{ "nbformat": 4, "nbformat_minor": 0, "metadata": { "colab": { "name": "Sweden", "provenance": [], "collapsed_sections": [], "toc_visible": true }, "kernelspec": { "display_name": "Python 3", "name": "python3" } }, "cells": [ { "cell_type": "markdown", "metadata": { "id": "AJX1jgLnX70s" }, "source": [ "# Epidemiology model\n", "\n", "https://nbviewer.jupyter.org/github/pyro-ppl/pyro/blob/sir-tutorial-ii/tutorial/source/epi_regional.ipynb?fbclid=IwAR3Gv8tLuiEjOmZh7-NQUa_ggm_QUqtSc5TxRZ0_pSxVA7Y3lWWzSFGKjrA \n" ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "z6UoAzRe1pMh", "outputId": "bbe41141-6c17-4505-c204-d9a68a80c1a5" }, "source": [ "!git clone https://github.com/pyro-ppl/pyro.git" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "fatal: destination path 'pyro' already exists and is not an empty directory.\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "ryMxWMvbD8Nc", "outputId": "436e3f6a-bbbf-4f7b-e708-0e4c3b5c5b8f" }, "source": [ "%cd /content/pyro\n" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "/content/pyro\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "w8MT-jR48mLX", "outputId": "60661038-82b2-434e-c9f8-b708b3e38662" }, "source": [ "!pip install .[extras]" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "Processing /content/pyro\n", "Requirement already satisfied: numpy>=1.7 in /usr/local/lib/python3.7/dist-packages (from pyro-ppl==1.6.0+c340831b) (1.19.5)\n", "Requirement already satisfied: opt_einsum>=2.3.2 in /usr/local/lib/python3.7/dist-packages (from pyro-ppl==1.6.0+c340831b) (3.3.0)\n", "Requirement already satisfied: pyro-api>=0.1.1 in /usr/local/lib/python3.7/dist-packages (from pyro-ppl==1.6.0+c340831b) (0.1.2)\n", "Requirement already 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packages: pyro-ppl\n", " Building wheel for pyro-ppl (setup.py) ... \u001b[?25l\u001b[?25hdone\n", " Created wheel for pyro-ppl: filename=pyro_ppl-1.6.0+c340831b-cp37-none-any.whl size=657943 sha256=d9082525b2e2c070c2437bcd5581d12dba5dadb74811b959a37b813622d4fe8d\n", " Stored in directory: /tmp/pip-ephem-wheel-cache-ba3b3xge/wheels/7f/c8/0f/f4e71d6e55e68c8a64c8382f3f6eb829e6aa18323499202e37\n", "Successfully built pyro-ppl\n", "Installing collected packages: pyro-ppl\n", " Found existing installation: pyro-ppl 1.6.0+c340831b\n", " Uninstalling pyro-ppl-1.6.0+c340831b:\n", " Successfully uninstalled pyro-ppl-1.6.0+c340831b\n", "Successfully installed pyro-ppl-1.6.0+c340831b\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "id": "7AUI1jmXcX4u" }, "source": [ "import os\n", "import logging\n", "import urllib.request\n", "from collections import OrderedDict\n", "\n", "import pandas as pd\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "import seaborn as sns\n", "import torch\n", "import pyro\n", "import pyro.distributions as dist\n", "from pyro.contrib.epidemiology import CompartmentalModel, binomial_dist, infection_dist\n", "from pyro.ops.tensor_utils import convolve\n", "\n", "%matplotlib inline\n", "pyro.enable_validation(True) \n", "torch.set_default_dtype(torch.double) \n" ], "execution_count": null, "outputs": [] }, { "cell_type": "markdown", "metadata": { "id": "hzpnb36feNgS" }, "source": [ " ## Model without Policies\n", " " ] }, { "cell_type": "code", "metadata": { "id": "bsaJcjx6xVLo" }, "source": [ "class CovidModel(CompartmentalModel):\n", " def __init__(self, population, new_cases, new_recovered, new_deaths):\n", " '''\n", " population (int) – Total population = S + E + I + R.\n", " '''\n", " assert len(new_cases) == len(new_recovered) == len(new_deaths)\n", "\n", " compartments = (\"S\", \"E\", \"I\", \"D\") # R is implicit.\n", " duration = len(new_cases)\n", " super().__init__(compartments, duration, population)\n", "\n", " self.new_cases = new_cases\n", " self.new_deaths = new_deaths\n", " self.new_recovered = new_recovered\n", " \n", "\n", " def global_model(self):\n", " tau_i = pyro.sample(\"rec_time\", dist.Normal(15.0, 3.0))\n", " tau_e = pyro.sample(\"incub_time\", dist.Normal(5.0, 1.0))\n", " # R0 = pyro.sample(\"R0\", dist.LogNormal(0., 1.))\n", " R0 = pyro.sample(\"R0\", dist.Normal(2.5, 0.5))\n", " rho = pyro.sample(\"rho\", dist.Beta(10, 10)) # About 50% response rate.\n", " mort_rate = pyro.sample(\"mort_rate\", dist.Beta(2, 50)) # About 2% mortality rate.\n", " rec_rate = pyro.sample(\"rec_rate\",dist.Beta(10, 10)) # About 50% recovery rate.\n", " return R0, tau_e, tau_i, rho, mort_rate, rec_rate\n", "\n", " def initialize(self, params):\n", " # Start with a single infection.\n", " return {\"S\": self.population - 1, \"E\": 0, \"I\": 1, \"D\": 0}\n", "\n", " def transition(self, params, state, t):\n", " R0, tau_e, tau_i, rho, mort_rate, rec_rate = params\n", "\n", " # Sample flows between compartments.\n", " S2E = pyro.sample(\"S2E_{}\".format(t),\n", " infection_dist(individual_rate=R0 / tau_i,\n", " num_susceptible=state[\"S\"],\n", " num_infectious=state[\"I\"],\n", " population=self.population))\n", " E2I = pyro.sample(\"E2I_{}\".format(t),\n", " binomial_dist(state[\"E\"], 1 / tau_e )) \n", " I2R = pyro.sample(\"I2R_{}\".format(t),\n", " binomial_dist(state[\"I\"], 1 / tau_i))\n", " I2D = pyro.sample(\"I2D_{}\".format(t),\n", " binomial_dist(state[\"I\"], mort_rate / tau_i))\n", "\n", " # Update compartments with flows.\n", " state[\"S\"] = state[\"S\"] - S2E \n", " state[\"E\"] = state[\"E\"] + S2E - E2I\n", " state[\"I\"] = state[\"I\"] + E2I - I2R - I2D\n", " state[\"D\"] = state[\"D\"] + I2D\n", "\n", " # Condition on observations.\n", " t_is_observed = isinstance(t, slice) or t < self.duration\n", " pyro.sample(\"new_cases_{}\".format(t),\n", " binomial_dist(S2E, rho),\n", " obs=self.new_cases[t] if t_is_observed else None)\n", " pyro.sample(\"new_deaths_{}\".format(t),\n", " binomial_dist(I2D, 1),\n", " obs=self.new_deaths[t] if t_is_observed else None)\n", " pyro.sample(\"new_recovered_{}\".format(t),\n", " binomial_dist(I2R, rho),\n", " obs=self.new_recovered[t] if t_is_observed else None)\n", " \n", " def compute_flows(self, prev, curr, t):\n", " S2E = prev[\"S\"] - curr[\"S\"] # S can only go to E.\n", " I2D = curr[\"D\"] - prev[\"D\"] # D can only have come from I.\n", " # We deduce the remaining flows by conservation of mass:\n", " # curr - prev = inflows - outflows\n", " E2I = prev[\"E\"] - curr[\"E\"] + S2E\n", " I2R = prev[\"I\"] - curr[\"I\"] + E2I - I2D\n", " return {\n", " \"S2E_{}\".format(t): S2E,\n", " \"E2I_{}\".format(t): E2I,\n", " \"I2D_{}\".format(t): I2D,\n", " \"I2R_{}\".format(t): I2R,\n", " }" ], "execution_count": null, "outputs": [] }, { "cell_type": "markdown", "metadata": { "id": "kgKCZvRfMi_3" }, "source": [ "## Create Country" ] }, { "cell_type": "code", "metadata": { "id": "koX5yGHrsuib" }, "source": [ "# function to make the time series of confirmed and daily confirmed cases for a specific country\n", "def create_country (country, start_date, end_date, state = False) : \n", "\n", " url = 'https://raw.githubusercontent.com/assemzh/ProbProg-COVID-19/master/full_grouped.csv'\n", " data = pd.read_csv(url)\n", "\n", " data.Date = pd.to_datetime(data.Date)\n", "\n", " if state :\n", " df = data.loc[data[\"Province/State\"] == country, [\"Province/State\", \"Date\", \"Confirmed\", \"Deaths\", \"Recovered\", \"Active\", \"New cases\", \"New deaths\", \"New recovered\"]]\n", " else : \n", " df = data.loc[data[\"Country/Region\"] == country, [\"Country/Region\", \"Date\", \"Confirmed\", \"Deaths\", \"Recovered\", \"Active\", \"New cases\", \"New deaths\", \"New recovered\"]]\n", " df.columns = [\"country\", \"date\", \"confirmed\", \"deaths\", \"recovered\", \"active\", \"new_cases\", \"new_deaths\", \"new_recovered\"]\n", "\n", " # group by country and date\n", " df = df.groupby(['country','date'])['confirmed', 'deaths', 'recovered',\"active\", \"new_cases\", \"new_deaths\", \"new_recovered\"].sum().reset_index()\n", "\n", " # convert date string to