Fix gamma parameter

gyorilab · Jul 7, 2023 · c2d0e3d · c2d0e3d
1 parent e1822b8
commit c2d0e3d
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Showing 2 changed files with 21 additions and 11 deletions.
diff --git a/notebooks/hackathon_2023.07/scenario2.ipynb b/notebooks/hackathon_2023.07/scenario2.ipynb
@@ -28,7 +28,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 10,
+ "execution_count": 18,
  "id": "0991209a",
  "metadata": {},
  "outputs": [
@@ -38,7 +38,7 @@
  "'\\nS = y(ind); ind=ind+1; % original susceptible\\nSVR = y(ind); ind=ind+1; % lost immunity after vaccination or recovery\\nV1 = y(ind:ind+n_vax-1); ind=ind+n_vax; % one-dose vaccination\\nV2 = y(ind:ind+n_vax-1); ind=ind+n_vax; % fully vaccinated\\nI = y(ind:ind+n_var-1); ind=ind+n_var; % infected\\nIV = y(ind:ind+n_var-1); ind=ind+n_var; % infected even with vaccination\\nIR = y(ind:ind+n_var-1); ind=ind+n_var; % infected again after recovery from a different variant\\nA = y(ind:ind+n_var-1); ind=ind+n_var; % asymptomatic infections\\nAR = y(ind:ind+n_var-1); ind=ind+n_var; % asymptomatic infections after recovery from a different variant\\nR = y(ind:ind+n_var-1); ind=ind+n_var; % recovered\\nR2 = y(ind); ind=ind+1; % recovered after getting both variants\\n\\n\\n'"
  ]
  },
- "execution_count": 10,
+ "execution_count": 18,
  "metadata": {},
  "output_type": "execute_result"
  }
@@ -68,7 +68,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 11,
+ "execution_count": 19,
  "id": "716217a7",
  "metadata": {},
  "outputs": [],
@@ -90,7 +90,7 @@
  " Parameter(name='beta_v2', value=0.05*3.3e-9),\n",
  " Parameter(name='beta_R', value=0.05*3.3e-9),\n",
  " Parameter(name='gamma', value=1/28),\n",
- " Parameter(name='mu', value=298.7),\n",
+ " Parameter(name='mu', value=109019/(14570000*365)),\n",
  " Parameter(name='mu_I', value=0.001),\n",
  " Parameter(name='mu_IV', value=0.15*0.001),\n",
  " Parameter(name='nu_R', value=1/(4*365)),\n",
@@ -119,7 +119,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 12,
+ "execution_count": 20,
  "id": "f91e5e06",
  "metadata": {},
  "outputs": [],
@@ -129,7 +129,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 13,
+ "execution_count": 21,
  "id": "45045c21",
  "metadata": {},
  "outputs": [],
@@ -140,7 +140,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 14,
+ "execution_count": 22,
  "id": "563bef26",
  "metadata": {},
  "outputs": [],
@@ -250,16 +250,26 @@
  },
  {
  "cell_type": "code",
- "execution_count": null,
+ "execution_count": 23,
  "id": "25dfad3d",
  "metadata": {},
  "outputs": [],
  "source": [
- "tm = TemplateModel(templates=templates\n",
+ "tm = TemplateModel(templates=templates,\n",
  " parameters={p.name: p for p in parameters},\n",
- " initial_conditions=initials,\n",
+ " initial_conditions=initials)\n",
+ "tm = simplify_rate_laws(tm)\n",
+ "tm.annotations= Annotations(name=\"Scenario 2a\")\n",
  "AskeNetPetriNetModel(Model(tm)).to_json_file('scenario2_a.json')"
  ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "34c423df",
+ "metadata": {},
+ "outputs": [],
+ "source": []
  }
  ],
  "metadata": {

diff --git a/notebooks/hackathon_2023.07/scenario2_a.json b/notebooks/hackathon_2023.07/scenario2_a.json
@@ -1346,7 +1346,7 @@
  },
  {
  "id": "mu",
- "value": 298.7
+ "value": 2.049980726017995e-05
  },
  {
  "id": "mu_I",