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.64 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 1: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 1: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 1: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 1: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.780687 seconds (Warm-up)\n",
      "Chain 1:                0.125624 seconds (Sampling)\n",
      "Chain 1:                0.906311 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 2).\n",
      "Chain 2: \n",
      "Chain 2: Gradient evaluation took 7.8e-05 seconds\n",
      "Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.78 seconds.\n",
      "Chain 2: Adjust your expectations accordingly!\n",
      "Chain 2: \n",
      "Chain 2: \n",
      "Chain 2: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 2: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 2: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 2: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 2: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 2: \n",
      "Chain 2:  Elapsed Time: 0.637369 seconds (Warm-up)\n",
      "Chain 2:                0.12729 seconds (Sampling)\n",
      "Chain 2:                0.764659 seconds (Total)\n",
      "Chain 2: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 3).\n",
      "Chain 3: \n",
      "Chain 3: Gradient evaluation took 8.9e-05 seconds\n",
      "Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.89 seconds.\n",
      "Chain 3: Adjust your expectations accordingly!\n",
      "Chain 3: \n",
      "Chain 3: \n",
      "Chain 3: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 3: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 3: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 3: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 3: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 3: \n",
      "Chain 3:  Elapsed Time: 0.822759 seconds (Warm-up)\n",
      "Chain 3:                0.170253 seconds (Sampling)\n",
      "Chain 3:                0.993012 seconds (Total)\n",
      "Chain 3: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 4).\n",
      "Chain 4: \n",
      "Chain 4: Gradient evaluation took 0.000143 seconds\n",
      "Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.43 seconds.\n",
      "Chain 4: Adjust your expectations accordingly!\n",
      "Chain 4: \n",
      "Chain 4: \n",
      "Chain 4: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 4: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 4: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 4: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 4: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 4: \n",
      "Chain 4:  Elapsed Time: 0.801485 seconds (Warm-up)\n",
      "Chain 4:                0.110385 seconds (Sampling)\n",
      "Chain 4:                0.91187 seconds (Total)\n",
      "Chain 4: \n",
      "Inference for Stan model: misreport.\n",
      "4 chains, each with iter=300; warmup=150; thin=1; \n",
      "post-warmup draws per chain=150, total post-warmup draws=600.\n",
      "\n",
      "             mean se_mean    sd     10%     50%     90% n_eff  Rhat\n",
      "b[1]        0.901   0.001 0.026   0.869   0.901   0.932   603 0.998\n",
      "b[2]       -0.414   0.001 0.024  -0.444  -0.415  -0.383   779 0.998\n",
      "b[3]       -0.245   0.001 0.026  -0.279  -0.245  -0.214   660 0.996\n",
      "b[4]       -0.065   0.001 0.025  -0.096  -0.066  -0.034   690 0.995\n",
      "sd_r        0.126   0.001 0.018   0.103   0.124   0.151   400 1.002\n",
      "integrity   0.802   0.003 0.078   0.697   0.814   0.894   791 0.998\n",
      "rho         5.258   0.140 2.925   2.559   4.666   8.531   437 0.998\n",
      "alpha       1.339   0.035 0.890   0.486   1.120   2.585   662 0.999\n",
      "sigma       1.708   0.009 0.245   1.401   1.682   2.041   698 0.998\n",
      "ilogodds    1.476   0.018 0.517   0.835   1.477   2.136   790 1.000\n",
      "r_new[1]    0.636   0.005 0.135   0.456   0.637   0.807   605 0.996\n",
      "r_new[2]    0.797   0.005 0.132   0.633   0.802   0.957   668 1.005\n",
      "r_new[3]   -0.276   0.005 0.134  -0.448  -0.276  -0.112   624 1.001\n",
      "lp__      -16.967   0.177 2.373 -20.120 -16.651 -14.254   180 1.027\n",
      "\n",
      "Samples were drawn using NUTS(diag_e) at Sun Apr  7 14:50:18 2019.\n",
      "For each parameter, n_eff is a crude measure of effective sample size,\n",
      "and Rhat is the potential scale reduction factor on split chains (at \n",
      "convergence, Rhat=1).\n",
