rerunned notebooks

53134a62 · dcoudrin · 79f3db54 · 53134a62 · 53134a62 · 53134a62
Commit 53134a62 authored Apr 25, 2018 by dcoudrin
--- a/library/examples/MPCE/clock.ipynb
+++ b/library/examples/MPCE/clock.ipynb
--- a/library/examples/MPRI/TD1_lotka_volterra.ipynb
+++ b/library/examples/MPRI/TD1_lotka_volterra.ipynb
--- a/library/examples/pac_learning_cmsb_2017/Lotka-Volterra.ipynb
+++ b/library/examples/pac_learning_cmsb_2017/Lotka-Volterra.ipynb
@@ -2,25 +2,16 @@
 "cells": [
  {
   "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 1,
   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Cannot read (library:examples/lotka_volterra/LVi.bc)"
-      ]
-     },
-     "execution_count": 7,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": []
+   "outputs": [],
+   "source": [
+    "load(library:examples/lotka_volterra/LVi.bc)."
+   ]
  },
  {
   "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
@@ -39,7 +30,7 @@
       ").\r\n"
      ]
     },
-     "execution_count": 6,
+     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
@@ -52,13 +43,7 @@
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": []
-    }
-   ],
+   "outputs": [],
   "source": [
    "clear_model."
   ]
@@ -69,24 +54,27 @@
   "metadata": {},
   "outputs": [
    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "% Maxmimum K used: 1\r\n",
-      "% minimum number of samples for h=1: 18\r\n",
-      "\r\n",
-      "% 1 samples (max h ~ 0.05555555555555555)\r\n",
-      "P / R -< P\r\n",
-      "\r\n",
-      "% 0 samples (max h ~ 0)\r\n",
-      "% _ -> P\r\n",
-      "\r\n",
-      "% 1 samples (max h ~ 0.05555555555555555)\r\n",
-      "P,R -< R\r\n",
-      "\r\n",
-      "% 0 samples (max h ~ 0)\r\n",
-      "% _ -> R\r\n"
-     ]
+     "data": {
+      "text/plain": [
+       "% Maxmimum K used: 1\r\n",
+       "% minimum number of samples for h=1: 18\r\n",
+       "\r\n",
+       "% 1 samples (max h ~ 0.05555555555555555)\r\n",
+       "P / R -< P\r\n",
+       "\r\n",
+       "% 0 samples (max h ~ 0)\r\n",
+       "% _ -> P\r\n",
+       "\r\n",
+       "% 0 samples (max h ~ 0)\r\n",
+       "% _ -< R\r\n",
+       "\r\n",
+       "% 0 samples (max h ~ 0)\r\n",
+       "% _ -> R\r\n"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
    }
   ],
   "source": [
@@ -95,28 +83,31 @@
  },
  {
   "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "% Maxmimum K used: 1\r\n",
-      "% minimum number of samples for h=1: 18\r\n",
-      "\r\n",
-      "% 10 samples (max h ~ 0.5555555555555556)\r\n",
-      "P -< P\r\n",
-      "\r\n",
-      "% 0 samples (max h ~ 0)\r\n",
-      "% _ -> P\r\n",
-      "\r\n",
-      "% 2 samples (max h ~ 0.1111111111111111)\r\n",
-      "P,R -< R\r\n",
-      "\r\n",
-      "% 0 samples (max h ~ 0)\r\n",
-      "% _ -> R\r\n"
-     ]
+     "data": {
+      "text/plain": [
+       "% Maxmimum K used: 1\r\n",
+       "% minimum number of samples for h=1: 18\r\n",
+       "\r\n",
+       "% 10 samples (max h ~ 0.5555555555555556)\r\n",
+       "P -< P\r\n",
+       "\r\n",
+       "% 0 samples (max h ~ 0)\r\n",
+       "% _ -> P\r\n",
+       "\r\n",
+       "% 1 samples (max h ~ 0.05555555555555555)\r\n",
+       "P,R -< R\r\n",
+       "\r\n",
+       "% 0 samples (max h ~ 0)\r\n",
+       "% _ -> R\r\n"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
    }
   ],
   "source": [
@@ -125,28 +116,31 @@
  },
  {
   "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "% Maxmimum K used: 1\r\n",
-      "% minimum number of samples for h=1: 18\r\n",
-      "\r\n",
-      "% 18 samples (max h ~ 1)\r\n",
-      "P -< P\r\n",
-      "\r\n",
-      "% 2 samples (max h ~ 0.1111111111111111)\r\n",
-      "P,R -> P\r\n",
-      "\r\n",
-      "% 5 samples (max h ~ 0.2777777777777778)\r\n",
-      "P,R -< R\r\n",
-      "\r\n",
-      "% 15 samples (max h ~ 0.8333333333333334)\r\n",
-      "R -> R\r\n"
-     ]
+     "data": {
+      "text/plain": [
+       "% Maxmimum K used: 1\r\n",
+       "% minimum number of samples for h=1: 18\r\n",
+       "\r\n",
+       "% 17 samples (max h ~ 0.9444444444444444)\r\n",
+       "P -< P\r\n",
+       "\r\n",
+       "% 3 samples (max h ~ 0.16666666666666666)\r\n",
+       "P,R -> P\r\n",
+       "\r\n",
+       "% 2 samples (max h ~ 0.1111111111111111)\r\n",
+       "P,R -< R\r\n",
+       "\r\n",
+       "% 20 samples (max h ~ 1.1111111111111112)\r\n",
+       "R -> R\r\n"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
    }
   ],
   "source": [
@@ -156,9 +150,7 @@
  {
   "cell_type": "code",
   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
   "outputs": [],
   "source": []
  }
@@ -175,6 +167,13 @@
   "mimetype": "text/plain",
   "name": "biocham",
   "pygments_lexer": "prolog"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
  }
 },
 "nbformat": 4,

