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Bug I'm running into using hddm v 0.5.5 running code at http://ski.clps.brown.edu/hddm_docs/tutorial_python.html
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hddm_debug.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Trying to debug problem\n",
"\n",
"URL for version 0.5.5 is https://github.com/hddm-devs/hddm/tree/v0.5.5"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/IPython/parallel.py:13: ShimWarning: The `IPython.parallel` package has been deprecated. You should import from ipyparallel instead.\n",
" \"You should import from ipyparallel instead.\", ShimWarning)\n"
]
}
],
"source": [
"import hddm"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"'0.5.5'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# version \n",
"hddm.__version__"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"I created the `test1.csv` by copying the lines show in http://ski.clps.brown.edu/hddm_docs/tutorial_python.html\n",
"\n",
"```\n",
"subj_idx,stim,rt,response,theta,dbs,conf\n",
"0,LL,1.21,1.0,0.65627512226100004,1,HC\n",
"0,WL,1.6299999999999999,1.0,-0.32788867166199998,1,LC\n",
"0,WW,1.03,1.0,-0.480284512399,1,HC\n",
"0,WL,2.77,1.0,1.9274273452399999,1,LC\n",
"0,WW,1.1399999999999999,0.0,-0.21323572605999999,1,HC\n",
"0,WL,1.1499999999999999,1.0,-0.43620365940099998,1,LC\n",
"0,LL,2.0,1.0,-0.27447891439400002,1,HC\n",
"0,WL,1.04,0.0,0.66695707371400004,1,LC\n",
"0,WW,0.85699999999999998,1.0,0.11861689909799999,1,HC\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# http://ski.clps.brown.edu/hddm_docs/tutorial_python.html\n",
"# test1.csv is \n",
"\n",
"data = hddm.load_csv('./test1.csv')"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>subj_idx</th>\n",
" <th>stim</th>\n",
" <th>rt</th>\n",
" <th>response</th>\n",
" <th>theta</th>\n",
" <th>dbs</th>\n",
" <th>conf</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>0</td>\n",
" <td>LL</td>\n",
" <td>1.210</td>\n",
" <td>1</td>\n",
" <td>0.656275</td>\n",
" <td>1</td>\n",
" <td>HC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>0</td>\n",
" <td>WL</td>\n",
" <td>1.630</td>\n",
" <td>1</td>\n",
" <td>-0.327889</td>\n",
" <td>1</td>\n",
" <td>LC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>0</td>\n",
" <td>WW</td>\n",
" <td>1.030</td>\n",
" <td>1</td>\n",
" <td>-0.480285</td>\n",
" <td>1</td>\n",
" <td>HC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>0</td>\n",
" <td>WL</td>\n",
" <td>2.770</td>\n",
" <td>1</td>\n",
" <td>1.927427</td>\n",
" <td>1</td>\n",
" <td>LC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>0</td>\n",
" <td>WW</td>\n",
" <td>1.140</td>\n",
" <td>0</td>\n",
" <td>-0.213236</td>\n",
" <td>1</td>\n",
" <td>HC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>0</td>\n",
" <td>WL</td>\n",
" <td>1.150</td>\n",
" <td>1</td>\n",
" <td>-0.436204</td>\n",
" <td>1</td>\n",
" <td>LC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>0</td>\n",
" <td>LL</td>\n",
" <td>2.000</td>\n",
" <td>1</td>\n",
" <td>-0.274479</td>\n",
" <td>1</td>\n",
" <td>HC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>0</td>\n",
" <td>WL</td>\n",
" <td>1.040</td>\n",
" <td>0</td>\n",
" <td>0.666957</td>\n",
" <td>1</td>\n",
" <td>LC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>0</td>\n",
" <td>WW</td>\n",
" <td>0.857</td>\n",
" <td>1</td>\n",
" <td>0.118617</td>\n",
" <td>1</td>\n",
" <td>HC</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" subj_idx stim rt response theta dbs conf\n",
"0 0 LL 1.210 1 0.656275 1 HC\n",
"1 0 WL 1.630 1 -0.327889 1 LC\n",
"2 0 WW 1.030 1 -0.480285 1 HC\n",
"3 0 WL 2.770 1 1.927427 1 LC\n",
"4 0 WW 1.140 0 -0.213236 1 HC\n",
"5 0 WL 1.150 1 -0.436204 1 LC\n",
"6 0 LL 2.000 1 -0.274479 1 HC\n",
"7 0 WL 1.040 0 0.666957 1 LC\n",
"8 0 WW 0.857 1 0.118617 1 HC"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "IndexError",
"evalue": "only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-5-ff1966694241>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mm\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhddm\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mHDDM\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/hddm/models/hddm_info.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m 111\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_informative\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'informative'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 113\u001b[0;31m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mHDDM\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 115\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_create_stochastic_knodes\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minclude\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/hddm/models/base.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, data, bias, include, wiener_params, p_outlier, **kwargs)\u001b[0m\n\u001b[1;32m 687\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwfpt_class\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhddm\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlikelihoods\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgenerate_wfpt_stochastic_class\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcdf_range\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcdf_range\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 688\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 689\u001b[0;31m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mHDDMBase\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 690\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 691\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m__getstate__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/hddm/models/base.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, data, **kwargs)\u001b[0m\n\u001b[1;32m 38\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstd_depends\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'std_depends'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 40\u001b[0;31m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mAccumulatorModel\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 41\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 42\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/kabuki/hierarchical.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, data, is_group_model, depends_on, trace_subjs, plot_subjs, plot_var, group_only_nodes)\u001b[0m\n\u001b[1;32m 346\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdb\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 347\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 348\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_setup_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 349\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 350\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_setup_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/kabuki/hierarchical.pyc\u001b[0m in \u001b[0;36m_setup_model\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 357\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 358\u001b[0m \u001b[0;31m# constructs pymc nodes etc and connects them appropriately\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 359\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcreate_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 360\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 361\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m__getstate__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/kabuki/hierarchical.pyc\u001b[0m in \u001b[0;36mcreate_model\u001b[0;34m(self, max_retries)\u001b[0m\n\u001b[1;32m 431\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mtries\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmax_retries\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 432\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 433\u001b[0;31m \u001b[0m_create\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 434\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mpm\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mZeroProbability\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 435\u001b[0m \u001b[0;32mcontinue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/kabuki/hierarchical.pyc\u001b[0m in \u001b[0;36m_create\u001b[0;34m()\u001b[0m\n\u001b[1;32m 427\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_create\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 