      "[1] \"n_eff / iter looks reasonable for all parameters\"\n",
      "[1] \"Rhat looks reasonable for all parameters\"\n",
      "[1] \"0 of 600 iterations ended with a divergence (0%)\"\n",
      "[1] \"0 of 600 iterations saturated the maximum tree depth of 10 (0%)\"\n",
      "[1] \"E-BFMI indicated no pathological behavior\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Warning: RCall.jl: Loading required package: ggplot2\n",
      "│ Loading required package: StanHeaders\n",
      "│ rstan (Version 2.18.2, GitRev: 2e1f913d3ca3)\n",
      "│ For execution on a local, multicore CPU with excess RAM we recommend calling\n",
      "│ options(mc.cores = parallel::detectCores()).\n",
      "│ To avoid recompilation of unchanged Stan programs, we recommend calling\n",
      "│ rstan_options(auto_write = TRUE)\n",
      "│ \n",
      "│ Attaching package: 'rstan'\n",
      "│ \n",
      "│ The following object is masked from 'package:magrittr':\n",
      "│ \n",
      "│     extract\n",
      "│ \n",
      "└ @ RCall /home/jrun/.julia/packages/RCall/29zDq/src/io.jl:113\n"
     ]
    }
   ],
   "source": [
    "using RCall;\n",
    "R\"\"\"\n",
    "\n",
    ".libPaths(c(\"/mnt/juliabox/R_library\", .libPaths()))\n",
    "print(.libPaths())\n",
    "print(sessionInfo())\n",
    "\n",
    "#library(dplyr)\n",
    "library(magrittr)\n",
    "\n",
    "source(\"/mnt/juliabox/tryStan_2.R\")\n",
    "\"\"\";"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"/mnt/juliabox/R_library\"       \"/usr/local/lib/R/site-library\"\n",
      "[3] \"/usr/lib/R/site-library\"       \"/usr/lib/R/library\"           \n",
      "R version 3.4.4 (2018-03-15)\n",
      "Platform: x86_64-pc-linux-gnu (64-bit)\n",
      "Running under: Ubuntu 16.04.5 LTS\n",
      "\n",
      "Matrix products: default\n",
      "BLAS: /usr/lib/libblas/libblas.so.3.6.0\n",
      "LAPACK: /usr/lib/lapack/liblapack.so.3.6.0\n",
      "\n",
      "locale:\n",
      "[1] C\n",
      "\n",
      "attached base packages:\n",
      "[1] stats     graphics  grDevices utils     datasets  methods   base     \n",
      "\n",
      "loaded via a namespace (and not attached):\n",
      "[1] compiler_3.4.4\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Warning: RCall.jl: Loading required package: ggplot2\n",
      "│ Loading required package: StanHeaders\n",
      "│ rstan (Version 2.18.2, GitRev: 2e1f913d3ca3)\n",
      "│ For execution on a local, multicore CPU with excess RAM we recommend calling\n",
      "│ options(mc.cores = parallel::detectCores()).\n",
      "│ To avoid recompilation of unchanged Stan programs, we recommend calling\n",
      "│ rstan_options(auto_write = TRUE)\n",
      "│ \n",
      "│ Attaching package: 'rstan'\n",
      "│ \n",
      "│ The following object is masked from 'package:magrittr':\n",
      "│ \n",
      "│     extract\n",
      "│ \n",
      "└ @ RCall /home/jrun/.julia/packages/RCall/29zDq/src/io.jl:113\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "SAMPLING FOR MODEL 'simu_GP' NOW (CHAIN 1).\n",
      "Chain 1: Iteration: 1 / 1 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0 seconds (Warm-up)\n",
      "Chain 1:                3.1e-05 seconds (Sampling)\n",
      "Chain 1:                3.1e-05 seconds (Total)\n",
      "Chain 1: \n",
      " [1] \"G_total\"     \"M\"           \"N\"           \"Z\"           \"a\"          \n",
      " [6] \"alpha_T\"     \"avec\"        \"g\"           \"integrity\"   \"mod_OLS\"    \n",
      "[11] \"r\"           \"rho_T\"       \"sd_r\"        \"sigma_T\"     \"sim_GP_data\"\n",
      "[16] \"simu_fit\"    \"t_total\"    \n",
      "DIAGNOSTIC(S) FROM PARSER:\n",
      "Info (non-fatal): Comments beginning with # are deprecated.  Please use // in place of # for line comments.\n",
      "\n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.000152 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.52 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: WARNING: No variance estimation is\n",
      "Chain 1:          performed for num_warmup < 20\n",
      "Chain 1: \n",
      "Chain 1: Iteration: 1 / 10 [ 10%]  (Warmup)\n",
      "Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)\n",
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      "Chain 1: Iteration: 10 / 10 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.003204 seconds (Warm-up)\n",
      "Chain 1:                0.002461 seconds (Sampling)\n",
