From 313429aa203781128f6193b2200577d090d5358e Mon Sep 17 00:00:00 2001
From: Ben Gyori <ben.gyori@gmail.com>
Date: Fri, 7 Jul 2023 12:49:11 -0400
Subject: [PATCH] Fill in missing parameter declarations and values

---
 notebooks/hackathon_2023.07/scenario1.ipynb  | 14 ++++++++------
 notebooks/hackathon_2023.07/scenario1_a.json |  3 ++-
 notebooks/hackathon_2023.07/scenario1_c.json | 20 ++++++++++++++++++++
 notebooks/hackathon_2023.07/scenario1_d.json | 20 ++++++++++++++++++++
 4 files changed, 50 insertions(+), 7 deletions(-)

diff --git a/notebooks/hackathon_2023.07/scenario1.ipynb b/notebooks/hackathon_2023.07/scenario1.ipynb
index 99ac88fa5..6093c9e0e 100644
--- a/notebooks/hackathon_2023.07/scenario1.ipynb
+++ b/notebooks/hackathon_2023.07/scenario1.ipynb
@@ -60,7 +60,7 @@
     "    # D=11, gamma = 1/D, R_0 = 5 and\n",
     "    # beta = R_0 * gamma * mask(t) so kappa = 5/11\n",
     "    'kappa': Parameter(name='kappa', value=5/11),\n",
-    "    'k': Parameter(name='k')\n",
+    "    'k': Parameter(name='k', value=5.0)\n",
     "}\n",
     "\n",
     "initials = {\n",
@@ -136,10 +136,11 @@
    "outputs": [],
    "source": [
     "k_1, k_2, t_1, beta_nc = sympy.symbols('k_1 k_2 t_1 beta_nc')\n",
-    "parameters['k_1'] = Parameter(name='k_1')\n",
-    "parameters['k_2'] = Parameter(name='k_2')\n",
+    "parameters['k_1'] = Parameter(name='k_1', value=5.0)\n",
+    "parameters['k_2'] = Parameter(name='k_2', value=1.0)\n",
     "parameters['t_1'] = Parameter(name='t_1', value=154, units=day_units)\n",
     "parameters['beta_nc'] = Parameter(name='beta_nc', value=0.5)\n",
+    "tm.parameters = parameters\n",
     "m_2 = (beta_s - beta_c) / (1 + sympy.exp(-k_1*(t_0-t))) + (beta_c - beta_nc) / (1 + sympy.exp(-k_2*(t_1-t))) + beta_nc"
    ]
   },
@@ -179,7 +180,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "id": "b1c1abab",
    "metadata": {},
    "outputs": [],
@@ -198,13 +199,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "id": "6fab9358",
    "metadata": {},
    "outputs": [],
    "source": [
     "epsilon = sympy.Symbol('epsilon')\n",
     "parameters['epsilon'] = Parameter(name='epsilon', value=1/90)\n",
+    "tm.parameters = parameters\n",
     "t5 = NaturalConversion(subject=c['R'],\n",
     "                       outcome=c['S'],\n",
     "                       rate_law=epsilon*R)"
@@ -212,7 +214,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "id": "00c70176",
    "metadata": {},
    "outputs": [],
diff --git a/notebooks/hackathon_2023.07/scenario1_a.json b/notebooks/hackathon_2023.07/scenario1_a.json
index 48f08cf63..789a5c16c 100644
--- a/notebooks/hackathon_2023.07/scenario1_a.json
+++ b/notebooks/hackathon_2023.07/scenario1_a.json
@@ -190,7 +190,8 @@
      "value": 1.0
     },
     {
-     "id": "k"
+     "id": "k",
+     "value": 5.0
     },
     {
      "id": "kappa",
diff --git a/notebooks/hackathon_2023.07/scenario1_c.json b/notebooks/hackathon_2023.07/scenario1_c.json
index ac92a8268..9b53fa4b9 100644
--- a/notebooks/hackathon_2023.07/scenario1_c.json
+++ b/notebooks/hackathon_2023.07/scenario1_c.json
@@ -177,10 +177,22 @@
      "id": "beta_c",
      "value": 0.4
     },
+    {
+     "id": "beta_nc",
+     "value": 0.5
+    },
     {
      "id": "beta_s",
      "value": 1.0
     },
+    {
+     "id": "k_1",
+     "value": 5.0
+    },
+    {
+     "id": "k_2",
+     "value": 1.0
+    },
     {
      "id": "kappa",
      "value": 0.45454545454545453
@@ -189,6 +201,14 @@
      "id": "t_0",
      "value": 89.0
     },
+    {
+     "id": "t_1",
+     "value": 154.0,
+     "units": {
+      "expression": "day",
+      "expression_mathml": "<ci>day</ci>"
+     }
+    },
     {
      "id": "delta",
      "value": 0.2,
diff --git a/notebooks/hackathon_2023.07/scenario1_d.json b/notebooks/hackathon_2023.07/scenario1_d.json
index ac92a8268..9b53fa4b9 100644
--- a/notebooks/hackathon_2023.07/scenario1_d.json
+++ b/notebooks/hackathon_2023.07/scenario1_d.json
@@ -177,10 +177,22 @@
      "id": "beta_c",
      "value": 0.4
     },
+    {
+     "id": "beta_nc",
+     "value": 0.5
+    },
     {
      "id": "beta_s",
      "value": 1.0
     },
+    {
+     "id": "k_1",
+     "value": 5.0
+    },
+    {
+     "id": "k_2",
+     "value": 1.0
+    },
     {
      "id": "kappa",
      "value": 0.45454545454545453
@@ -189,6 +201,14 @@
      "id": "t_0",
      "value": 89.0
     },
+    {
+     "id": "t_1",
+     "value": 154.0,
+     "units": {
+      "expression": "day",
+      "expression_mathml": "<ci>day</ci>"
+     }
+    },
     {
      "id": "delta",
      "value": 0.2,