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nwlandry committed Nov 21, 2021
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87 changes: 66 additions & 21 deletions demos/Library-Demo.ipynb
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Expand Up @@ -9,11 +9,11 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"from hypercontagion.Hypergraph import Hypergraph, HypergraphGenerator\n",
"import xgi\n",
"from hypercontagion.simulation.epidemics import *\n",
"import hypercontagion\n",
"import matplotlib.pyplot as plt\n",
Expand All @@ -35,18 +35,16 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"n = 100\n",
"parameters = [{\"degree-distribution\":\"power-law\",\"min-degree\":10,\"max-degree\":1000,\"hyperedge-size\":2,\"size\":n,\"is-correlated\":True,\"exponent\":3},{\"degree-distribution\":\"power-law\",\"min-degree\":10,\"max-degree\":1000,\"hyperedge-size\":3,\"size\":n,\"is-correlated\":True,\"exponent\":3}]\n",
"\n",
"h = HypergraphGenerator(parameters)\n",
"H = Hypergraph(h.getHyperedges())\n",
"m = 1000\n",
"test = [tuple(random.sample(range(n), k=random.choice([2, 3]))) for i in range(m)]\n",
"H = Hypergraph(test)"
"k1 = k1 = {i : random.randint(10, 30) for i in range(n)}\n",
"k2 = {i : sorted(k1.values())[i] for i in range(n)}\n",
"\n",
"H = xgi.chung_lu_hypergraph(k1, k2)"
]
},
{
Expand All @@ -68,13 +66,13 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"initial_size = 10\n",
"gamma = 0.01\n",
"tau = {2:0.01,3:0.01}"
"tau = {i: 0.01 for i in range(100)}"
]
},
{
Expand All @@ -88,9 +86,22 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"execution_count": 8,
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'Hypergraph' object has no attribute 'nodeLabels'",
"output_type": "error",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[1;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m~\\AppData\\Local\\Temp/ipykernel_928/3077490486.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mt1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mS1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mI1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mR1\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdiscrete_SIR\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mH\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtau\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mgamma\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmin\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmax\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m10\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdt\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m0.1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0minitial_infecteds\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mrange\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0minitial_size\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2\u001b[0m \u001b[0mt\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mS2\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mI2\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mR2\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mGillespie_SIR\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mH\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtau\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mgamma\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmin\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmax\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m10\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0minitial_infecteds\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mrange\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0minitial_size\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[1;31m#cProfile.run('discrete_SIR(H, tau, gamma, tmin=0, tmax=100, dt=0.1, rho=0.5)', sort=\"cumtime\")\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[1;31m#t, S2, I2, R2 = Gillespie_SIR(H, tau, gamma, tmin=0, tmax = 100, initial_infecteds = range(initial_size))\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32mc:\\users\\nicho\\documents\\github\\hypercontagion\\hypercontagion\\simulation\\epidemics.py\u001b[0m in \u001b[0;36mdiscrete_SIR\u001b[1;34m(H, tau, gamma, transmission_function, initial_infecteds, initial_recovereds, recovery_weight, transmission_weight, rho, tmin, tmax, dt, **args)\u001b[0m\n\u001b[0;32m 338\u001b[0m \u001b[0mR\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mR\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 339\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 340\u001b[1;33m \u001b[1;32mfor\u001b[0m \u001b[0mnode\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mH\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mnodeLabels\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 341\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mstatus\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mnode\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;34m\"I\"\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 342\u001b[0m \u001b[1;31m# heal\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mAttributeError\u001b[0m: 'Hypergraph' object has no attribute 'nodeLabels'"
]
}
],
"source": [
"t1, S1, I1, R1 = discrete_SIR(H, tau, gamma, tmin=0, tmax=10, dt=0.1, initial_infecteds = range(initial_size))\n",
"t, S2, I2, R2 = Gillespie_SIR(H, tau, gamma, tmin=0, tmax = 10, initial_infecteds = range(initial_size))\n",
Expand All @@ -107,9 +118,30 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"execution_count": 9,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 't' is not defined",
"output_type": "error",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m~\\AppData\\Local\\Temp/ipykernel_928/1764217710.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[1;31m# plt.plot(t1, I1/n, label=\"I (discrete)\")\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[1;31m# plt.plot(t1, R1/n, label=\"R (discrete)\")\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 5\u001b[1;33m \u001b[0mplt\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mt\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mS2\u001b[0m\u001b[1;33m/\u001b[0m\u001b[0mn\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mlabel\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"S (continuous)\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 6\u001b[0m \u001b[0mplt\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mt\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mI2\u001b[0m\u001b[1;33m/\u001b[0m\u001b[0mn\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mlabel\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"I (continuous)\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 7\u001b[0m \u001b[0mplt\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mt\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mR2\u001b[0m\u001b[1;33m/\u001b[0m\u001b[0mn\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mlabel\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"R (continuous)\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mNameError\u001b[0m: name 't' is not defined"
]
},
{
"data": {
"text/plain": [
"<Figure size 432x288 with 0 Axes>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"plt.figure()\n",
"# plt.plot(t1, S1/n, label=\"S (discrete)\")\n",
Expand All @@ -135,9 +167,22 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"execution_count": 10,
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'list' object has no attribute 'elements'",
"output_type": "error",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[1;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m~\\AppData\\Local\\Temp/ipykernel_928/1678647023.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mt1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mS1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mI1\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdiscrete_SIS\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mH\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtau\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mgamma\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmin\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmax\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m10\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdt\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0minitial_infecteds\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mrange\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0minitial_size\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2\u001b[0m \u001b[0mt\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mS2\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mI2\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mGillespie_SIS\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mH\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtau\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mgamma\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmin\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtmax\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m10\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0minitial_infecteds\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mrange\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0minitial_size\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32mc:\\users\\nicho\\documents\\github\\hypercontagion\\hypercontagion\\simulation\\epidemics.py\u001b[0m in \u001b[0;36mdiscrete_SIS\u001b[1;34m(H, tau, gamma, transmission_function, initial_infecteds, recovery_weight, transmission_weight, rho, tmin, tmax, dt, **args)\u001b[0m\n\u001b[0;32m 250\u001b[0m \u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mH\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0medges\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0medge\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 251\u001b[0m \u001b[1;33m]\u001b[0m \u001b[1;33m*\u001b[0m \u001b[0mtransmission_function\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 252\u001b[1;33m \u001b[0mstatus\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mH\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0medges\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0medge\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0melements\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdifference\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m{\u001b[0m\u001b[0mnode\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m**\u001b[0m\u001b[0margs\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 253\u001b[0m \u001b[1;33m)\u001b[0m \u001b[1;33m*\u001b[0m \u001b[0mdt\u001b[0m \u001b[1;33m*\u001b[0m \u001b[0medgeweight\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 254\u001b[0m \u001b[0medge\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mAttributeError\u001b[0m: 'list' object has no attribute 'elements'"
]
}
],
"source": [
"t1, S1, I1 = discrete_SIS(H, tau, gamma, tmin=0, tmax=10, dt=1, initial_infecteds = range(initial_size))\n",
"t, S2, I2 = Gillespie_SIS(H, tau, gamma, tmin=0, tmax = 10, initial_infecteds = range(initial_size))"
Expand Down Expand Up @@ -375,7 +420,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.4"
"version": "3.9.7"
}
},
"nbformat": 4,
Expand Down
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