      "Chain 1:                0.005665 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.000145 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.45 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 1: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 1: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 1: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 1: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.702141 seconds (Warm-up)\n",
      "Chain 1:                0.119526 seconds (Sampling)\n",
      "Chain 1:                0.821667 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 2).\n",
      "Chain 2: \n",
      "Chain 2: Gradient evaluation took 8.2e-05 seconds\n",
      "Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.82 seconds.\n",
      "Chain 2: Adjust your expectations accordingly!\n",
      "Chain 2: \n",
      "Chain 2: \n",
      "Chain 2: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 2: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 2: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 2: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 2: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 2: \n",
      "Chain 2:  Elapsed Time: 0.545619 seconds (Warm-up)\n",
      "Chain 2:                0.129839 seconds (Sampling)\n",
      "Chain 2:                0.675458 seconds (Total)\n",
      "Chain 2: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 3).\n",
      "Chain 3: \n",
      "Chain 3: Gradient evaluation took 7.3e-05 seconds\n",
      "Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds.\n",
      "Chain 3: Adjust your expectations accordingly!\n",
      "Chain 3: \n",
      "Chain 3: \n",
      "Chain 3: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 3: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 3: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 3: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 3: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 3: \n",
      "Chain 3:  Elapsed Time: 0.572665 seconds (Warm-up)\n",
      "Chain 3:                0.138942 seconds (Sampling)\n",
      "Chain 3:                0.711607 seconds (Total)\n",
      "Chain 3: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 4).\n",
      "Chain 4: \n",
      "Chain 4: Gradient evaluation took 0.000111 seconds\n",
      "Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.11 seconds.\n",
      "Chain 4: Adjust your expectations accordingly!\n",
      "Chain 4: \n",
      "Chain 4: \n",
      "Chain 4: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 4: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 4: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 4: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 4: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 4: \n",
      "Chain 4:  Elapsed Time: 0.614179 seconds (Warm-up)\n",
      "Chain 4:                0.121525 seconds (Sampling)\n",
      "Chain 4:                0.735704 seconds (Total)\n",
      "Chain 4: \n",
      "Inference for Stan model: misreport.\n",
      "4 chains, each with iter=300; warmup=150; thin=1; \n",
      "post-warmup draws per chain=150, total post-warmup draws=600.\n",
      "\n",
      "             mean se_mean    sd     10%     50%     90% n_eff  Rhat\n",
      "b[1]        0.886   0.001 0.030   0.846   0.887   0.925   650 0.997\n",
      "b[2]       -0.434   0.001 0.023  -0.462  -0.435  -0.404   668 1.002\n",
      "b[3]       -0.223   0.001 0.028  -0.261  -0.222  -0.190   646 1.002\n",
      "b[4]       -0.043   0.001 0.026  -0.076  -0.043  -0.009  1058 0.997\n",
      "sd_r        0.141   0.002 0.022   0.115   0.137   0.168   191 1.014\n",
      "integrity   0.744   0.003 0.077   0.641   0.754   0.838   902 1.001\n",
      "rho         6.491   0.122 3.178   3.406   5.739  10.548   682 0.999\n",
      "alpha       3.346   0.067 1.410   1.922   3.077   4.993   445 1.007\n",
      "sigma       2.216   0.015 0.323   1.829   2.190   2.653   471 1.015\n",
      "ilogodds    1.111   0.015 0.418   0.580   1.121   1.646   830 1.001\n",
      "r_new[1]    0.757   0.006 0.143   0.574   0.763   0.937   595 1.001\n",
      "r_new[2]    1.309   0.006 0.149   1.127   1.313   1.496   703 0.998\n",
      "r_new[3]    1.037   0.006 0.145   0.843   1.049   1.209   557 1.001\n",
      "lp__      -32.090   0.162 2.264 -35.133 -31.682 -29.584   195 1.005\n",
      "\n",
      "Samples were drawn using NUTS(diag_e) at Sun Apr  7 15:09:36 2019.\n",
      "For each parameter, n_eff is a crude measure of effective sample size,\n",
      "and Rhat is the potential scale reduction factor on split chains (at \n",
      "convergence, Rhat=1).\n",