datetime\n", " df.date = pd.to_datetime(df.date)\n", " df = df.sort_values(by = \"date\")\n", " df = df[df.date >= start_date]\n", " df = df[df.date <= end_date]\n", "\n", " active = df['active'].tolist()\n", " recovered = df['recovered'].tolist()\n", " deaths = df['deaths'].tolist()\n", " new_cases = df['new_cases'].tolist()\n", " new_recovered = df['new_recovered'].tolist()\n", " new_deaths = df['new_deaths'].tolist()\n", " \n", " active = torch.tensor(list(map(float, active))).view(len(active),1) \n", " recovered = torch.tensor(list(map(float, recovered))).view(len(recovered),1) \n", " deaths = torch.tensor(list(map(float, deaths))).view(len(deaths),1) \n", " new_cases = torch.tensor(list(map(float, new_cases))).view(len(new_cases),1) \n", " new_recovered = torch.tensor(list(map(float, new_recovered))).view(len(new_recovered),1) \n", " new_deaths = torch.tensor(list(map(float, new_deaths))).view(len(new_deaths),1) \n", "\n", "\n", " return_data = {\n", " 'active':active,\n", " 'recovered':recovered,\n", " 'deaths':deaths,\n", " 'new_cases':new_cases,\n", " 'new_recovered': new_recovered,\n", " 'new_deaths':new_deaths }\n", " \n", " return return_data\n" ], "execution_count": null, "outputs": [] }, { "cell_type": "markdown", "metadata": { "id": "nxRxbNr8zt3O" }, "source": [ "## Get data for countries\n" ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "V4O6XUbM9Ff3", "outputId": "bae83a68-aef8-44b0-a7a4-126e0fa81a99" }, "source": [ "Japan = create_country(\"Japan\", start_date = \"2020-02-01\", end_date = \"2020-04-01\")\n", "Sweden = create_country(\"Sweden\", start_date = \"2020-02-01\", end_date = \"2020-04-01\")\n" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "/usr/local/lib/python3.7/dist-packages/ipykernel_launcher.py:16: FutureWarning: Indexing with multiple keys (implicitly converted to a tuple of keys) will be deprecated, use a list instead.\n", " app.launch_new_instance()\n" ], "name": "stderr" } ] }, { "cell_type": "markdown", "metadata": { "id": "XTUPDWD9e_9o" }, "source": [ "##Train the model using MCMC.\n", "\n" ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "wE7Jen8XfB62", "outputId": "6a459604-03fc-49b1-eaba-3082df7141aa" }, "source": [ "%%time\n", "Sweden_model = CovidModel(10230000, Sweden[\"new_cases\"], Sweden[\"new_recovered\"], Sweden[\"new_deaths\"] )\n", "pyro.set_rng_seed(20210521)\n", "Sweden_mcmc = Sweden_model.fit_mcmc(num_samples=500, warmup_steps = 200)\n", "Sweden_mcmc.summary()" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "INFO \t Running inference...\n", "Warmup: 0%| | 0/700 [00:00, ?it/s]INFO \t Heuristic init: R0=2.77, incub_time=6.2, mort_rate=0.0282, rec_rate=0.465, rec_time=16.4, rho=0.248\n", "Sample: 100%|██████████| 700/700 [00:49, 14.03it/s, step size=7.64e-05, acc. prob=0.720]\n" ], "name": "stderr" }, { "output_type": "stream", "text": [ "\n", " mean std median 5.0% 95.0% n_eff r_hat\n", " R0 2.77 0.00 2.77 2.77 2.77 12.46 1.01\n", " auxiliary[0,0] 10229991.22 0.00 10229991.22 10229991.22 10229991.22 5.34 1.41\n", " auxiliary[0,1] 10229983.34 0.00 10229983.34 10229983.34 10229983.34 3.00 2.03\n", " auxiliary[0,2] 10229974.97 0.00 10229974.97 10229974.97 10229974.97 2.80 2.54\n", " auxiliary[0,3] 10229966.19 0.00 10229966.19 10229966.19 10229966.19 7.19 1.33\n", " auxiliary[0,4] 10229957.06 0.00 10229957.06 10229957.06 10229957.07 2.59 2.66\n", " auxiliary[0,5] 10229947.77 0.00 10229947.77 10229947.77 10229947.77 9.10 1.09\n", " auxiliary[0,6] 10229938.37 0.00 10229938.37 10229938.36 10229938.37 2.74 2.15\n", " auxiliary[0,7] 10229928.89 0.00 10229928.89 10229928.89 10229928.89 3.56 1.55\n", " auxiliary[0,8] 10229950.86 0.00 10229950.86 10229950.86 10229950.86 3.40 1.73\n", " auxiliary[0,9] 10229941.07 0.00 10229941.07 10229941.07 10229941.07 3.91 1.64\n", "auxiliary[0,10] 10229931.08 0.00 10229931.08 10229931.07 10229931.08 2.50 3.05\n", "auxiliary[0,11] 10229920.97 0.00 10229920.97 10229920.96 10229920.97 2.70 2.33\n", "auxiliary[0,12] 10229910.77 0.00 10229910.77 10229910.77 10229910.77 6.54 1.06\n", "auxiliary[0,13] 10229900.50 0.00 10229900.50 10229900.50 10229900.50 3.58 1.41\n", "auxiliary[0,14] 10229890.17 0.00 10229890.17 10229890.17 10229890.17 5.88 1.06\n", "auxiliary[0,15] 10229879.80 0.00 10229879.80 10229879.79 10229879.80 3.40 1.58\n", "auxiliary[0,16] 10229869.35 0.01 10229869.35 10229869.35 10229869.37 3.10 1.90\n", "auxiliary[0,17] 10229858.92 0.00 10229858.92 10229858.92 10229858.92 5.27 1.29\n", "auxiliary[0,18] 10229848.41 0.02 10229848.41 10229848.38 10229848.43 2.51 2.72\n", "auxiliary[0,19] 10229848.01 0.02 10229848.01 10229847.98 10229848.03 2.52 2.68\n", "auxiliary[0,20] 10229836.65 0.03 10229836.65 10229836.60 10229836.69 2.67 2.36\n", "auxiliary[0,21] 10229824.48 0.03 10229824.49 10229824.43 10229824.54 2.61 2.50\n", "auxiliary[0,22] 10229811.45 0.03 10229811.45 10229811.40 10229811.49 2.67 2.41\n", "auxiliary[0,23] 10229797.37 0.03 10229797.37 10229797.33 10229797.42 2.68 2.35\n", "auxiliary[0,24] 10229782.24 0.03 10229782.24 10229782.19 10229782.29 2.56 2.56\n", "auxiliary[0,25] 10229765.94 0.03 10229765.94 10229765.89 10229765.98 2.80 2.22\n", "auxiliary[0,26] 10229748.36 0.04 10229748.37 10229748.31 10229748.42 2.63 2.47\n", "auxiliary[0,27] 10229729.43 0.03 10229729.44 10229729.38 10229729.48 2.65 2.45\n", "auxiliary[0,28] 10229708.98 0.04 10229708.99 10229708.92 10229709.03 2.63 2.47\n", "auxiliary[0,29] 10229686.85 0.03 10229686.85 10229686.81 10229686.91 2.67 2.42\n", "auxiliary[0,30] 10229662.82 0.04 10229662.83 10229662.75 10229662.88 2.47 2.83\n", "auxiliary[0,31] 10229636.78 0.04 10229636.79 10229636.72 10229636.83 2.82 2.20\n", "auxiliary[0,32] 10229608.69 0.03 10229608.68 10229608.64 10229608.74 2.74 2.22\n", "auxiliary[0,33] 10229577.72 0.04 10229577.74 10229577.66 10229577.76 2.50 2.66\n", "auxiliary[0,34] 10229543.97 0.04 10229543.98 10229543.92 10229544.04 2.76 2.30\n", "auxiliary[0,35] 10229506.91 0.04 10229506.90 10229506.86 10229506.96 2.53 2.86\n", "auxiliary[0,36] 10229466.13 0.03 10229466.13 10229466.06 10229466.16 2.94 2.02\n", "auxiliary[0,37] 10229421.07 0.03 10229421.08 10229421.03 10229421.13 2.56 2.72\n", "auxiliary[0,38] 10229371.49 0.04 10229371.50 10229371.43 10229371.54 2.55 2.52\n", "auxiliary[0,39] 10229316.38 0.04 10229316.38 10229316.32 10229316.44 2.78 2.26\n", "auxiliary[0,40] 10229256.01 0.05 10229256.03 10229255.93 10229256.09 2.63 2.41\n", "auxiliary[0,41] 10229189.35 0.03 10229189.34 10229189.31 10229189.41 3.46 1.66\n", "auxiliary[0,42] 10229117.19 0.02 10229117.19 10229117.15 10229117.22 3.67 1.75\n", "auxiliary[0,43] 10229038.11 0.02 10229038.11 10229038.07 10229038.14 4.00 1.27\n", "auxiliary[0,44] 10228952.34 0.02 10228952.33 10228952.32 10228952.39 5.52 1.16\n", "auxiliary[0,45] 10228860.11 0.03 10228860.12 10228860.06 10228860.15 2.95 1.95\n", "auxiliary[0,46] 10228760.57 0.03 10228760.58 10228760.50 10228760.60 5.36 1.41\n", "auxiliary[0,47] 10228651.40 0.02 10228651.41 10228651.37 10228651.44 3.35 2.06\n", "auxiliary[0,48] 10228535.41 0.02 10228535.42 10228535.39 10228535.43 3.93 1.69\n", "auxiliary[0,49] 10228412.15 0.04 10228412.13 10228412.10 10228412.21 2.76 2.38\n", "auxiliary[0,50] 10228281.30 0.03 10228281.31 10228281.27 10228281.36 5.88 1.15\n", "auxiliary[0,51] 10228142.73 0.05 10228142.75 10228142.65 10228142.79 5.03 1.32\n", "auxiliary[0,52] 10227994.73 0.03 10227994.73 10227994.68 10227994.77 8.68 1.15\n", "auxiliary[0,53] 10227838.64 0.04 10227838.63 10227838.59 10227838.72 5.94 1.38\n", "auxiliary[0,54] 10227673.45 0.08 10227673.45 10227673.28 10227673.55 4.39 1.57\n", "auxiliary[0,55] 10227499.73 0.06 10227499.72 10227499.66 10227499.86 5.49 1.15\n", "auxiliary[0,56] 10227314.55 0.06 10227314.57 10227314.40 10227314.61 6.61 1.12\n", "auxiliary[0,57] 10227117.23 0.04 10227117.23 10227117.17 10227117.28 7.32 1.13\n", "auxiliary[0,58] 10226907.98 0.05 10226907.97 10226907.91 10226908.05 