 %% Cell type:code id: tags:

 ``` 
+load(library:examples/lotka_volterra/LVi.bc).
 ```

-%% Output
-
-    Cannot read (library:examples/lotka_volterra/LVi.bc)
-
 %% Cell type:code id: tags:

 ``` 
 list_model.
 ```

 %% Output

    k1*R*P for R,P -< R.
    k1*R*P for R,P -> P.
    k2*R for R -> R.
    k3*P for P -< P.
    present(R).
    present(P).
    parameter(
      k1 = 2,
      k2 = 2,
      k3 = 1
    ).

 %% Cell type:code id: tags:

 ``` 
 clear_model.
 ```

-%% Output
-
-
 %% Cell type:code id: tags:

 ``` 
 pac_learning(library:examples/lotka_volterra/LVi.bc, 1, 50, boolean_simulation: yes).
 ```

 %% Output

    % Maxmimum K used: 1
    % minimum number of samples for h=1: 18
    
    % 1 samples (max h ~ 0.05555555555555555)
    P / R -< P
    
    % 0 samples (max h ~ 0)
    % _ -> P
    
-    % 1 samples (max h ~ 0.05555555555555555)
-    P,R -< R
+    % 0 samples (max h ~ 0)
+    % _ -< R
    
    % 0 samples (max h ~ 0)
    % _ -> R

 %% Cell type:code id: tags:

 ``` 
 pac_learning(library:examples/lotka_volterra/LVi.bc, 25, 2, boolean_simulation: yes).
 ```

 %% Output

    % Maxmimum K used: 1
    % minimum number of samples for h=1: 18
    
    % 10 samples (max h ~ 0.5555555555555556)
    P -< P
    
    % 0 samples (max h ~ 0)
    % _ -> P
    
-    % 2 samples (max h ~ 0.1111111111111111)
+    % 1 samples (max h ~ 0.05555555555555555)
    P,R -< R
    
    % 0 samples (max h ~ 0)
    % _ -> R

 %% Cell type:code id: tags:

 ``` 
 pac_learning(library:examples/lotka_volterra/LVi.bc, 50, 1).
 ```

 %% Output

    % Maxmimum K used: 1
    % minimum number of samples for h=1: 18
    
-    % 18 samples (max h ~ 1)
+    % 17 samples (max h ~ 0.9444444444444444)
    P -< P
    
-    % 2 samples (max h ~ 0.1111111111111111)
+    % 3 samples (max h ~ 0.16666666666666666)
    P,R -> P
    
-    % 5 samples (max h ~ 0.2777777777777778)
+    % 2 samples (max h ~ 0.1111111111111111)
    P,R -< R
    
-    % 15 samples (max h ~ 0.8333333333333334)
+    % 20 samples (max h ~ 1.1111111111111112)
    R -> R

 %% Cell type:code id: tags:

 ``` 
 ```