Fill in missing parameter declarations and values

gyorilab · Jul 7, 2023 · 313429a · 313429a
1 parent 5c854e0
commit 313429a
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Showing 4 changed files with 50 additions and 7 deletions.
diff --git 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": [],
@@ -198,21 +199,22 @@
  },
  {
  "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)"
  ]
  },
  {
  "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
@@ -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
@@ -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
@@ -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,