5.14 1.51\n", "auxiliary[0,59] 10226686.86 0.04 10226686.85 10226686.81 10226686.93 7.22 1.13\n", "auxiliary[0,60] 10226463.04 0.07 10226463.05 10226462.92 10226463.15 3.68 1.39\n", " auxiliary[1,0] 9.28 0.00 9.28 9.28 9.28 11.61 1.14\n", " auxiliary[1,1] 10.72 0.00 10.72 10.72 10.72 5.60 1.16\n", " auxiliary[1,2] 16.10 0.00 16.10 16.10 16.10 9.35 1.42\n", " auxiliary[1,3] 24.53 0.00 24.53 24.53 24.53 3.39 1.86\n", " auxiliary[1,4] 34.44 0.00 34.44 34.43 34.44 7.18 1.14\n", " auxiliary[1,5] 36.73 0.00 36.73 36.73 36.73 7.36 1.16\n", " auxiliary[1,6] 40.48 0.00 40.48 40.48 40.48 2.73 2.54\n", " auxiliary[1,7] 44.13 0.00 44.13 44.13 44.14 2.86 2.11\n", " auxiliary[1,8] 32.66 0.00 32.66 32.65 32.66 2.73 2.40\n", " auxiliary[1,9] 36.78 0.00 36.78 36.77 36.78 2.63 2.81\n", "auxiliary[1,10] 39.66 0.00 39.66 39.66 39.66 2.40 3.48\n", "auxiliary[1,11] 42.58 0.00 42.58 42.58 42.58 4.25 1.62\n", "auxiliary[1,12] 42.65 0.00 42.65 42.65 42.65 3.34 1.79\n", "auxiliary[1,13] 45.90 0.00 45.90 45.90 45.90 2.69 2.56\n", "auxiliary[1,14] 50.20 0.00 50.20 50.20 50.20 4.31 1.75\n", "auxiliary[1,15] 55.24 0.00 55.24 55.24 55.24 3.61 1.66\n", "auxiliary[1,16] 55.35 0.00 55.35 55.34 55.35 3.58 2.35\n", "auxiliary[1,17] 55.40 0.00 55.40 55.40 55.40 5.93 1.14\n", "auxiliary[1,18] 50.70 0.00 50.70 50.69 50.70 3.58 1.88\n", "auxiliary[1,19] 45.41 0.00 45.41 45.41 45.41 2.93 2.38\n", "auxiliary[1,20] 47.10 0.00 47.10 47.10 47.10 9.53 1.05\n", "auxiliary[1,21] 49.98 0.00 49.98 49.98 49.98 8.52 1.31\n", "auxiliary[1,22] 53.79 0.00 53.79 53.79 53.80 7.57 1.26\n", "auxiliary[1,23] 55.84 0.00 55.84 55.84 55.85 3.50 1.72\n", "auxiliary[1,24] 56.29 0.00 56.29 56.29 56.29 6.35 1.60\n", "auxiliary[1,25] 54.52 0.00 54.52 54.51 54.52 6.55 1.24\n", "auxiliary[1,26] 70.57 0.00 70.57 70.57 70.57 7.45 1.19\n", "auxiliary[1,27] 86.03 0.00 86.03 86.03 86.04 3.55 2.17\n", "auxiliary[1,28] 88.07 0.00 88.07 88.07 88.08 4.56 1.48\n", "auxiliary[1,29] 89.82 0.00 89.82 89.82 89.83 8.43 1.08\n", "auxiliary[1,30] 93.25 0.00 93.25 93.24 93.25 6.31 1.18\n", "auxiliary[1,31] 96.14 0.00 96.14 96.14 96.14 7.58 1.08\n", "auxiliary[1,32] 107.74 0.00 107.74 107.74 107.74 12.70 1.01\n", "auxiliary[1,33] 122.78 0.00 122.78 122.78 122.79 4.28 1.08\n", "auxiliary[1,34] 132.22 0.00 132.22 132.21 132.22 3.78 2.16\n", "auxiliary[1,35] 151.28 0.00 151.28 151.28 151.29 5.92 1.13\n", "auxiliary[1,36] 166.64 0.00 166.64 166.63 166.64 5.03 1.58\n", "auxiliary[1,37] 185.71 0.00 185.71 185.70 185.72 3.98 1.60\n", "auxiliary[1,38] 215.91 0.00 215.91 215.91 215.92 4.77 1.44\n", "auxiliary[1,39] 240.58 0.01 240.58 240.57 240.59 5.84 1.00\n", "auxiliary[1,40] 256.23 0.01 256.23 256.23 256.25 5.57 1.19\n", "auxiliary[1,41] 278.20 0.00 278.20 278.20 278.21 6.91 1.01\n", "auxiliary[1,42] 314.01 0.01 314.01 314.00 314.02 2.93 2.40\n", "auxiliary[1,43] 354.73 0.00 354.73 354.73 354.74 11.19 1.05\n", "auxiliary[1,44] 381.32 0.01 381.32 381.31 381.33 5.48 1.25\n", "auxiliary[1,45] 400.67 0.01 400.67 400.66 400.69 2.99 2.10\n", "auxiliary[1,46] 425.65 0.01 425.64 425.64 425.66 2.72 2.35\n", "auxiliary[1,47] 457.26 0.01 457.26 457.24 457.28 3.56 1.73\n", "auxiliary[1,48] 507.00 0.01 507.00 506.98 507.02 4.18 1.07\n", "auxiliary[1,49] 549.12 0.02 549.13 549.09 549.14 2.81 2.31\n", "auxiliary[1,50] 611.96 0.02 611.95 611.94 611.98 3.29 1.66\n", "auxiliary[1,51] 657.49 0.01 657.49 657.48 657.50 11.34 1.05\n", "auxiliary[1,52] 700.38 0.01 700.38 700.36 700.41 3.74 1.84\n", "auxiliary[1,53] 732.40 0.02 732.40 732.37 732.42 2.55 2.39\n", "auxiliary[1,54] 765.93 0.03 765.93 765.89 765.98 2.63 2.35\n", "auxiliary[1,55] 798.41 0.01 798.41 798.40 798.43 10.48 1.00\n", "auxiliary[1,56] 838.83 0.02 838.83 838.80 838.86 4.23 1.44\n", "auxiliary[1,57] 899.95 0.02 899.95 899.92 899.97 6.43 1.28\n", "auxiliary[1,58] 961.68 0.02 961.67 961.65 961.71 4.28 1.78\n", "auxiliary[1,59] 1027.89 0.02 1027.89 1027.86 1027.91 6.32 1.08\n", "auxiliary[1,60] 1105.04 0.05 1105.02 1105.00 1105.12 3.00 1.85\n", " auxiliary[2,0] 0.83 0.00 0.83 0.83 0.83 4.64 1.40\n", " auxiliary[2,1] 3.24 0.00 3.24 3.24 3.24 5.12 1.03\n", " auxiliary[2,2] 6.08 0.00 6.08 6.08 6.08 2.72 2.85\n", " auxiliary[2,3] 5.69 0.00 5.69 5.69 5.69 8.29 1.07\n", " auxiliary[2,4] 5.90 0.00 5.90 5.90 5.90 6.30 1.24\n", " auxiliary[2,5] 9.45 0.00 9.45 9.45 9.45 3.03 1.89\n", " auxiliary[2,6] 15.07 0.00 15.07 15.07 15.07 6.39 1.15\n", " auxiliary[2,7] 16.98 0.00 16.98 16.98 16.98 3.05 2.06\n", " auxiliary[2,8] 22.83 0.00 22.83 22.83 22.83 7.65 1.05\n", " auxiliary[2,9] 28.02 0.00 28.02 28.02 28.02 13.15 1.01\n", "auxiliary[2,10] 29.02 0.00 29.02 29.01 29.02 2.72 2.23\n", "auxiliary[2,11] 31.26 0.00 31.26 31.26 31.26 12.94 1.05\n", "auxiliary[2,12] 33.17 0.00 33.17 33.17 33.17 2.83 2.23\n", "auxiliary[2,13] 34.59 0.00 34.59 34.59 34.59 5.39 1.47\n", "auxiliary[2,14] 37.78 0.00 37.78 37.78 37.78 3.78 2.57\n", "auxiliary[2,15] 42.25 0.00 42.25 42.25 42.25 3.68 1.77\n", "auxiliary[2,16] 49.62 0.00 49.62 49.62 49.62 6.48 1.12\n", "auxiliary[2,17] 54.11 0.00 54.11 54.11 54.11 8.24 1.38\n", "auxiliary[2,18] 62.68 0.00 62.68 62.68 62.68 5.97 1.01\n", "auxiliary[2,19] 53.69 0.00 53.69 53.69 53.69 7.18 1.46\n", "auxiliary[2,20] 57.39 0.00 57.39 57.39 57.39 5.88 1.10\n", "auxiliary[2,21] 64.64 0.00 64.64 64.64 64.65 4.36 1.52\n", "auxiliary[2,22] 71.07 0.00 71.07 71.07 71.07 6.47 1.11\n", "auxiliary[2,23] 71.68 0.00 71.68 71.68 71.68 10.42 1.04\n", "auxiliary[2,24] 76.15 0.00 76.15 76.14 76.15 3.94 1.57\n", "auxiliary[2,25] 81.53 0.00 81.53 81.52 81.53 6.00 1.09\n", "auxiliary[2,26] 81.02 0.00 81.02 81.01 81.02 2.64 2.44\n", "auxiliary[2,27] 80.96 0.00 80.96 80.96 80.96 8.12 1.21\n", "auxiliary[2,28] 92.33 0.00 92.33 92.33 92.34 7.67 1.34\n", "auxiliary[2,29] 101.72 0.00 101.72 101.72 101.72 6.24 2.13\n", "auxiliary[2,30] 115.37 0.00 115.37 115.37 115.38 4.33 1.37\n", "auxiliary[2,31] 130.31 0.00 130.31 130.30 130.31 3.37 2.13\n", "auxiliary[2,32] 146.38 0.00 146.38 146.38 146.38 5.86 1.39\n", "auxiliary[2,33] 154.69 0.00 154.69 154.68 154.69 15.89 1.02\n", "auxiliary[2,34] 166.47 0.00 166.47 166.47 166.47 17.12 1.05\n", "auxiliary[2,35] 177.30 0.00 177.30 177.29 177.30 3.60 1.62\n", "auxiliary[2,36] 192.63 0.01 192.63 192.62 192.64 3.08 1.78\n", "auxiliary[2,37] 213.02 0.00 213.02 213.01 213.02 3.23 2.23\n", "auxiliary[2,38] 224.42 0.00 224.42 224.41 224.43 6.48 1.02\n", "auxiliary[2,39] 236.27 0.01 236.27 236.26 236.29 3.03 1.87\n", "auxiliary[2,40] 265.57 0.01 265.57 265.56 265.58 3.67 1.69\n", "auxiliary[2,41] 291.46 0.01 291.46 291.45 291.47 3.50 2.12\n", "auxiliary[2,42] 316.95 0.01 316.95 316.93 316.96 3.37 1.78\n", "auxiliary[2,43] 341.49 0.02 341.49 341.47 341.51 2.42 2.95\n", "auxiliary[2,44] 374.58 0.00 374.58 374.58 374.59 4.45 1.70\n", "auxiliary[2,45] 421.81 0.01 421.81 421.80 421.83 4.31 2.18\n", "auxiliary[2,46] 466.38 0.01 466.38 466.37 466.39 6.76 1.02\n", "auxiliary[2,47] 513.48 0.01 513.49 513.47 513.50 6.16 1.01\n", "auxiliary[2,48] 560.70 0.01 560.70 560.69 560.71 5.15 1.35\n", "auxiliary[2,49] 605.92 0.01 605.91 605.90 605.93 9.73 1.31\n", "auxiliary[2,50] 647.28 0.02 647.28 647.26 647.31 2.93 2.14\n", "auxiliary[2,51] 681.99 0.01 681.99 681.98 682.00 3.98 1.57\n", "auxiliary[2,52] 740.33 0.03 740.33 740.29 740.39 3.21 1.83\n", "auxiliary[2,53] 799.50 0.01 799.50 799.48 799.51 7.19 1.08\n", "auxiliary[2,54] 868.84 0.01 868.85 868.81 868.86 3.06 2.40\n", "auxiliary[2,55] 939.05 0.01 939.05 939.04 939.07 8.98 1.15\n", "auxiliary[2,56] 1043.75 0.02 1043.75 1043.73 1043.78 7.55 1.01\n", "auxiliary[2,57] 1135.80 0.03 1135.81 1135.75 1135.84 3.07 2.02\n", "auxiliary[2,58] 1199.02 0.02 1199.02 1198.99 1199.04 3.30 2.17\n", "auxiliary[2,59] 1268.89 0.03 1268.89 1268.84 1268.94 6.69 1.18\n", "auxiliary[2,60] 1376.02 0.02 1376.02 1375.97 1376.05 8.23 1.29\n", " auxiliary[3,0] 0.50 0.00 0.50 0.50 0.50 3.60 1.92\n", " auxiliary[3,1] 0.50 0.00 0.50 0.50 0.50 3.61 1.58\n", " auxiliary[3,2] 0.50 0.00 0.50 0.50 