Add post-hoc analysis

.gitignore

@@ -1,4 +1,5 @@
 *.svg
 *.pgf
 .ipynb_checkpoints
-rnaseq.csv
+rnaseq.csv
+ita91.csv

index.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Multinomial Splitting Models for Multivariate Count Data\n",
+    "# Splitting Models for Multivariate Count Data\n",
     "\n",
     "This **Jupyter** notebook lists all notebooks available to illustrate the modeling apporoach presented in the eponymous article.\n",
     "\n",
@@ -20,14 +20,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {
     "collapsed": true
    },
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ['FIGURE'] = 'svg'"
+    "os.environ['FIGURE'] = 'pgf'\n",
+    "figure = os.environ.get('FIGURE')"
    ]
   },
   {
@@ -42,33 +43,55 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "os.environ['DIMENSION'] = str(5)\n",
-    "os.environ['SIMULATIONS'] = str(10)\n",
-    "for alpha in [0.1, 1., 10., 100.]:\n",
+    "os.environ['SIMULATIONS'] = str(10000)\n",
+    "for alpha in [0.1, 1., 10., 100., 1000.]:\n",
     "    os.environ['ALPHA'] = str(alpha)\n",
-    "    for observation in [10, 100, 1000]:\n",
+    "    for observation in [10, 100, 1000, 10000]:\n",
     "        os.environ['OBSERVATIONS'] = str(observation)\n",
-    "        simulation = !jupyter nbconvert --ExecutePreprocessor.timeout=3600 --to notebook --execute misc/simulation.ipynb --output simulation.ipynb"
+    "        simulation = !jupyter nbconvert --ExecutePreprocessor.timeout=3600 --to notebook --execute misc/simulation.ipynb --output misc/simulation.ipynb"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "* By a [comparison](misc/comparison.ipynb) of multinomial splitting distributions to usual discrete multivariate distributions."
+    "Summaries of these simulations are presented in [post-hoc analyses](misc/post_hoc.ipynb)."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "post_hoc = !jupyter nbconvert --ExecutePreprocessor.timeout=3600 --to notebook --execute misc/post_hoc.ipynb --output misc/post_hoc.ipynb"
+   ]
+  },
+  {
+   "cell_type": "markdown",
    "metadata": {},
+   "source": [
+    "* By a [comparison](misc/comparison.ipynb) of multinomial splitting distributions to usual discrete multivariate distributions."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
-    "comparison = !jupyter nbconvert --to notebook misc/comparison.ipynb --output comparison.ipynb"
+    "comparison = !jupyter nbconvert --to notebook misc/comparison.ipynb --output misc/comparison.ipynb"
    ]
   },
   {
@@ -80,11 +103,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
-    "application = !jupyter nbconvert --to notebook miasc/application.ipynb --output application.ipynb"
+    "application = !jupyter nbconvert --to notebook misc/application.ipynb --output misc/application.ipynb"
    ]
   },
   {