      "[1] \"n_eff / iter looks reasonable for all parameters\"\n",
      "[1] \"Rhat looks reasonable for all parameters\"\n",
      "[1] \"0 of 600 iterations ended with a divergence (0%)\"\n",
      "[1] \"0 of 600 iterations saturated the maximum tree depth of 10 (0%)\"\n",
      "[1] \"E-BFMI indicated no pathological behavior\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Warning: RCall.jl: Warning: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See\n",
      "│ http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup\n",
      "│ Warning: Examine the pairs() plot to diagnose sampling problems\n",
      "│ \n",
      "└ @ RCall /home/jrun/.julia/packages/RCall/29zDq/src/io.jl:113\n"
     ]
    }
   ],
   "source": [
    "using RCall;\n",
    "R\"\"\"\n",
    "\n",
    ".libPaths(c(\"/mnt/juliabox/R_library\", .libPaths()))\n",
    "print(.libPaths())\n",
    "print(sessionInfo())\n",
    "\n",
    "library(magrittr)\n",
    "\n",
    "library(rstan)\n",
    "# The following can affect distributional computing over a cluster\n",
    "#options(mc.cores = 1)  # only 1 core on Juliabox; don't set more unless 2-core machine is launched\n",
    "\n",
    "source(\"/mnt/juliabox/tryStan_2.R\")\n",
    "\"\"\";"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"/mnt/juliabox/R_library\"       \"/usr/local/lib/R/site-library\"\n",
      "[3] \"/usr/lib/R/site-library\"       \"/usr/lib/R/library\"           \n",
      "R version 3.4.4 (2018-03-15)\n",
      "Platform: x86_64-pc-linux-gnu (64-bit)\n",
      "Running under: Ubuntu 16.04.5 LTS\n",
      "\n",
      "Matrix products: default\n",
      "BLAS: /usr/lib/libblas/libblas.so.3.6.0\n",
      "LAPACK: /usr/lib/lapack/liblapack.so.3.6.0\n",
      "\n",
      "locale:\n",
      "[1] C\n",
      "\n",
      "attached base packages:\n",
      "[1] stats     graphics  grDevices utils     datasets  methods   base     \n",
      "\n",
      "other attached packages:\n",
      "[1] rstan_2.18.2       StanHeaders_2.18.1 ggplot2_3.1.0      magrittr_1.5      \n",
      "\n",
      "loaded via a namespace (and not attached):\n",
      " [1] Rcpp_1.0.1         tidyselect_0.2.5   munsell_0.5.0      colorspace_1.4-1  \n",
      " [5] R6_2.4.0           rlang_0.3.3        plyr_1.8.4         dplyr_0.8.0.1     \n",
      " [9] tools_3.4.4        parallel_3.4.4     pkgbuild_1.0.3     grid_3.4.4        \n",
      "[13] gtable_0.3.0       loo_2.1.0          cli_1.1.0          withr_2.1.2       \n",
      "[17] matrixStats_0.54.0 lazyeval_0.2.2     assertthat_0.2.1   tibble_2.1.1      \n",
      "[21] crayon_1.3.4       processx_3.3.0     gridExtra_2.3      purrr_0.3.2       \n",
      "[25] callr_3.2.0        codetools_0.2-15   ps_1.3.0           inline_0.3.15     \n",
      "[29] glue_1.3.1         compiler_3.4.4     pillar_1.3.1       prettyunits_1.0.2 \n",
      "[33] scales_1.0.0       stats4_3.4.4       pkgconfig_2.0.2   \n",
      "\n",
      "SAMPLING FOR MODEL 'simu_GP' NOW (CHAIN 1).\n",
      "Chain 1: Iteration: 1 / 1 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0 seconds (Warm-up)\n",
      "Chain 1:                2.5e-05 seconds (Sampling)\n",
      "Chain 1:                2.5e-05 seconds (Total)\n",
      "Chain 1: \n",
      "   user  system elapsed \n",
      "  0.085   0.000   0.119 \n",
      "\n",
      "\n",
      " [1] \"G_total\"               \"M\"                     \"N\"                    \n",
      " [4] \"N_new\"                 \"Z\"                     \"a\"                    \n",
      " [7] \"alpha_T\"               \"avec\"                  \"check_all_diagnostics\"\n",
      "[10] \"check_div\"             \"check_energy\"          \"check_n_eff\"          \n",
      "[13] \"check_rhat\"            \"check_treedepth\"       \"fit0_debug\"           \n",
      "[16] \"fit1\"                  \"g\"                     \"integrity\"            \n",
      "[19] \"m\"                     \"m_total\"               \"mod_OLS\"              \n",
      "[22] \"observed_t\"            \"partition_div\"         \"r\"                    \n",
      "[25] \"rho_T\"                 \"sd_r\"                  \"sigma_T\"              \n",
      "[28] \"sim_EM_data\"           \"sim_GP_data\"           \"simu_fit\"             \n",
      "[31] \"ss_complete_pool\"      \"t\"                     \"t_total\"              \n",
      "[34] \"timeused\"             \n",
      "DIAGNOSTIC(S) FROM PARSER:\n",
      "Info (non-fatal): Comments beginning with # are deprecated.  Please use // in place of # for line comments.\n",