0.50 3.00 2.07\n", " auxiliary[3,3] 0.50 0.00 0.50 0.50 0.50 7.26 1.34\n", " auxiliary[3,4] 0.50 0.00 0.50 0.50 0.50 2.52 2.75\n", " auxiliary[3,5] 0.50 0.00 0.50 0.50 0.50 5.37 1.56\n", " auxiliary[3,6] 0.50 0.00 0.50 0.50 0.50 3.30 2.19\n", " auxiliary[3,7] 0.50 0.00 0.50 0.50 0.50 6.92 1.22\n", " auxiliary[3,8] 0.50 0.00 0.50 0.50 0.50 6.55 1.46\n", " auxiliary[3,9] 0.50 0.00 0.50 0.50 0.50 7.07 1.00\n", "auxiliary[3,10] 0.50 0.00 0.50 0.50 0.50 6.12 1.09\n", "auxiliary[3,11] 0.50 0.00 0.50 0.50 0.50 8.53 1.01\n", "auxiliary[3,12] 0.50 0.00 0.50 0.50 0.50 2.61 2.97\n", "auxiliary[3,13] 0.50 0.00 0.50 0.50 0.50 2.78 2.28\n", "auxiliary[3,14] 0.50 0.00 0.50 0.50 0.50 3.02 1.98\n", "auxiliary[3,15] 0.50 0.00 0.50 0.50 0.50 4.72 1.80\n", "auxiliary[3,16] 0.50 0.00 0.50 0.50 0.50 2.54 3.38\n", "auxiliary[3,17] 0.50 0.00 0.50 0.50 0.50 8.79 1.31\n", "auxiliary[3,18] 0.50 0.00 0.50 0.50 0.50 10.64 1.20\n", "auxiliary[3,19] 0.50 0.00 0.50 0.50 0.50 3.98 1.45\n", "auxiliary[3,20] 0.50 0.00 0.50 0.50 0.50 2.92 2.08\n", "auxiliary[3,21] 0.50 0.00 0.50 0.50 0.50 9.54 1.17\n", "auxiliary[3,22] 0.50 0.00 0.50 0.50 0.50 8.20 1.07\n", "auxiliary[3,23] 0.50 0.00 0.50 0.50 0.50 11.49 1.13\n", "auxiliary[3,24] 0.50 0.00 0.50 0.50 0.50 8.84 1.32\n", "auxiliary[3,25] 0.50 0.00 0.50 0.50 0.50 5.19 1.02\n", "auxiliary[3,26] 0.50 0.00 0.50 0.50 0.50 3.15 2.20\n", "auxiliary[3,27] 0.50 0.00 0.50 0.50 0.50 6.71 1.15\n", "auxiliary[3,28] 0.50 0.00 0.50 0.50 0.50 5.98 1.00\n", "auxiliary[3,29] 0.50 0.00 0.50 0.50 0.50 6.23 1.02\n", "auxiliary[3,30] 0.50 0.00 0.50 0.50 0.50 2.42 4.13\n", "auxiliary[3,31] 0.50 0.00 0.50 0.50 0.50 3.67 2.11\n", "auxiliary[3,32] 0.50 0.00 0.50 0.50 0.50 2.94 2.04\n", "auxiliary[3,33] 0.70 0.00 0.70 0.70 0.70 2.99 2.16\n", "auxiliary[3,34] 0.51 0.00 0.51 0.51 0.51 3.09 2.14\n", "auxiliary[3,35] 0.94 0.00 0.94 0.94 0.94 5.58 1.05\n", "auxiliary[3,36] 1.66 0.00 1.66 1.66 1.66 5.80 1.51\n", "auxiliary[3,37] 1.32 0.00 1.32 1.32 1.32 6.51 1.19\n", "auxiliary[3,38] 2.12 0.00 2.12 2.12 2.12 4.83 1.70\n", "auxiliary[3,39] 2.68 0.00 2.68 2.68 2.68 3.57 2.04\n", "auxiliary[3,40] 2.33 0.00 2.33 2.33 2.33 3.24 1.85\n", "auxiliary[3,41] 1.93 0.00 1.93 1.93 1.93 2.87 2.20\n", "auxiliary[3,42] 2.18 0.00 2.18 2.18 2.18 4.90 1.35\n", "auxiliary[3,43] 3.20 0.00 3.20 3.20 3.20 4.14 1.71\n", "auxiliary[3,44] 4.29 0.00 4.29 4.29 4.29 4.73 1.66\n", "auxiliary[3,45] 5.25 0.00 5.25 5.25 5.25 5.61 1.04\n", "auxiliary[3,46] 7.55 0.00 7.55 7.55 7.55 2.67 3.81\n", "auxiliary[3,47] 7.61 0.00 7.61 7.61 7.61 2.94 1.97\n", "auxiliary[3,48] 9.42 0.00 9.42 9.42 9.42 7.95 1.00\n", "auxiliary[3,49] 11.32 0.00 11.32 11.32 11.32 3.25 1.73\n", "auxiliary[3,50] 13.73 0.00 13.73 13.73 13.73 10.30 1.01\n", "auxiliary[3,51] 17.01 0.00 17.01 17.01 17.01 5.22 1.38\n", "auxiliary[3,52] 20.83 0.00 20.83 20.83 20.83 9.88 1.01\n", "auxiliary[3,53] 25.58 0.00 25.58 25.58 25.58 3.39 1.99\n", "auxiliary[3,54] 29.47 0.00 29.47 29.47 29.47 12.12 1.10\n", "auxiliary[3,55] 33.04 0.00 33.04 33.04 33.04 2.93 2.16\n", "auxiliary[3,56] 35.69 0.00 35.69 35.69 35.70 5.18 1.50\n", "auxiliary[3,57] 39.57 0.00 39.57 39.57 39.57 4.22 1.42\n", "auxiliary[3,58] 44.65 0.00 44.65 44.65 44.65 3.46 2.21\n", "auxiliary[3,59] 50.05 0.00 50.05 50.05 50.05 3.08 2.16\n", "auxiliary[3,60] 55.01 0.00 55.01 55.01 55.02 3.63 1.52\n", " incub_time 6.20 0.00 6.20 6.20 6.20 3.84 1.35\n", " mort_rate 0.03 0.00 0.03 0.03 0.03 2.45 3.31\n", " rec_rate 0.46 0.00 0.46 0.46 0.46 5.82 1.01\n", " rec_time 16.42 0.00 16.42 16.42 16.42 2.52 2.66\n", " rho 0.47 0.00 0.47 0.47 0.47 2.56 2.55\n", "\n", "Number of divergences: 500\n", "CPU times: user 49.8 s, sys: 456 ms, total: 50.3 s\n", "Wall time: 50.3 s\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "id": "8vIwqiAyASOb", "colab": { "base_uri": "https://localhost:8080/" }, "outputId": "639524af-313f-40fb-8530-10b1f9532e5a" }, "source": [ "%%time\n", "Sweden_model = CovidModel(10230000, Sweden[\"new_cases\"], Sweden[\"new_recovered\"], Sweden[\"new_deaths\"] )\n", "Sweden_mcmc = Sweden_model.fit_mcmc(num_samples=500, warmup_steps = 200)\n", "Sweden_mcmc.summary()" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "INFO \t Running inference...\n", "Warmup: 0%| | 0/700 [00:00, ?it/s]INFO \t Heuristic init: R0=2.67, incub_time=7.16, mort_rate=0.0627, rec_rate=0.42, rec_time=17.4, rho=0.207\n", "Sample: 100%|██████████| 700/700 [00:25, 27.48it/s, step size=1.86e-04, acc. prob=0.370]\n" ], "name": "stderr" }, { "output_type": "stream", "text": [ "\n", " mean std median 5.0% 95.0% n_eff r_hat\n", " R0 2.67 0.00 2.67 2.67 2.67 6.16 1.34\n", " auxiliary[0,0] 10229990.38 0.00 10229990.38 10229990.38 10229990.38 16.52 1.13\n", " auxiliary[0,1] 10229981.77 0.00 10229981.77 10229981.77 10229981.77 6.82 1.67\n", " auxiliary[0,2] 10229973.01 0.00 10229973.01 10229973.00 10229973.01 2.63 2.26\n", " auxiliary[0,3] 10229964.13 0.00 10229964.13 10229964.13 10229964.13 8.23 1.18\n", " auxiliary[0,4] 10229955.09 0.00 10229955.09 10229955.09 10229955.09 7.89 1.12\n", " auxiliary[0,5] 10229945.92 0.00 10229945.92 10229945.92 10229945.92 5.02 1.57\n", " auxiliary[0,6] 10229936.61 0.00 10229936.61 10229936.61 10229936.62 2.63 2.49\n", " auxiliary[0,7] 10229927.17 0.00 10229927.17 10229927.16 10229927.17 2.46 2.83\n", " auxiliary[0,8] 10229917.56 0.00 10229917.56 10229917.55 10229917.56 2.74 2.26\n", " auxiliary[0,9] 10229907.76 0.00 10229907.76 10229907.75 10229907.76 2.63 2.53\n", "auxiliary[0,10] 10229897.68 0.01 10229897.68 10229897.67 10229897.70 2.65 2.42\n", "auxiliary[0,11] 10229897.28 0.01 10229897.28 10229897.27 10229897.30 2.64 2.46\n", "auxiliary[0,12] 10229886.65 0.03 10229886.64 10229886.60 10229886.72 2.57 2.57\n", "auxiliary[0,13] 10229875.72 0.04 10229875.71 10229875.66 10229875.78 2.54 2.61\n", "auxiliary[0,14] 10229864.38 0.04 10229864.37 10229864.32 10229864.43 2.47 2.86\n", "auxiliary[0,15] 10229852.56 0.05 10229852.57 10229852.49 10229852.63 2.57 2.51\n", "auxiliary[0,16] 10229840.16 0.03 10229840.16 10229840.11 10229840.22 2.70 2.35\n", "auxiliary[0,17] 10229827.08 0.04 10229827.07 10229827.02 10229827.14 2.53 2.69\n", "auxiliary[0,18] 10229813.21 0.03 10229813.21 10229813.16 10229813.26 2.51 2.79\n", "auxiliary[0,19] 10229798.45 0.03 10229798.45 10229798.40 10229798.49 2.69 2.39\n", "auxiliary[0,20] 10229782.72 0.03 10229782.72 10229782.69 10229782.77 2.54 2.64\n", "auxiliary[0,21] 10229765.93 0.03 10229765.93 10229765.88 10229765.98 2.66 2.33\n", "auxiliary[0,22] 10229748.07 0.03 10229748.07 10229748.03 10229748.10 2.70 2.39\n", "auxiliary[0,23] 10229729.07 0.02 10229729.07 10229729.03 10229729.10 2.65 2.51\n", "auxiliary[0,24] 10229708.94 0.03 10229708.94 10229708.90 10229708.98 2.40 3.18\n", "auxiliary[0,25] 10229687.76 0.02 10229687.76 10229687.72 10229687.79 3.57 1.69\n", "auxiliary[0,26] 10229665.40 0.03 10229665.39 10229665.36 10229665.44 2.50 2.91\n", "auxiliary[0,27] 10229641.75 0.02 10229641.75 10229641.72 10229641.79 2.82 2.19\n", "auxiliary[0,28] 10229616.97 0.04 10229616.96 10229616.92 10229617.02 2.54 2.61\n", "auxiliary[0,29] 10229590.99 0.02 10229590.99 10229590.96 10229591.03 2.58 2.51\n", "auxiliary[0,30] 10229563.74 0.03 10229563.75 10229563.69 10229563.77 2.59 2.50\n", "auxiliary[0,31] 10229535.09 0.02 10229535.09 10229535.07 10229535.12 2.51 3.17\n", "auxiliary[0,32] 10229504.92 0.03 10229504.92 10229504.88 10229504.97 2.48 2.86\n", "auxiliary[0,33] 10229473.01 0.04 10229473.01 10229472.95 10229473.06 2.46 2.92\n", "auxiliary[0,34] 10229439.39 0.04 10229439.39 10229439.34 10229439.44 2.52 2.66\n", "auxiliary[0,35] 10229404.00 0.03 10229404.00 10229403.96 10229404.03 2.52 2.67\n", "auxiliary[0,36] 10229366.44 0.03 10229366.43 10229366.40 10229366.49 2.49 2.90\n", "auxiliary[0,37] 10229326.71 0.05 10229326.72 10229326.64 10229326.77 2.63 2.39\n", "auxiliary[0,38] 10229284.25 0.02 10229284.25 10229284.22 10229284.27 4.36 1.43\n", "auxiliary[0,39] 10229239.32 0.03 