428\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mknode\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mknodes\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 429\u001b[0;31m \u001b[0mknode\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcreate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 430\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 431\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mtries\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmax_retries\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/kabuki/hierarchical.pyc\u001b[0m in \u001b[0;36mcreate\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 166\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'doc'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnode_name\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 167\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 168\u001b[0;31m \u001b[0mnode\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcreate_node\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnode_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgrouped_data\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 169\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 170\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mnode\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/kabuki/hierarchical.pyc\u001b[0m in \u001b[0;36mcreate_node\u001b[0;34m(self, node_name, kwargs, data)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcreate_node\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnode_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 175\u001b[0m \u001b[0;31m#actually create the node\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 176\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpymc_node\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mnode_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 177\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 178\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcreate_tag_and_subj_idx\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0muniq_elem\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/pymc/distributions.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, *args, **kwds)\u001b[0m\n\u001b[1;32m 318\u001b[0m \u001b[0mlogp_partial_gradients\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlogp_partial_gradients\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 319\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 320\u001b[0;31m **arg_dict_out)\n\u001b[0m\u001b[1;32m 321\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 322\u001b[0m \u001b[0mnew_class\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/pymc/PyMCObjects.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, logp, doc, name, parents, random, trace, value, dtype, rseed, observed, cache_depth, plot, verbose, isdata, check_logp, logp_partial_gradients)\u001b[0m\n\u001b[1;32m 762\u001b[0m \u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 763\u001b[0m \u001b[0mplot\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mplot\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 764\u001b[0;31m verbose=verbose)\n\u001b[0m\u001b[1;32m 765\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 766\u001b[0m \u001b[0;31m# self._logp.force_compute()\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/pymc/Node.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, doc, name, parents, cache_depth, trace, dtype, plot, verbose)\u001b[0m\n\u001b[1;32m 212\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextended_children\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 213\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 214\u001b[0;31m \u001b[0mNode\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdoc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparents\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcache_depth\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mverbose\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mverbose\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 215\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 216\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdtype\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/pymc/Node.pyc\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, doc, name, parents, cache_depth, verbose)\u001b[0m\n\u001b[1;32m 127\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 128\u001b[0m \u001b[0;31m# Initialize\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 129\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparents\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparents\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 130\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 131\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_get_parents\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/pymc/Node.pyc\u001b[0m in \u001b[0;36m_set_parents\u001b[0;34m(self, new_parents)\u001b[0m\n\u001b[1;32m 145\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 146\u001b[0m \u001b[0;31m# Get new lazy function\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 147\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgen_lazy_function\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 148\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 149\u001b[0m parents = property(\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/pymc/PyMCObjects.pyc\u001b[0m in \u001b[0;36mgen_lazy_function\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 811\u001b[0m [self]),\n\u001b[1;32m 812\u001b[0m cache_depth=self._cache_depth)\n\u001b[0;32m--> 813\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_logp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mforce_compute\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 814\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 815\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_logp_partial_gradients\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32mLazyFunction.pyx\u001b[0m in \u001b[0;36mpymc.LazyFunction.LazyFunction.force_compute (pymc/LazyFunction.c:2409)\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/pymc/distributions.pyc\u001b[0m in \u001b[0;36mwrapper\u001b[0;34m(**kwds)\u001b[0m\n\u001b[1;32m 2979\u001b[0m \u001b[0;31m# Handle Pandas DataFrames\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2980\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'values'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2981\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2982\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2983\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0marguments\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/raymondyee/anaconda/envs/hddm_test/lib/python2.7/site-packages/hddm/likelihoods.pyc\u001b[0m in \u001b[0;36mwfpt_like\u001b[0;34m(x, v, sv, a, z, sz, t, st, p_outlier)\u001b[0m\n\u001b[1;32m 50\u001b[0m \u001b[0;31m#create likelihood function\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 51\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mwfpt_like\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mz\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msz\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mt\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mst\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mp_outlier\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 52\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mhddm\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwfpt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwiener_like\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'rt'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mz\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msz\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mt\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mst\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mp_outlier\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mp_outlier\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mwp\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 53\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mIndexError\u001b[0m: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices"
]
}
],
"source": [
"m = hddm.HDDM(data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
@rdhyee
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rdhyee commented Oct 26, 2015

reported at hddm-devs/hddm#37

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