      "\n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.00038 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.8 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: WARNING: No variance estimation is\n",
      "Chain 1:          performed for num_warmup < 20\n",
      "Chain 1: \n",
      "Chain 1: Iteration: 1 / 10 [ 10%]  (Warmup)\n",
      "Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)\n",
      "Chain 1: Iteration: 3 / 10 [ 30%]  (Warmup)\n",
      "Chain 1: Iteration: 4 / 10 [ 40%]  (Warmup)\n",
      "Chain 1: Iteration: 5 / 10 [ 50%]  (Warmup)\n",
      "Chain 1: Iteration: 6 / 10 [ 60%]  (Sampling)\n",
      "Chain 1: Iteration: 7 / 10 [ 70%]  (Sampling)\n",
      "Chain 1: Iteration: 8 / 10 [ 80%]  (Sampling)\n",
      "Chain 1: Iteration: 9 / 10 [ 90%]  (Sampling)\n",
      "Chain 1: Iteration: 10 / 10 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.005053 seconds (Warm-up)\n",
      "Chain 1:                0.00101 seconds (Sampling)\n",
      "Chain 1:                0.006063 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.000136 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.36 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 1: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 1: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 1: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 1: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.754456 seconds (Warm-up)\n",
      "Chain 1:                0.140776 seconds (Sampling)\n",
      "Chain 1:                0.895232 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 2).\n",
      "Chain 2: \n",
      "Chain 2: Gradient evaluation took 8.8e-05 seconds\n",
      "Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.88 seconds.\n",
      "Chain 2: Adjust your expectations accordingly!\n",
      "Chain 2: \n",
      "Chain 2: \n",
      "Chain 2: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 2: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 2: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 2: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 2: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 2: \n",
      "Chain 2:  Elapsed Time: 0.765036 seconds (Warm-up)\n",
      "Chain 2:                0.116517 seconds (Sampling)\n",
      "Chain 2:                0.881553 seconds (Total)\n",
      "Chain 2: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 3).\n",
      "Chain 3: \n",
      "Chain 3: Gradient evaluation took 8.5e-05 seconds\n",
      "Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.85 seconds.\n",
      "Chain 3: Adjust your expectations accordingly!\n",
      "Chain 3: \n",
      "Chain 3: \n",
      "Chain 3: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 3: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 3: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 3: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 3: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 3: \n",
      "Chain 3:  Elapsed Time: 0.668543 seconds (Warm-up)\n",
      "Chain 3:                0.143605 seconds (Sampling)\n",
      "Chain 3:                0.812148 seconds (Total)\n",
      "Chain 3: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 4).\n",
      "Chain 4: \n",
      "Chain 4: Gradient evaluation took 8.9e-05 seconds\n",
      "Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.89 seconds.\n",
      "Chain 4: Adjust your expectations accordingly!\n",
      "Chain 4: \n",
      "Chain 4: \n",
      "Chain 4: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 4: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 4: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 4: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 4: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 4: \n",
      "Chain 4:  Elapsed Time: 0.790453 seconds (Warm-up)\n",
      "Chain 4:                0.203009 seconds (Sampling)\n",
      "Chain 4:                0.993462 seconds (Total)\n",
      "Chain 4: \n",
      "   user  system elapsed \n",
      "  3.597   0.003   3.718 \n",
      "\n",
      "\n",
      "\n",
      "Inference for Stan model: misreport.\n",
      "4 chains, each with iter=300; warmup=150; thin=1; \n",
      "post-warmup draws per chain=150, total post-warmup draws=600.\n",
      "\n",
      "             mean se_mean    sd     10%     50%     90% n_eff  Rhat\n",
      "b[1]        0.894   0.001 0.037   0.848   0.893   0.944   631 1.000\n",
      "b[2]       -0.397   0.002 0.043  -0.452  -0.397  -0.342   409 1.001\n",
      "b[3]       -0.173   0.001 0.032  -0.211  -0.174  -0.131   578 0.995\n",
