ENH: Use toy example instead of stan MCMC simulation

README.md

@@ -139,10 +139,8 @@ task workers complete records and become available.
 
 ```sh
 # From the command-line
-python2.7 -m pip install --user --upgrade pip
-python2.7 -m pip install --user --upgrade pystan
 module purge
-module load gcc/4.9.3		# Needed for pystan 2.19.0
+module load python/2.7.6-gcc-unicode
 cd ~/parallel-slurm/examples
 rm -rf joblog submit.out results/ results.csv
 for i in {1..5}; do sbatch 03-submit-param-sweep.slurm; done

examples/model.py

@@ -1,27 +1,80 @@
-# Example of Surgical institutional ranking from
-# http://www.openbugs.net/Examples/Surgical.html
-
+#!/usr/bin/env python
+"""Model fit example program."""
+import argparse
+import collections
+import itertools
 import os
+import time
+
+
+RESULTS_DIR = 'results'
+PARAMETERS = collections.OrderedDict((
+    ('x', [0.1 * i for i in range(1, 11)]),
+    ('y', [-0.1, 0.1]),
+    ('z', ['control', 'positive', 'negative'])))
+COMBINATIONS = list(itertools.product(*PARAMETERS.values()))
+
+
+def n_remaining():
+    """Return number of completed combinations."""
+    total = len(COMBINATIONS)
+    if not os.path.exists(RESULTS_DIR):
+        completed = 0
+    else:
+        completed = len([name
+                         for name in os.listdir(RESULTS_DIR)
+                         if os.path.isfile(os.path.join(RESULTS_DIR, name))])
+    return total - completed
+
+
+def run(index):
+    """Run example model fit."""
+    prefix = '{}: '.format(index)
+    record = collections.OrderedDict(
+        zip(PARAMETERS.keys(),
+            COMBINATIONS[index - 1]))
+    print(prefix + 'Fitting model to parameters: {} ...'.format(
+        ", ".join(["{} = {}".format(param, value)
+                   for param, value in record.items()])))
+    value = {'positive': 0.8, 'negative': 0.1, 'control': 0.3}
+    result = record['x'] ** record['y'] / value[record['z']]
+    time.sleep(1)
+    path_result = os.path.join(RESULTS_DIR, '{:02d}.dat'.format(index))
+    if not os.path.exists(RESULTS_DIR):
+        os.mkdir(RESULTS_DIR)
+    with open(path_result, 'w') as handle:
+        handle.writelines([str(result)])
+    print(prefix + '... done!  Saved result {:6.3f} to {}'.format(result, path_result))
+
+
+def parse_args():
+    """Parse command-line arguments."""
+    parser = argparse.ArgumentParser(
+        description='Model fit example program.')
+    parser.add_argument('--sim', action='store_true',
+                        help='Number of simulations to run')
+    parser.add_argument('--remaining', action='store_true',
+                        help='Remaining simulations to run')
+    parser.add_argument('indices', metavar='I', nargs='*', type=int,
+                        help='Model indices to run')
+    return parser
+
+
+def main(argv=None):
+    """Entry point for model.py"""
+    parser = parse_args()
+    args = parser.parse_args(argv)
+    if args.sim:
+        print(len(COMBINATIONS))
+        return
+    if args.remaining:
+        print(n_remaining())
+        return
+    if not args.indices:
+        parser.error('Need at least 1 index to run!')
+    for index in args.indices:
+        run(index)
+
 
-import pystan
-
-# This example considers mortality rates in 12 hospitals performing
-# cardiac surgery in babies. The data are shown below.
-#
-DATA = {
-    # Number of hospitals.
-    'N': 12,
-    # Number of operations.
-    'n': [ 47, 148, 119, 810, 211, 196, 148, 215, 207,  97, 256, 360],  # noqa: E201, E501
-    # Number of deaths.
-    'r': [  0,  18,   8,  46,   8,  13,   9,  31,  14,   8,  29,  24]   # noqa: E201, E501
-}
-
-if __name__ == "__main__":
-    # Disable threading.
-    os.environ['STAN_NUM_THREADS'] = "1"
-
-    fixed_effects = pystan.StanModel(file="model_indep.stan")
-    random_effects = pystan.StanModel(file="model_dep.stan")
-    burn_in = fixed_effects.sampling(data=DATA, warmup=1000, iter=0)
-    fit = random_effects.sampling(fit=burn_in, data=DATA, warmup=0, iter=10000)
+if __name__ == '__main__':
+    main()