10229239.30 10229239.26 10229239.36 2.60 2.63\n", "auxiliary[0,40] 10229191.00 0.02 10229191.00 10229190.96 10229191.05 3.26 1.88\n", "auxiliary[0,41] 10229138.65 0.02 10229138.64 10229138.62 10229138.68 3.67 1.69\n", "auxiliary[0,42] 10229082.62 0.03 10229082.61 10229082.59 10229082.67 2.61 2.81\n", "auxiliary[0,43] 10229022.66 0.02 10229022.66 10229022.63 10229022.68 3.16 1.98\n", "auxiliary[0,44] 10228958.74 0.03 10228958.74 10228958.69 10228958.79 2.47 2.77\n", "auxiliary[0,45] 10228888.87 0.02 10228888.87 10228888.85 10228888.90 4.33 1.62\n", "auxiliary[0,46] 10228812.68 0.02 10228812.67 10228812.64 10228812.71 3.63 1.43\n", "auxiliary[0,47] 10228730.30 0.04 10228730.29 10228730.23 10228730.34 2.47 3.44\n", "auxiliary[0,48] 10228641.46 0.01 10228641.46 10228641.44 10228641.48 10.18 1.03\n", "auxiliary[0,49] 10228546.64 0.02 10228546.64 10228546.62 10228546.68 4.13 1.47\n", "auxiliary[0,50] 10228444.57 0.03 10228444.58 10228444.53 10228444.61 3.69 1.54\n", "auxiliary[0,51] 10228334.87 0.01 10228334.87 10228334.85 10228334.90 11.17 1.08\n", "auxiliary[0,52] 10228218.37 0.05 10228218.37 10228218.30 10228218.43 2.47 3.32\n", "auxiliary[0,53] 10228094.85 0.03 10228094.84 10228094.82 10228094.91 4.89 1.43\n", "auxiliary[0,54] 10227963.29 0.03 10227963.30 10227963.25 10227963.33 3.97 1.32\n", "auxiliary[0,55] 10227823.44 0.04 10227823.45 10227823.37 10227823.47 3.25 1.68\n", "auxiliary[0,56] 10227673.75 0.06 10227673.75 10227673.64 10227673.83 2.63 2.55\n", "auxiliary[0,57] 10227513.66 0.03 10227513.66 10227513.62 10227513.71 8.76 1.11\n", "auxiliary[0,58] 10227344.50 0.02 10227344.50 10227344.46 10227344.53 9.83 1.08\n", "auxiliary[0,59] 10227164.86 0.03 10227164.86 10227164.83 10227164.93 4.35 1.53\n", "auxiliary[0,60] 10226964.40 0.12 10226964.44 10226964.21 10226964.53 2.41 3.25\n", " auxiliary[1,0] 11.66 0.00 11.66 11.66 11.66 4.66 1.04\n", " auxiliary[1,1] 15.07 0.00 15.07 15.07 15.07 3.00 2.46\n", " auxiliary[1,2] 27.48 0.00 27.48 27.48 27.48 8.31 1.09\n", " auxiliary[1,3] 27.69 0.00 27.69 27.69 27.69 2.83 2.32\n", " auxiliary[1,4] 27.59 0.00 27.59 27.59 27.59 2.97 2.44\n", " auxiliary[1,5] 29.15 0.00 29.15 29.15 29.15 3.61 1.66\n", " auxiliary[1,6] 30.15 0.00 30.15 30.15 30.15 12.95 1.14\n", " auxiliary[1,7] 36.32 0.00 36.32 36.31 36.32 3.99 2.18\n", " auxiliary[1,8] 33.77 0.00 33.77 33.77 33.77 3.52 1.60\n", " auxiliary[1,9] 34.19 0.00 34.19 34.18 34.19 2.76 2.29\n", "auxiliary[1,10] 36.36 0.00 36.36 36.36 36.37 3.10 1.91\n", "auxiliary[1,11] 23.75 0.00 23.75 23.74 23.75 3.33 1.64\n", "auxiliary[1,12] 30.35 0.00 30.35 30.35 30.35 9.62 1.02\n", "auxiliary[1,13] 33.66 0.00 33.66 33.66 33.66 4.31 1.75\n", "auxiliary[1,14] 32.03 0.00 32.03 32.03 32.03 17.45 1.02\n", "auxiliary[1,15] 39.47 0.00 39.47 39.47 39.47 5.06 1.39\n", "auxiliary[1,16] 40.59 0.00 40.59 40.59 40.60 4.04 1.54\n", "auxiliary[1,17] 37.59 0.00 37.59 37.59 37.59 2.97 2.10\n", "auxiliary[1,18] 35.50 0.00 35.50 35.50 35.50 5.78 1.15\n", "auxiliary[1,19] 33.91 0.00 33.91 33.91 33.91 6.77 1.19\n", "auxiliary[1,20] 34.40 0.00 34.40 34.40 34.40 8.53 1.02\n", "auxiliary[1,21] 34.98 0.00 34.98 34.98 34.98 5.36 1.48\n", "auxiliary[1,22] 38.61 0.00 38.61 38.61 38.61 4.10 1.39\n", "auxiliary[1,23] 46.63 0.00 46.63 46.62 46.63 3.97 1.92\n", "auxiliary[1,24] 55.12 0.00 55.12 55.12 55.12 3.57 1.85\n", "auxiliary[1,25] 58.71 0.00 58.71 58.70 58.71 10.03 1.29\n", "auxiliary[1,26] 66.40 0.00 66.40 66.40 66.40 5.85 1.40\n", "auxiliary[1,27] 75.62 0.00 75.62 75.62 75.62 5.46 1.24\n", "auxiliary[1,28] 83.35 0.00 83.35 83.35 83.35 5.40 1.33\n", "auxiliary[1,29] 79.85 0.00 79.85 79.85 79.85 6.01 1.03\n", "auxiliary[1,30] 94.09 0.00 94.09 94.09 94.09 9.79 1.50\n", "auxiliary[1,31] 98.70 0.00 98.70 98.70 98.70 4.78 1.60\n", "auxiliary[1,32] 107.96 0.00 107.96 107.96 107.96 10.42 1.10\n", "auxiliary[1,33] 125.06 0.00 125.06 125.05 125.06 5.65 1.24\n", "auxiliary[1,34] 135.72 0.00 135.72 135.72 135.73 4.64 1.34\n", "auxiliary[1,35] 156.41 0.00 156.41 156.41 156.41 8.21 1.13\n", "auxiliary[1,36] 179.35 0.00 179.35 179.34 179.35 4.01 1.65\n", "auxiliary[1,37] 190.99 0.00 190.99 190.99 191.00 3.76 1.63\n", "auxiliary[1,38] 209.83 0.00 209.83 209.83 209.84 3.67 1.35\n", "auxiliary[1,39] 227.71 0.01 227.71 227.70 227.72 3.89 1.38\n", "auxiliary[1,40] 245.49 0.00 245.49 245.48 245.49 11.39 1.04\n", "auxiliary[1,41] 276.49 0.00 276.49 276.48 276.50 3.03 2.00\n", "auxiliary[1,42] 309.37 0.00 309.37 309.37 309.38 4.30 2.01\n", "auxiliary[1,43] 336.38 0.01 336.38 336.37 336.39 2.68 2.46\n", "auxiliary[1,44] 344.92 0.00 344.92 344.91 344.92 5.81 1.43\n", "auxiliary[1,45] 366.48 0.01 366.48 366.47 366.49 2.67 3.14\n", "auxiliary[1,46] 412.28 0.01 412.28 412.27 412.29 2.71 2.68\n", "auxiliary[1,47] 442.26 0.01 442.26 442.25 442.27 4.91 1.23\n", "auxiliary[1,48] 475.22 0.01 475.22 475.20 475.23 3.04 1.76\n", "auxiliary[1,49] 498.40 0.00 498.40 498.40 498.41 10.29 1.00\n", "auxiliary[1,50] 536.38 0.01 536.39 536.36 536.40 2.74 2.45\n", "auxiliary[1,51] 584.47 0.02 584.47 584.45 584.49 3.03 2.13\n", "auxiliary[1,52] 598.38 0.01 598.38 598.37 598.39 3.19 2.01\n", "auxiliary[1,53] 614.45 0.01 614.45 614.44 614.46 3.24 2.01\n", "auxiliary[1,54] 635.20 0.01 635.20 635.19 635.21 10.63 1.23\n", "auxiliary[1,55] 666.48 0.01 666.48 666.47 666.49 11.31 1.02\n", "auxiliary[1,56] 732.19 0.01 732.19 732.18 732.20 5.18 1.37\n", "auxiliary[1,57] 792.48 0.01 792.49 792.46 792.50 2.87 1.94\n", "auxiliary[1,58] 830.34 0.01 830.34 830.33 830.36 9.65 1.00\n", "auxiliary[1,59] 879.10 0.01 879.10 879.08 879.11 4.66 1.74\n", "auxiliary[1,60] 981.97 0.01 981.97 981.94 981.99 3.21 2.08\n", " auxiliary[2,0] 0.86 0.00 0.86 0.86 0.86 4.18 2.15\n", " auxiliary[2,1] 3.51 0.00 3.51 3.51 3.51 4.29 1.58\n", " auxiliary[2,2] 1.03 0.00 1.03 1.03 1.03 7.44 1.21\n", " auxiliary[2,3] 5.16 0.00 5.16 5.16 5.16 13.28 1.05\n", " auxiliary[2,4] 7.69 0.00 7.69 7.69 7.69 2.89 2.44\n", " auxiliary[2,5] 10.50 0.00 10.50 10.50 10.50 3.16 2.12\n", " auxiliary[2,6] 16.07 0.00 16.07 16.07 16.07 12.99 1.18\n", " auxiliary[2,7] 18.43 0.00 18.43 18.43 18.43 9.84 1.03\n", " auxiliary[2,8] 21.98 0.00 21.98 21.98 21.98 3.48 1.76\n", " auxiliary[2,9] 28.99 0.00 28.99 28.99 28.99 6.79 1.01\n", "auxiliary[2,10] 38.74 0.00 38.74 38.74 38.74 5.36 1.77\n", "auxiliary[2,11] 30.36 0.00 30.36 30.36 30.36 6.26 1.32\n", "auxiliary[2,12] 33.80 0.00 33.80 33.80 33.80 2.95 2.03\n", "auxiliary[2,13] 36.35 0.00 36.35 36.34 36.35 5.97 1.04\n", "auxiliary[2,14] 39.24 0.00 39.24 39.24 39.24 5.87 1.20\n", "auxiliary[2,15] 41.61 0.00 41.61 41.61 41.61 2.61 2.30\n", "auxiliary[2,16] 46.00 0.00 46.00 46.00 46.00 6.30 1.01\n", "auxiliary[2,17] 50.17 0.00 50.17 50.17 50.17 15.52 1.00\n", "auxiliary[2,18] 52.81 0.00 52.81 52.81 52.81 6.49 1.00\n", "auxiliary[2,19] 57.63 0.00 57.63 57.63 57.63 3.40 1.62\n", "auxiliary[2,20] 63.04 0.00 63.04 63.04 63.04 6.64 1.22\n", "auxiliary[2,21] 69.72 0.00 69.72 69.72 69.72 2.75 2.32\n", "auxiliary[2,22] 69.81 0.00 69.81 69.80 69.81 2.50 2.80\n", "auxiliary[2,23] 69.98 0.00 69.98 69.97 69.98 3.24 1.75\n", "auxiliary[2,24] 73.27 0.00 73.27 73.27 73.27 3.04 1.95\n", "auxiliary[2,25] 78.19 0.00 78.19 78.19 78.19 5.95 1.68\n", "auxiliary[2,26] 85.06 0.00 85.06 85.06 85.06 5.09 1.42\n", "auxiliary[2,27] 84.56 0.00 84.56 84.55 84.56 4.58 1.56\n", "auxiliary[2,28] 87.52 0.00 87.52 87.52 87.52 2.83 2.25\n", "auxiliary[2,29] 96.94 0.00 96.94 96.94 96.94 3.31 1.71\n", "auxiliary[2,30] 103.26 0.00 103.26 103.26 103.26 2.72 2.01\n", "auxiliary[2,31] 121.85 0.00 121.85 121.85 121.85 4.28 1.61\n", "auxiliary[2,32] 134.88 0.00 134.88 134.88 134.89 3.16 1.81\n", "auxiliary[2,33] 138.05 0.00 138.05 138.05 138.05 3.39 2.65\n", "auxiliary[2,34] 143.97 0.00 143.97 143.97 143.98 12.59 1.02\n", "auxiliary[2,35] 155.06 0.00 155.06 155.05 155.06 2.86 2.06\n", "auxiliary[2,36] 168.65 0.00 168.65 168.64 168.65 3.16 1.67\n", "auxiliary[2,37] 184.25 0.00 184.25 184.24 184.25 5.36 1.13\n", "auxiliary[2,38] 