      "b[4]        0.016   0.002 0.037  -0.032   0.016   0.063   522 0.999\n",
      "sd_r        0.167   0.001 0.026   0.135   0.166   0.201   541 0.995\n",
      "integrity   0.868   0.002 0.059   0.787   0.877   0.938   589 0.999\n",
      "rho         5.840   0.155 3.055   2.865   5.030   9.771   388 1.008\n",
      "alpha       1.583   0.053 1.082   0.538   1.352   2.896   417 1.004\n",
      "sigma       2.252   0.017 0.353   1.849   2.208   2.717   428 1.001\n",
      "ilogodds    1.988   0.023 0.541   1.305   1.969   2.724   551 1.002\n",
      "r_new[1]    0.199   0.007 0.174  -0.016   0.203   0.412   580 0.997\n",
      "r_new[2]    1.022   0.008 0.182   0.803   1.013   1.276   579 1.001\n",
      "r_new[3]    1.075   0.007 0.181   0.843   1.071   1.302   624 1.002\n",
      "lp__      -29.000   0.157 2.410 -32.094 -28.637 -26.220   237 1.023\n",
      "\n",
      "Samples were drawn using NUTS(diag_e) at Sun Apr  7 15:23:28 2019.\n",
      "For each parameter, n_eff is a crude measure of effective sample size,\n",
      "and Rhat is the potential scale reduction factor on split chains (at \n",
      "convergence, Rhat=1).\n",
      "[1] \"n_eff / iter looks reasonable for all parameters\"\n",
      "[1] \"Rhat looks reasonable for all parameters\"\n",
      "[1] \"0 of 600 iterations ended with a divergence (0%)\"\n",
      "[1] \"0 of 600 iterations saturated the maximum tree depth of 10 (0%)\"\n",
      "[1] \"E-BFMI indicated no pathological behavior\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Warning: RCall.jl: Warning: There were 5 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See\n",
      "│ http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup\n",
      "│ Warning: Examine the pairs() plot to diagnose sampling problems\n",
      "│ \n",
      "└ @ RCall /home/jrun/.julia/packages/RCall/29zDq/src/io.jl:113\n"
     ]
    }
   ],
   "source": [
    "#using RCall;\n",
    "# 4 threads (1 core) time shown\n",
    "#   user  system elapsed \n",
    "#  3.597   0.003   3.718 \n",
    "\n",
    "R\"\"\"\n",
    "\n",
    ".libPaths(c(\"/mnt/juliabox/R_library\", .libPaths()))\n",
    "print(.libPaths())\n",
    "print(sessionInfo())\n",
    "\n",
    "library(magrittr)\n",
    "\n",
    "library(rstan)\n",
    "# The following can affect distributional computing over a cluster\n",
    "#options(mc.cores = 1)  # only 1 core on Juliabox; don't set more unless 2-core machine is launched\n",
    "\n",
    "source(\"/mnt/juliabox/tryStan_2.R\")\n",
    "\"\"\";"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-04-07T20:55:04.011000Z",
     "start_time": "2019-04-07T20:54:44.471Z"
    }
   },
   "outputs": [],
   "source": [
    "#using JuliaRunClient\n",
    "#initParallel()\n",
    "# Apparently, no parallel mode for free-tier users\n",
    "# error: Parallel mode is already being used in a different Julia instance\n",
    "\n",
    "using RCall;\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-04-07T20:56:54.683000Z",
     "start_time": "2019-04-07T20:56:41.109Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"/mnt/juliabox/R_library\"       \"/usr/local/lib/R/site-library\"\n",
      "[3] \"/usr/lib/R/site-library\"       \"/usr/lib/R/library\"           \n",
      "R version 3.4.4 (2018-03-15)\n",
      "Platform: x86_64-pc-linux-gnu (64-bit)\n",
      "Running under: Ubuntu 16.04.5 LTS\n",
      "\n",
      "Matrix products: default\n",
      "BLAS: /usr/lib/libblas/libblas.so.3.6.0\n",
      "LAPACK: /usr/lib/lapack/liblapack.so.3.6.0\n",
      "\n",
      "locale:\n",
      "[1] C\n",
      "\n",
      "attached base packages:\n",
      "[1] stats     graphics  grDevices utils     datasets  methods   base     \n",
      "\n",
      "other attached packages:\n",
      "[1] rstan_2.18.2       StanHeaders_2.18.1 ggplot2_3.1.0      magrittr_1.5      \n",
      "\n",
      "loaded via a namespace (and not attached):\n",
      " [1] Rcpp_1.0.1         tidyselect_0.2.5   munsell_0.5.0      colorspace_1.4-1  \n",
      " [5] R6_2.4.0           rlang_0.3.3        plyr_1.8.4         dplyr_0.8.0.1     \n",
      " [9] parallel_3.4.4     pkgbuild_1.0.3     grid_3.4.4         gtable_0.3.0      \n",
      "[13] loo_2.1.0          cli_1.1.0          withr_2.1.2        matrixStats_0.54.0\n",
      "[17] lazyeval_0.2.2     assertthat_0.2.1   tibble_2.1.1       crayon_1.3.4      \n",
      "[21] processx_3.3.0     gridExtra_2.3      purrr_0.3.2        callr_3.2.0       \n",
      "[25] ps_1.3.0           inline_0.3.15      glue_1.3.1         compiler_3.4.4    \n",
