Created
September 9, 2013 02:48
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{ | |
"metadata": { | |
"name": "" | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
{ | |
"cells": [ | |
{ | |
"cell_type": "code", | |
"collapsed": false, | |
"input": [ | |
"import pymc\n", | |
"with pymc.Model() as m1:\n", | |
" a1 = pymc.Normal('a1')\n", | |
" step = pymc.HamiltonianMC()" | |
], | |
"language": "python", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"ename": "NameError", | |
"evalue": "global name 'guess_scaling' is not defined", | |
"output_type": "pyerr", | |
"traceback": [ | |
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", | |
"\u001b[0;32m<ipython-input-1-84b25692bfd8>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mpymc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mModel\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mm1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0ma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpymc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mNormal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'a'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mstep\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpymc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mHamiltonianMC\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", | |
"\u001b[0;32m/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/step_methods/hmc.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, vars, scaling, step_scale, path_length, is_cov, step_rand, state, model)\u001b[0m\n\u001b[1;32m 53\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscaling\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdict\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 55\u001b[0;31m \u001b[0mscaling\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mguess_scaling\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mPoint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscaling\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 56\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 57\u001b[0m \u001b[0mn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mscaling\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
"\u001b[0;31mNameError\u001b[0m: global name 'guess_scaling' is not defined" | |
] | |
} | |
], | |
"prompt_number": 1 | |
}, | |
{ | |
"cell_type": "code", | |
"collapsed": false, | |
"input": [ | |
"from pymc import *\n", | |
"with Model() as m2:\n", | |
" a2 = Normal('a2')\n", | |
" step = HamiltonianMC()" | |
], | |
"language": "python", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"ename": "NameError", | |
"evalue": "global name 'guess_scaling' is not defined", | |
"output_type": "pyerr", | |
"traceback": [ | |
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", | |
"\u001b[0;32m<ipython-input-2-b7e235b1d0b8>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mModel\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mm2\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0ma2\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mNormal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'a2'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mstep\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mHamiltonianMC\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", | |
"\u001b[0;32m/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/step_methods/hmc.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, vars, scaling, step_scale, path_length, is_cov, step_rand, state, model)\u001b[0m\n\u001b[1;32m 53\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscaling\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdict\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 55\u001b[0;31m \u001b[0mscaling\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mguess_scaling\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mPoint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscaling\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmodel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 56\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 57\u001b[0m \u001b[0mn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mscaling\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
"\u001b[0;31mNameError\u001b[0m: global name 'guess_scaling' is not defined" | |
] | |
} | |
], | |
"prompt_number": 2 | |
}, | |
{ | |
"cell_type": "code", | |
"collapsed": false, | |
"input": [ | |
"with Model() as m3:\n", | |
" a3 = Normal('a3')\n", | |
" start = find_MAP()\n", | |
" h = guess_scaling(start)\n", | |
" step = HamiltonianMC(scaling=h)" | |
], | |
"language": "python", | |
"metadata": {}, | |
"outputs": [], | |
"prompt_number": 3 | |
} | |
], | |
"metadata": {} | |
} | |
] | |
} |
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