198.40 0.00 198.40 198.39 198.40 3.58 1.39\n", "auxiliary[2,39] 221.31 0.00 221.31 221.31 221.32 11.71 1.23\n", "auxiliary[2,40] 237.15 0.00 237.15 237.15 237.16 5.06 1.35\n", "auxiliary[2,41] 256.52 0.00 256.52 256.52 256.53 9.26 1.00\n", "auxiliary[2,42] 277.68 0.01 277.67 277.66 277.69 2.53 2.60\n", "auxiliary[2,43] 303.07 0.01 303.07 303.06 303.08 2.65 3.04\n", "auxiliary[2,44] 356.19 0.00 356.19 356.19 356.20 7.50 1.08\n", "auxiliary[2,45] 388.05 0.00 388.05 388.05 388.06 5.28 1.33\n", "auxiliary[2,46] 405.34 0.01 405.34 405.33 405.35 3.77 1.70\n", "auxiliary[2,47] 441.71 0.00 441.71 441.71 441.72 9.53 1.08\n", "auxiliary[2,48] 480.71 0.01 480.71 480.70 480.72 5.87 1.33\n", "auxiliary[2,49] 524.23 0.00 524.23 524.23 524.24 6.49 1.05\n", "auxiliary[2,50] 556.59 0.01 556.59 556.57 556.60 3.46 1.49\n", "auxiliary[2,51] 589.08 0.01 589.08 589.06 589.09 3.05 2.40\n", "auxiliary[2,52] 645.94 0.02 645.95 645.92 645.97 2.53 2.99\n", "auxiliary[2,53] 674.68 0.01 674.68 674.67 674.71 6.78 1.21\n", "auxiliary[2,54] 733.07 0.02 733.07 733.04 733.10 2.42 2.84\n", "auxiliary[2,55] 773.44 0.01 773.44 773.43 773.45 5.00 1.82\n", "auxiliary[2,56] 822.85 0.01 822.85 822.83 822.87 4.77 1.38\n", "auxiliary[2,57] 883.45 0.01 883.45 883.44 883.47 5.09 1.62\n", "auxiliary[2,58] 938.80 0.01 938.81 938.79 938.82 4.07 1.53\n", "auxiliary[2,59] 994.27 0.02 994.27 994.24 994.31 3.62 1.66\n", "auxiliary[2,60] 1087.46 0.03 1087.47 1087.42 1087.50 2.97 2.19\n", " auxiliary[3,0] 0.50 0.00 0.50 0.50 0.50 6.27 1.02\n", " auxiliary[3,1] 0.50 0.00 0.50 0.50 0.50 6.82 1.27\n", " auxiliary[3,2] 0.50 0.00 0.50 0.50 0.50 2.95 2.76\n", " auxiliary[3,3] 0.50 0.00 0.50 0.50 0.50 4.65 1.01\n", " auxiliary[3,4] 0.50 0.00 0.50 0.50 0.50 5.75 1.08\n", " auxiliary[3,5] 0.50 0.00 0.50 0.50 0.50 2.52 2.81\n", " auxiliary[3,6] 0.50 0.00 0.50 0.50 0.50 4.94 1.00\n", " auxiliary[3,7] 0.50 0.00 0.50 0.50 0.50 5.97 1.03\n", " auxiliary[3,8] 0.50 0.00 0.50 0.50 0.50 6.28 1.12\n", " auxiliary[3,9] 0.50 0.00 0.50 0.50 0.50 4.64 1.07\n", "auxiliary[3,10] 0.50 0.00 0.50 0.50 0.50 3.57 1.94\n", "auxiliary[3,11] 0.49 0.00 0.49 0.49 0.49 3.72 1.67\n", "auxiliary[3,12] 0.63 0.00 0.63 0.63 0.63 2.47 3.68\n", "auxiliary[3,13] 0.81 0.00 0.81 0.81 0.81 2.76 3.08\n", "auxiliary[3,14] 0.78 0.00 0.78 0.78 0.78 14.40 1.25\n", "auxiliary[3,15] 0.91 0.00 0.91 0.91 0.91 10.38 1.09\n", "auxiliary[3,16] 0.89 0.00 0.89 0.89 0.89 7.30 1.20\n", "auxiliary[3,17] 0.59 0.00 0.59 0.59 0.59 5.47 1.19\n", "auxiliary[3,18] 0.50 0.00 0.50 0.50 0.50 2.77 2.44\n", "auxiliary[3,19] 0.50 0.00 0.50 0.50 0.50 2.77 2.26\n", "auxiliary[3,20] 0.64 0.00 0.64 0.64 0.64 5.46 1.31\n", "auxiliary[3,21] 0.50 0.00 0.50 0.50 0.50 9.27 1.08\n", "auxiliary[3,22] 0.50 0.00 0.50 0.50 0.50 7.14 1.14\n", "auxiliary[3,23] 0.50 0.00 0.50 0.50 0.50 2.67 2.34\n", "auxiliary[3,24] 0.82 0.00 0.82 0.82 0.82 2.88 2.42\n", "auxiliary[3,25] 0.55 0.00 0.55 0.55 0.55 6.56 1.17\n", "auxiliary[3,26] 0.71 0.00 0.71 0.71 0.71 8.54 1.04\n", "auxiliary[3,27] 0.51 0.00 0.51 0.51 0.51 6.50 1.36\n", "auxiliary[3,28] 0.66 0.00 0.66 0.66 0.66 7.67 1.26\n", "auxiliary[3,29] 0.82 0.00 0.82 0.82 0.82 6.70 1.00\n", "auxiliary[3,30] 0.57 0.00 0.57 0.57 0.57 7.84 1.26\n", "auxiliary[3,31] 0.50 0.00 0.50 0.50 0.50 3.76 1.68\n", "auxiliary[3,32] 0.86 0.00 0.86 0.86 0.86 3.86 1.72\n", "auxiliary[3,33] 1.76 0.00 1.76 1.76 1.76 3.93 1.24\n", "auxiliary[3,34] 1.76 0.00 1.76 1.76 1.76 4.30 1.64\n", "auxiliary[3,35] 2.58 0.00 2.58 2.58 2.58 4.15 1.72\n", "auxiliary[3,36] 3.22 0.00 3.22 3.22 3.22 6.09 1.07\n", "auxiliary[3,37] 3.72 0.00 3.72 3.72 3.72 2.75 2.15\n", "auxiliary[3,38] 4.11 0.00 4.11 4.11 4.11 2.85 2.15\n", "auxiliary[3,39] 4.10 0.00 4.10 4.10 4.10 3.13 2.12\n", "auxiliary[3,40] 5.45 0.00 5.45 5.45 5.45 2.68 2.22\n", "auxiliary[3,41] 7.39 0.00 7.39 7.39 7.39 5.10 1.64\n", "auxiliary[3,42] 9.22 0.00 9.22 9.22 9.22 6.54 1.16\n", "auxiliary[3,43] 11.18 0.00 11.18 11.18 11.18 2.63 3.86\n", "auxiliary[3,44] 13.12 0.00 13.12 13.12 13.12 3.50 1.43\n", "auxiliary[3,45] 14.77 0.00 14.77 14.77 14.77 3.72 1.75\n", "auxiliary[3,46] 16.76 0.00 16.76 16.76 16.76 5.32 1.13\n", "auxiliary[3,47] 18.46 0.00 18.46 18.46 18.46 7.10 1.02\n", "auxiliary[3,48] 20.50 0.00 20.50 20.50 20.50 11.03 1.01\n", "auxiliary[3,49] 22.83 0.00 22.83 22.83 22.83 2.57 2.76\n", "auxiliary[3,50] 25.81 0.00 25.81 25.81 25.81 4.22 1.53\n", "auxiliary[3,51] 30.05 0.00 30.05 30.05 30.06 2.57 2.52\n", "auxiliary[3,52] 35.58 0.00 35.58 35.58 35.58 3.02 2.24\n", "auxiliary[3,53] 41.75 0.00 41.75 41.75 41.75 6.58 1.27\n", "auxiliary[3,54] 47.87 0.00 47.87 47.87 47.87 4.55 1.46\n", "auxiliary[3,55] 53.81 0.00 53.81 53.81 53.81 3.65 1.47\n", "auxiliary[3,56] 59.47 0.00 59.47 59.47 59.47 2.44 3.85\n", "auxiliary[3,57] 64.88 0.00 64.88 64.88 64.88 2.64 2.63\n", "auxiliary[3,58] 69.92 0.00 69.92 69.92 69.92 5.36 1.02\n", "auxiliary[3,59] 74.57 0.00 74.57 74.57 74.57 3.78 1.71\n", "auxiliary[3,60] 78.87 0.00 78.87 78.87 78.87 6.72 1.13\n", " incub_time 7.16 0.00 7.16 7.16 7.16 2.97 2.14\n", " mort_rate 0.06 0.00 0.06 0.06 0.06 2.97 2.17\n", " rec_rate 0.42 0.00 0.42 0.42 0.42 2.41 3.38\n", " rec_time 17.43 0.00 17.43 17.43 17.43 7.22 1.00\n", " rho 0.49 0.00 0.49 0.49 0.49 2.85 2.04\n", "\n", "Number of divergences: 500\n", "CPU times: user 25.6 s, sys: 221 ms, total: 25.8 s\n", "Wall time: 25.8 s\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "azXz2h-v2egJ", "outputId": "3e2cde05-d483-43c4-8364-f25a3ac1d7de" }, "source": [ "%%time\n", "Sweden_model = CovidModel(10230000, Sweden[\"new_cases\"], Sweden[\"new_recovered\"], Sweden[\"new_deaths\"] )\n", "Sweden_mcmc = Sweden_model.fit_mcmc(num_samples=500, warmup_steps = 200)\n", "Sweden_mcmc.summary()" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "INFO \t Running inference...\n", "Warmup: 0%| | 0/700 [00:00, ?it/s]INFO \t Heuristic init: R0=2.93, incub_time=4.53, mort_rate=0.0237, rec_rate=0.449, rec_time=16.9, rho=0.189\n", "Sample: 100%|██████████| 700/700 [01:29, 7.83it/s, step size=9.38e-04, acc. prob=0.895]\n" ], "name": "stderr" }, { "output_type": "stream", "text": [ "\n", " mean std median 5.0% 95.0% n_eff r_hat\n", " R0 2.93 0.00 2.93 2.93 2.93 3.30 1.68\n", " auxiliary[0,0] 10229990.62 0.23 10229990.69 10229990.18 10229990.86 3.31 1.55\n", " auxiliary[0,1] 10229982.16 0.80 10229982.45 10229980.74 10229982.95 2.66 2.32\n", " auxiliary[0,2] 10229973.08 1.87 10229973.41 10229970.00 10229975.43 2.54 2.59\n", " auxiliary[0,3] 10229962.96 3.45 10229963.32 10229957.16 10229967.39 2.51 2.67\n", " auxiliary[0,4] 10229951.60 5.55 10229951.96 10229942.53 10229959.03 2.50 2.69\n", " auxiliary[0,5] 10229938.92 8.15 10229939.24 10229925.82 10229950.08 2.50 2.70\n", " auxiliary[0,6] 10229924.89 11.19 10229925.16 10229907.12 10229940.45 2.50 2.70\n", " auxiliary[0,7] 10229909.57 14.63 10229909.70 10229886.55 10229930.14 2.50 2.70\n", " auxiliary[0,8] 10229893.01 18.42 10229893.00 10229864.18 10229919.10 2.51 2.69\n", " auxiliary[0,9] 10229875.30 22.49 10229875.09 10229840.41 10229907.46 2.51 2.69\n", "auxiliary[0,10] 10229856.52 26.78 10229856.05 10229815.20 10229895.07 2.51 2.69\n", "auxiliary[0,11] 10229836.73 31.27 10229836.03 10229786.94 10229880.08 2.51 2.68\n", "auxiliary[0,12] 10229816.01 35.86 10229815.00 10229761.32 10229868.11 2.51 2.68\n", "auxiliary[0,13] 10229794.40 40.55 10229793.08 10229730.48 10229851.15 2.51 2.67\n", "auxiliary[0,14] 10229771.97 45.31 10229770.30 10229700.92 10229835.52 2.52 2.67\n", "auxiliary[0,15] 10229748.76 50.10 10229746.75 10229670.50 10229819.23 2.52 2.66\n", "auxiliary[0,16] 10229724.84 54.90 10229722.47 10229639.25 10229802.23 2.52 2.66\n", "auxiliary[0,17] 10229700.25 59.70 10229697.60 10229607.36 10229784.57 2.52 2.65\n", "auxiliary[0,18] 10229675.03 64.47 10229672.04 10229574.84 10229766.19 2.52 2.65\n", "auxiliary[0,19] 10229649.23 69.19 10229645.85 10229541.70 10229747.16 2.52 2.65\n", "auxiliary[0,20] 10229622.85 73.88 