      "[29] pillar_1.3.1       prettyunits_1.0.2  scales_1.0.0       stats4_3.4.4      \n",
      "[33] pkgconfig_2.0.2   \n",
      "\n",
      "SAMPLING FOR MODEL 'simu_GP' NOW (CHAIN 1).\n",
      "Chain 1: Iteration: 1 / 1 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0 seconds (Warm-up)\n",
      "Chain 1:                2.9e-05 seconds (Sampling)\n",
      "Chain 1:                2.9e-05 seconds (Total)\n",
      "Chain 1: \n",
      "   user  system elapsed \n",
      "  1.581   0.120   2.190 \n",
      "\n",
      "\n",
      " [1] \"G_total\"     \"M\"           \"N\"           \"Z\"           \"a\"          \n",
      " [6] \"alpha_T\"     \"avec\"        \"g\"           \"integrity\"   \"mod_OLS\"    \n",
      "[11] \"r\"           \"rho_T\"       \"sd_r\"        \"sigma_T\"     \"sim_GP_data\"\n",
      "[16] \"simu_fit\"    \"t_total\"     \"timeused\"   \n",
      "DIAGNOSTIC(S) FROM PARSER:\n",
      "Info (non-fatal): Comments beginning with # are deprecated.  Please use // in place of # for line comments.\n",
      "\n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.000179 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.79 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: WARNING: No variance estimation is\n",
      "Chain 1:          performed for num_warmup < 20\n",
      "Chain 1: \n",
      "Chain 1: Iteration: 1 / 10 [ 10%]  (Warmup)\n",
      "Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)\n",
      "Chain 1: Iteration: 3 / 10 [ 30%]  (Warmup)\n",
      "Chain 1: Iteration: 4 / 10 [ 40%]  (Warmup)\n",
      "Chain 1: Iteration: 5 / 10 [ 50%]  (Warmup)\n",
      "Chain 1: Iteration: 6 / 10 [ 60%]  (Sampling)\n",
      "Chain 1: Iteration: 7 / 10 [ 70%]  (Sampling)\n",
      "Chain 1: Iteration: 8 / 10 [ 80%]  (Sampling)\n",
      "Chain 1: Iteration: 9 / 10 [ 90%]  (Sampling)\n",
      "Chain 1: Iteration: 10 / 10 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.00549 seconds (Warm-up)\n",
      "Chain 1:                0.00167 seconds (Sampling)\n",
      "Chain 1:                0.00716 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 1).\n",
      "Chain 1: \n",
      "Chain 1: Gradient evaluation took 0.000171 seconds\n",
      "Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.71 seconds.\n",
      "Chain 1: Adjust your expectations accordingly!\n",
      "Chain 1: \n",
      "Chain 1: \n",
      "Chain 1: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 1: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 1: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 1: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 1: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 1: \n",
      "Chain 1:  Elapsed Time: 0.574114 seconds (Warm-up)\n",
      "Chain 1:                0.126639 seconds (Sampling)\n",
      "Chain 1:                0.700753 seconds (Total)\n",
      "Chain 1: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 2).\n",
      "Chain 2: \n",
      "Chain 2: Gradient evaluation took 0.00011 seconds\n",
      "Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.1 seconds.\n",
      "Chain 2: Adjust your expectations accordingly!\n",
      "Chain 2: \n",
      "Chain 2: \n",
      "Chain 2: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 2: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 2: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 2: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 2: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 2: \n",
      "Chain 2:  Elapsed Time: 0.567018 seconds (Warm-up)\n",
      "Chain 2:                0.114958 seconds (Sampling)\n",
      "Chain 2:                0.681976 seconds (Total)\n",
      "Chain 2: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 3).\n",
      "Chain 3: \n",
      "Chain 3: Gradient evaluation took 0.0001 seconds\n",
      "Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1 seconds.\n",
      "Chain 3: Adjust your expectations accordingly!\n",
      "Chain 3: \n",
      "Chain 3: \n",
      "Chain 3: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 3: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 3: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 3: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 3: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 3: \n",
      "Chain 3:  Elapsed Time: 0.767447 seconds (Warm-up)\n",
      "Chain 3:                0.117967 seconds (Sampling)\n",
      "Chain 3:                0.885414 seconds (Total)\n",
      "Chain 3: \n",
      "\n",
      "SAMPLING FOR MODEL 'misreport' NOW (CHAIN 4).\n",
      "Chain 4: \n",
      "Chain 4: Gradient evaluation took 0.000118 seconds\n",
      "Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.18 seconds.\n",
      "Chain 4: Adjust your expectations accordingly!\n",
      "Chain 4: \n",
      "Chain 4: \n",
      "Chain 4: Iteration:   1 / 300 [  0%]  (Warmup)\n",
      "Chain 4: Iteration: 100 / 300 [ 33%]  (Warmup)\n",
      "Chain 4: Iteration: 151 / 300 [ 50%]  (Sampling)\n",
      "Chain 4: Iteration: 250 / 300 [ 83%]  (Sampling)\n",
      "Chain 4: Iteration: 300 / 300 [100%]  (Sampling)\n",
      "Chain 4: \n",
      "Chain 4:  Elapsed Time: 0.660254 seconds (Warm-up)\n",
      "Chain 4:                0.110862 seconds (Sampling)\n",
      "Chain 4:                0.771116 seconds (Total)\n",
      "Chain 4: \n",
      "   user  system elapsed \n",
      "  3.058   0.000   3.083 \n",
      "\n",
      "\n",
      "\n",
      "Inference for Stan model: misreport.\n",
      "4 chains, each with iter=300; warmup=150; thin=1; \n",
      "post-warmup draws per chain=150, total post-warmup draws=600.\n",
      "\n",
      "             mean se_mean    sd     10%     50%     90% n_eff  Rhat\n",
      "b[1]        0.892   0.001 0.033   0.849   0.892   0.935  1064 0.995\n",
      "b[2]       -0.405   0.001 0.032  -0.444  -0.407  -0.364   705 0.997\n",
      "b[3]       -0.210   0.001 0.035  -0.256  -0.209  -0.167   962 0.997\n",
      "b[4]       -0.028   0.002 0.036  -0.074  -0.029   0.014   567 0.996\n",
      "sd_r        0.172   0.001 0.027   0.141   0.169   0.206   510 0.999\n",
      "integrity   0.865   0.003 0.061   0.782   0.872   0.937   530 1.001\n",
      "rho         6.092   0.165 3.568   2.878   5.220  10.043   469 0.999\n",
      "alpha       1.820   0.036 0.983   0.856   1.595   3.102   731 0.995\n",
      "sigma       2.064   0.012 0.289   1.722   2.028   2.449   537 1.002\n",
      "ilogodds    1.970   0.025 0.562   1.275   1.921   2.703   497 1.000\n",
      "r_new[1]    1.503   0.008 0.185   1.270   1.502   1.729   586 1.003\n",
      "r_new[2]    1.889   0.008 0.202   1.640   1.896   2.134   613 1.000\n",
      "r_new[3]   -0.026   0.007 0.192  -0.274  -0.032   0.216   769 0.995\n",
      "lp__      -28.589   0.155 2.281 -31.762 -28.225 -26.006   215 1.020\n",
      "\n",
      "Samples were drawn using NUTS(diag_e) at Sun Apr  7 20:56:52 2019.\n",
      "For each parameter, n_eff is a crude measure of effective sample size,\n",
      "and Rhat is the potential scale reduction factor on split chains (at \n",
      "convergence, Rhat=1).\n",
      "[1] \"n_eff / iter looks reasonable for all parameters\"\n",
      "[1] \"Rhat looks reasonable for all parameters\"\n",
      "[1] \"0 of 600 iterations ended with a divergence (0%)\"\n",
      "[1] \"0 of 600 iterations saturated the maximum tree depth of 10 (0%)\"\n",
      "[1] \"E-BFMI indicated no pathological behavior\"\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Warning: RCall.jl: Warning: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.8 may help. See\n",
      "│ http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup\n",
      "│ Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See\n",
      "│ http://mc-stan.org/misc/warnings.html#bfmi-low\n",
      "│ Warning: Examine the pairs() plot to diagnose sampling problems\n",
      "│ \n",
      "└ @ RCall /home/jrun/.julia/packages/RCall/29zDq/src/io.jl:113\n"
     ]
    }
   ],
   "source": [
    "# 4 threads (1 core) time shown\n",
    "#   user  system elapsed \n",
    "#  2.511   0.000   2.528 \n",
    "#\n",
    "# 1 thread (1 core) time shown\n",
    "#   user  system elapsed \n",
    "#  2.287   0.007   2.321 \n",
    "#\n",
    "# 1 thread (2 cores - but ?Juliabox cannot start 2 workers, so take longer time) time shown\n",
    "#   user  system elapsed \n",
    "#  3.203   0.000   3.202\n",
    "#\n",
    "# 1 thread (1 core) time shown\n",
    "#   with cores = 2 in stan()\n",
    "# kernel simply died!!!\n",
    "\n",
    "R\"\"\"\n",
    "\n",
    ".libPaths(c(\"/mnt/juliabox/R_library\", .libPaths()))\n",
    "print(.libPaths())\n",
    "print(sessionInfo())\n",
    "\n",
    "library(magrittr)\n",
    "\n",
    "library(rstan)\n",
    "# The following can affect distributional computing over a cluster\n",
    "#options(mc.cores = 2)  # only 1 core on Juliabox; don't set more unless 2-core machine is launched\n",
    "\n",
    "source(\"/mnt/juliabox/JuliaBox_Sync/tryStan_2.R\")\n",
    "\"\"\";"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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