10229619.27 10229508.02 10229727.33 2.53 2.64\n", "auxiliary[0,21] 10229595.94 78.50 10229592.08 10229474.35 10229707.22 2.53 2.64\n", "auxiliary[0,22] 10229568.52 83.06 10229564.36 10229439.94 10229686.23 2.53 2.64\n", "auxiliary[0,23] 10229540.60 87.54 10229536.25 10229404.87 10229664.48 2.53 2.64\n", "auxiliary[0,24] 10229512.18 91.94 10229507.69 10229369.58 10229642.20 2.53 2.64\n", "auxiliary[0,25] 10229483.26 96.27 10229478.71 10229333.79 10229619.26 2.53 2.64\n", "auxiliary[0,26] 10229453.87 100.51 10229449.25 10229298.02 10229596.13 2.53 2.64\n", "auxiliary[0,27] 10229423.99 104.66 10229419.29 10229261.12 10229571.63 2.53 2.64\n", "auxiliary[0,28] 10229393.62 108.70 10229388.95 10229224.30 10229547.06 2.53 2.64\n", "auxiliary[0,29] 10229362.76 112.62 10229358.23 10229186.76 10229521.29 2.52 2.65\n", "auxiliary[0,30] 10229331.35 116.41 10229326.98 10229149.32 10229495.31 2.52 2.65\n", "auxiliary[0,31] 10229299.34 120.06 10229295.28 10229111.28 10229467.98 2.52 2.66\n", "auxiliary[0,32] 10229266.68 123.54 10229262.95 10229072.68 10229439.96 2.52 2.66\n", "auxiliary[0,33] 10229233.08 126.48 10229230.10 10229033.45 10229409.92 2.52 2.67\n", "auxiliary[0,34] 10229198.27 129.02 10229195.80 10228993.73 10229378.36 2.52 2.67\n", "auxiliary[0,35] 10229161.29 130.38 10229159.36 10228953.60 10229342.73 2.51 2.68\n", "auxiliary[0,36] 10229121.73 131.12 10229120.41 10228912.08 10229303.46 2.51 2.68\n", "auxiliary[0,37] 10229078.77 131.23 10229078.05 10228875.45 10229267.44 2.51 2.69\n", "auxiliary[0,38] 10229030.98 129.73 10229031.72 10228828.83 10229215.73 2.50 2.70\n", "auxiliary[0,39] 10228977.90 127.32 10228980.39 10228777.73 10229157.04 2.50 2.71\n", "auxiliary[0,40] 10228918.41 124.13 10228922.62 10228721.36 10229092.26 2.49 2.72\n", "auxiliary[0,41] 10228850.63 119.37 10228856.95 10228665.48 10229013.75 2.48 2.75\n", "auxiliary[0,42] 10228773.89 112.91 10228783.02 10228598.13 10228920.16 2.47 2.78\n", "auxiliary[0,43] 10228687.39 105.01 10228701.61 10228519.77 10228815.50 2.47 2.78\n", "auxiliary[0,44] 10228591.21 96.17 10228611.64 10228433.43 10228701.57 2.48 2.76\n", "auxiliary[0,45] 10228482.90 85.93 10228506.67 10228337.87 10228577.00 2.53 2.65\n", "auxiliary[0,46] 10228365.46 73.77 10228395.71 10228232.08 10228440.95 2.69 2.29\n", "auxiliary[0,47] 10228235.08 60.29 10228260.80 10228122.14 10228297.39 2.92 2.00\n", "auxiliary[0,48] 10228089.73 47.24 10228106.64 10227998.61 10228139.41 3.10 1.89\n", "auxiliary[0,49] 10227929.36 34.18 10227939.51 10227864.13 10227968.65 2.95 2.02\n", "auxiliary[0,50] 10227753.03 26.47 10227756.98 10227706.11 10227787.58 2.72 2.31\n", "auxiliary[0,51] 10227560.44 23.36 10227562.36 10227520.30 10227590.98 2.57 2.53\n", "auxiliary[0,52] 10227354.06 20.60 10227354.68 10227320.95 10227382.56 2.55 2.57\n", "auxiliary[0,53] 10227134.20 17.26 10227132.66 10227109.18 10227160.06 2.51 2.65\n", "auxiliary[0,54] 10226901.14 10.84 10226897.78 10226889.89 10226919.58 2.58 2.43\n", "auxiliary[0,55] 10226661.91 4.66 10226661.38 10226655.36 10226669.78 4.21 1.04\n", "auxiliary[0,56] 10226418.74 19.25 10226414.16 10226396.85 10226448.78 2.39 3.25\n", "auxiliary[0,57] 10226174.92 28.53 10226181.63 10226134.21 10226213.51 2.48 2.74\n", "auxiliary[0,58] 10225931.25 27.46 10225936.39 10225888.07 10225967.68 2.57 2.57\n", "auxiliary[0,59] 10225669.48 29.02 10225676.39 10225622.84 10225706.54 2.65 2.43\n", "auxiliary[0,60] 10225393.70 31.94 10225399.65 10225343.99 10225436.01 2.57 2.54\n", " auxiliary[1,0] 11.27 0.05 11.27 11.19 11.34 2.45 2.86\n", " auxiliary[1,1] 11.91 0.02 11.92 11.87 11.94 2.50 2.70\n", " auxiliary[1,2] 19.04 0.01 19.04 19.01 19.05 4.67 1.26\n", " auxiliary[1,3] 23.01 0.02 23.01 22.99 23.04 2.87 1.97\n", " auxiliary[1,4] 26.77 0.02 26.76 26.75 26.80 7.01 1.21\n", " auxiliary[1,5] 27.49 0.04 27.48 27.45 27.55 3.21 1.85\n", " auxiliary[1,6] 27.17 0.01 27.17 27.16 27.19 7.10 1.08\n", " auxiliary[1,7] 26.49 0.01 26.50 26.47 26.51 5.92 1.47\n", " auxiliary[1,8] 32.03 0.02 32.04 32.00 32.06 4.26 1.71\n", " auxiliary[1,9] 29.84 0.03 29.84 29.81 29.89 3.40 1.75\n", "auxiliary[1,10] 30.65 0.02 30.66 30.62 30.67 4.24 1.54\n", "auxiliary[1,11] 31.44 0.01 31.44 31.42 31.45 12.84 1.05\n", "auxiliary[1,12] 32.51 0.02 32.51 32.48 32.54 5.66 1.00\n", "auxiliary[1,13] 33.01 0.01 33.01 32.99 33.03 8.57 1.04\n", "auxiliary[1,14] 36.48 0.04 36.48 36.41 36.52 4.06 1.17\n", "auxiliary[1,15] 38.72 0.04 38.70 38.67 38.80 2.89 2.04\n", "auxiliary[1,16] 35.40 0.03 35.39 35.37 35.45 3.79 1.21\n", "auxiliary[1,17] 33.89 0.03 33.90 33.84 33.92 4.19 1.31\n", "auxiliary[1,18] 37.29 0.02 37.29 37.26 37.31 6.92 1.10\n", "auxiliary[1,19] 29.29 0.02 29.28 29.26 29.33 2.73 2.62\n", "auxiliary[1,20] 32.08 0.01 32.08 32.06 32.10 5.59 1.48\n", "auxiliary[1,21] 36.17 0.02 36.17 36.14 36.20 3.79 1.88\n", "auxiliary[1,22] 39.27 0.02 39.27 39.25 39.31 6.01 1.35\n", "auxiliary[1,23] 38.57 0.02 38.57 38.53 38.59 7.22 1.38\n", "auxiliary[1,24] 43.31 0.02 43.31 43.27 43.33 8.06 1.15\n", "auxiliary[1,25] 52.26 0.03 52.26 52.23 52.32 3.16 2.00\n", "auxiliary[1,26] 58.64 0.03 58.65 58.59 58.68 7.03 1.01\n", "auxiliary[1,27] 71.06 0.03 71.05 71.03 71.14 4.61 1.45\n", "auxiliary[1,28] 79.92 0.12 79.96 79.76 80.09 2.40 3.12\n", "auxiliary[1,29] 82.41 0.10 82.37 82.29 82.57 2.86 2.35\n", "auxiliary[1,30] 84.93 0.03 84.93 84.88 84.97 8.42 1.62\n", "auxiliary[1,31] 89.96 0.07 89.94 89.89 90.11 5.42 1.24\n", "auxiliary[1,32] 101.90 0.12 101.93 101.72 102.03 4.64 1.23\n", "auxiliary[1,33] 124.61 0.37 124.79 123.99 125.01 2.82 2.05\n", "auxiliary[1,34] 131.96 0.79 132.10 130.73 132.81 2.56 2.63\n", "auxiliary[1,35] 164.35 1.13 164.28 162.79 166.01 2.45 2.84\n", "auxiliary[1,36] 173.57 1.01 173.44 172.39 175.17 2.44 2.93\n", "auxiliary[1,37] 193.37 0.66 193.21 192.66 194.52 2.58 2.56\n", "auxiliary[1,38] 222.92 0.59 222.72 222.17 223.73 4.35 1.00\n", "auxiliary[1,39] 252.26 1.26 251.79 251.18 254.58 3.52 1.44\n", "auxiliary[1,40] 278.06 2.09 276.80 276.10 281.96 2.78 2.06\n", "auxiliary[1,41] 303.98 2.30 303.07 301.64 307.55 2.48 2.72\n", "auxiliary[1,42] 338.60 3.20 338.23 334.26 342.91 2.39 3.17\n", "auxiliary[1,43] 369.95 3.63 369.56 365.05 374.41 2.34 3.48\n", "auxiliary[1,44] 401.86 2.74 403.04 397.10 404.50 2.60 2.56\n", "auxiliary[1,45] 461.81 4.62 464.10 454.47 466.22 2.48 2.94\n", "auxiliary[1,46] 500.78 1.99 501.71 496.72 502.48 3.70 1.56\n", "auxiliary[1,47] 544.39 1.10 544.45 542.62 546.18 5.21 1.02\n", "auxiliary[1,48] 575.41 0.66 575.49 574.24 576.30 6.02 1.00\n", "auxiliary[1,49] 619.87 0.28 619.92 619.45 620.28 4.71 1.60\n", "auxiliary[1,50] 663.89 0.44 663.93 663.34 664.54 3.49 1.85\n", "auxiliary[1,51] 712.82 0.19 712.78 712.54 713.12 13.86 1.00\n", "auxiliary[1,52] 772.26 0.61 772.01 771.54 773.35 3.06 1.76\n", "auxiliary[1,53] 800.33 0.32 800.41 799.77 800.75 6.22 1.02\n", "auxiliary[1,54] 862.95 0.40 863.07 862.18 863.49 7.11 1.16\n", "auxiliary[1,55] 894.03 0.26 894.09 893.54 894.34 16.75 1.01\n", "auxiliary[1,56] 1016.70 1.72 1015.96 1014.98 1020.11 4.17 1.35\n", "auxiliary[1,57] 1103.67 3.57 1102.46 1099.81 1109.39 2.43 3.15\n", "auxiliary[1,58] 1184.93 5.69 1185.21 1176.81 1193.33 2.49 2.69\n", "auxiliary[1,59] 1283.89 5.30 1284.38 1276.05 1291.86 2.57 2.44\n", "auxiliary[1,60] 1379.95 3.52 1381.30 1373.29 1384.55 2.89 2.12\n", " auxiliary[2,0] 1.24 0.00 1.25 1.24 1.25 2.66 2.44\n", " auxiliary[2,1] 5.34 0.00 5.34 5.34 5.35 4.67 1.29\n", " auxiliary[2,2] 4.28 0.00 4.28 4.28 4.29 4.54 1.01\n", " auxiliary[2,3] 5.81 0.00 5.81 5.80 5.81 5.08 1.31\n", " auxiliary[2,4] 9.27 0.01 9.27 9.26 9.29 2.55 2.68\n", " auxiliary[2,5] 16.66 0.01 16.66 16.65 16.68 4.11 1.17\n", " auxiliary[2,6] 22.36 0.01 22.36 22.35 22.38 4.19 1.30\n", " auxiliary[2,7] 29.02 0.03 29.03 28.98 29.06 3.07 1.67\n", " auxiliary[2,8] 30.40 0.02 30.40 30.38 30.43 3.25 1.79\n", " auxiliary[2,9] 36.73 0.03 36.72 36.69 36.77 3.32 2.73\n", "auxiliary[2,10] 37.14 0.03 37.13 37.10 37.18 2.73 2.77\n", "auxiliary[2,11] 42.55 0.02 42.55 42.51 42.58 4.20 1.03\n", "auxiliary[2,12] 45.75 0.06 45.77 45.65 45.82 2.46 2.71\n", "auxiliary[2,13] 48.41 0.02 48.41 48.37 48.44 6.66 1.33\n", "auxiliary[2,14] 53.35 0.02 53.35 53.32 53.39 6.95 1.03\n", "auxiliary[2,15] 55.47 0.04 55.46 55.40 55.52 4.81 1.01\n", "auxiliary[2,16] 61.12 0.03 61.11 61.07 61.16 6.66 1.22\n", "auxiliary[2,17] 62.37 0.04 62.37 62.29 62.42 4.37 1.25\n", "auxiliary[2,18] 63.25 0.03 63.25 63.20 63.29 5.85 1.03\n", "auxiliary[2,19] 71.11 0.04 71.11 71.05 71.16 3.07 2.08\n", "auxiliary[2,20] 71.68 0.04 71.68 71.63 71.75 4.90 1.36\n", "auxiliary[2,21] 75.03 0.05 75.03 74.96 75.12 4.89 1.38\n", "auxiliary[2,22] 82.74 0.08 82.72 82.63 82.86 2.86 2.15\n", "auxiliary[2,23] 90.28 0.04 90.29 90.20 90.33 3.90 1.58\n", "auxiliary[2,24] 94.25 0.06 94.28 94.13 94.31 6.79 1.05\n", "auxiliary[2,25] 100.34 0.10 100.30 100.25 100.55 4.32 1.21\n", "auxiliary[2,26] 109.56 0.09 109.58 109.41 109.69 3.54 1.44\n", "auxiliary[2,27] 110.57 0.07 110.56 110.48 110.68 3.55 2.49\n", "auxiliary[2,28] 122.59 0.05 122.60 122.51 122.66 6.13 1.66\n", "auxiliary[2,29] 131.94 0.11 131.89 131.83 132.13 3.27 1.71\n", "auxiliary[2,30] 150.16 0.05 150.17 150.08 150.25 10.37 1.03\n", "auxiliary[2,31] 163.92 0.07 163.93 163.83 164.03 7.82 1.15\n", "auxiliary[2,32] 177.76 0.42 177.91 177.08 178.17 4.55 1.17\n", "auxiliary[2,33] 187.69 0.99 188.16 186.09 188.78 2.50 2.69\n", "auxiliary[2,34] 215.02 2.23 215.45 211.68 217.58 2.55 2.58\n", "auxiliary[2,35] 219.76 2.12 219.75 216.91 222.79 2.38 3.14\n", "auxiliary[2,36] 251.29 1.96 250.92 248.91 254.47 2.45 2.86\n", "auxiliary[2,37] 276.71 1.60 276.18 275.08 279.64 2.66 2.40\n", "auxiliary[2,38] 296.85 1.04 296.43 295.66 298.20 4.77 1.00\n", "auxiliary[2,39] 321.35 2.23 320.33 319.35 325.51 3.29 1.57\n", "auxiliary[2,40] 356.43 3.11 354.78 353.61 362.17 2.69 2.20\n", "auxiliary[2,41] 396.00 4.28 394.67 391.29 402.43 2.45 2.81\n", "auxiliary[2,42] 435.01 4.95 434.43 428.56 441.43 2.35 3.26\n", "auxiliary[2,43] 485.10 6.26 484.61 476.36 492.71 2.34 3.46\n", "auxiliary[2,44] 537.86 4.71 539.95 529.80 542.22 2.55 2.60\n", "auxiliary[2,45] 578.83 6.88 582.46 567.01 585.42 2.59 2.50\n", "auxiliary[2,46] 632.82 3.08 634.36 626.70 635.16 3.90 1.40\n", "auxiliary[2,47] 696.18 1.53 696.89 692.94 697.44 5.17 1.20\n", "auxiliary[2,48] 786.46 1.32 786.79 783.73 787.86 6.39 1.04\n", "auxiliary[2,49] 861.87 0.34 861.87 861.30 862.35 6.07 1.24\n", "auxiliary[2,50] 957.53 0.34 957.54 957.02 958.07 7.38 1.11\n", "auxiliary[2,51] 1051.57 0.48 1051.73 1050.82 1052.23 3.15 1.94\n", "auxiliary[2,52] 1123.89 1.14 1123.72 1122.48 1125.82 2.65 2.62\n", "auxiliary[2,53] 1232.07 0.44 1232.06 1231.39 1232.80 7.37 1.24\n", "auxiliary[2,54] 1334.96 1.43 1334.34 1333.57 1337.84 3.18 1.76\n", "auxiliary[2,55] 1461.82 0.69 1461.80 1460.82 1462.86 7.25 1.19\n", "auxiliary[2,56] 1542.81 4.31 1540.64 1539.34 1551.77 3.61 1.48\n", "auxiliary[2,57] 1680.75 7.92 1679.32 1672.39 1694.24 2.49 2.71\n", "auxiliary[2,58] 1833.69 13.22 1837.02 1813.85 1852.23 2.59 2.45\n", "auxiliary[2,59] 1991.63 12.47 1993.27 1974.61 2009.73 2.44 2.86\n", "auxiliary[2,60] 2166.95 11.45 2168.36 2150.83 2183.91 2.51 2.71\n", " auxiliary[3,0] 0.50 0.00 0.50 0.50 0.50 5.78 1.24\n", " auxiliary[3,1] 0.50 0.00 0.50 0.50 0.50 3.53 1.87\n", " auxiliary[3,2] 0.87 0.00 0.87 0.87 0.87 2.94 2.61\n", " auxiliary[3,3] 0.50 0.00 0.50 0.50 0.50 3.92 1.42\n", " auxiliary[3,4] 0.56 0.00 0.56 0.56 0.56 4.57 1.06\n", " auxiliary[3,5] 0.50 0.00 0.50 0.50 0.50 3.44 1.57\n", " auxiliary[3,6] 0.62 0.00 0.62 0.61 0.62 2.81 4.57\n", " auxiliary[3,7] 0.51 0.00 0.51 0.51 0.51 5.12 1.32\n", " auxiliary[3,8] 0.50 0.00 0.50 0.50 0.50 2.78 2.87\n", " auxiliary[3,9] 0.50 0.00 0.50 0.50 0.50 7.56 1.00\n", "auxiliary[3,10] 0.50 0.00 0.50 0.50 0.50 7.28 1.05\n", "auxiliary[3,11] 0.50 0.00 0.50 0.50 0.50 3.40 1.65\n", "auxiliary[3,12] 0.50 0.00 0.50 0.50 0.50 6.48 1.00\n", "auxiliary[3,13] 0.50 0.00 0.50 0.50 0.50 6.37 1.24\n", "auxiliary[3,14] 0.50 0.00 0.50 0.50 0.50 3.95 1.61\n", "auxiliary[3,15] 0.50 0.00 0.50 0.50 0.50 4.35 1.18\n", "auxiliary[3,16] 0.50 0.00 0.50 0.50 0.50 7.62 1.11\n", "auxiliary[3,17] 0.50 0.00 0.50 0.50 0.50 5.99 1.54\n", "auxiliary[3,18] 0.50 0.00 0.50 0.50 0.50 7.90 1.05\n", "auxiliary[3,19] 0.50 0.00 0.50 0.50 0.50 4.16 1.75\n", "auxiliary[3,20] 0.50 0.00 0.50 0.50 0.51 2.47 2.59\n", "auxiliary[3,21] 0.50 0.00 0.50 0.50 0.50 3.67 1.76\n", "auxiliary[3,22] 0.50 0.00 0.50 0.50 0.50 3.08 2.24\n", "auxiliary[3,23] 0.50 0.00 0.50 0.50 0.50 4.45 1.35\n", "auxiliary[3,24] 0.50 0.00 0.50 0.50 0.50 3.92 1.22\n", "auxiliary[3,25] 0.50 0.00 0.50 0.50 0.50 6.01 1.21\n", "auxiliary[3,26] 0.50 0.00 0.50 0.50 0.50 4.76 1.26\n", "auxiliary[3,27] 0.50 0.00 0.50 0.50 0.50 8.25 1.08\n", "auxiliary[3,28] 0.50 0.00 0.50 0.50 0.50 7.38 1.31\n", "auxiliary[3,29] 0.50 0.00 0.50 0.50 0.50 3.35 1.67\n", "auxiliary[3,30] 0.84 0.00 0.84 0.84 0.84 3.06 1.87\n", "auxiliary[3,31] 1.00 0.00 1.00 1.00 1.00 3.09 2.50\n", "auxiliary[3,32] 0.88 0.00 0.88 0.88 0.88 3.52 1.74\n", "auxiliary[3,33] 0.50 0.00 0.50 0.50 0.50 2.96 1.76\n", "auxiliary[3,34] 0.50 0.00 0.50 0.50 0.50 4.33 1.14\n", "auxiliary[3,35] 1.37 0.00 1.37 1.36 1.37 2.67 2.73\n", "auxiliary[3,36] 1.68 0.00 1.68 1.68 1.68 7.21 1.27\n", "auxiliary[3,37] 1.32 0.00 1.32 1.31 1.32 3.80 1.58\n", "auxiliary[3,38] 1.56 0.00 1.56 1.56 1.57 2.97 1.98\n", "auxiliary[3,39] 2.67 0.00 2.67 2.66 2.67 3.51 1.78\n", "auxiliary[3,40] 2.29 0.01 2.28 2.28 2.29 2.58 2.53\n", "auxiliary[3,41] 4.02 0.00 4.02 4.01 4.03 2.52 2.98\n", "auxiliary[3,42] 4.89 0.01 4.89 4.88 4.90 2.75 2.89\n", "auxiliary[3,43] 5.89 0.01 5.88 5.87 5.90 2.68 2.28\n", "auxiliary[3,44] 7.72 0.00 7.72 7.71 7.73 3.68 1.68\n", "auxiliary[3,45] 9.39 0.01 9.39 9.38 9.41 5.66 1.07\n", "auxiliary[3,46] 11.63 0.08 11.64 11.50 11.74 2.57 2.53\n", "auxiliary[3,47] 11.67 0.04 11.67 11.62 11.74 2.45 2.84\n", "auxiliary[3,48] 12.75 0.05 12.74 12.68 12.83 2.50 2.66\n", "auxiliary[3,49] 14.73 0.05 14.72 14.67 14.80 2.54 2.58\n", "auxiliary[3,50] 16.02 0.17 16.02 15.78 16.28 2.48 2.79\n", "auxiliary[3,51] 19.49 0.13 19.50 19.31 19.68 2.57 2.57\n", "auxiliary[3,52] 24.07 0.10 24.09 23.94 24.22 2.44 2.88\n", "auxiliary[3,53] 29.24 0.02 29.24 29.22 29.27 3.17 3.35\n", "auxiliary[3,54] 34.39 0.10 34.38 34.24 34.52 2.55 2.61\n", "auxiliary[3,55] 39.21 0.08 39.22 39.08 39.34 2.81 2.15\n", "auxiliary[3,56] 43.83 0.07 43.86 43.70 43.90 2.74 2.36\n", "auxiliary[3,57] 48.56 0.11 48.61 48.35 48.68 2.79 2.14\n", "auxiliary[3,58] 53.45 0.09 53.44 53.28 53.57 2.67 2.68\n", "auxiliary[3,59] 58.22 0.35 58.20 57.67 58.74 2.56 2.60\n", "auxiliary[3,60] 62.57 0.52 62.52 61.80 63.31 2.53 2.63\n", " incub_time 4.53 0.00 4.53 4.53 4.53 2.72 2.51\n", " mort_rate 0.02 0.00 0.02 0.02 0.02 5.12 1.12\n", " rec_rate 0.45 0.00 0.45 0.45 0.45 7.26 1.11\n", " rec_time 16.90 0.00 16.90 16.90 16.90 3.87 1.73\n", " rho 0.51 0.00 0.51 0.51 0.52 2.53 2.62\n", "\n", "Number of divergences: 0\n", "CPU times: user 1min 29s, sys: 606 ms, total: 1min 29s\n", "Wall time: 1min 29s\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "JmZuFDKNB51D", "outputId": "d9ea7121-cc4e-4b6f-a311-2110c6a0523f" }, "source": [ "%%time\n", "Sweden_model = CovidModel(10230000, Sweden[\"new_cases\"], Sweden[\"new_recovered\"], Sweden[\"new_deaths\"] )\n", "Sweden_mcmc = Sweden_model.fit_mcmc(num_samples=500, warmup_steps = 200)\n", "Sweden_mcmc.summary()" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "INFO \t Running inference...\n", "Warmup: 0%| | 0/700 [00:00, ?it/s]INFO \t Heuristic init: R0=2.38, incub_time=4.76, mort_rate=0.013, rec_rate=0.612, rec_time=22.2, rho=0.184\n", "Sample: 100%|██████████| 700/700 [01:51, 6.29it/s, step size=4.76e-04, acc. prob=0.779]\n" ], "name": "stderr" }, { "output_type": "stream", "text": [ "\n", " mean std median 5.0% 95.0% n_eff r_hat\n", " R0 2.38 0.00 2.38 2.38 2.38 3.33 1.67\n", " auxiliary[0,0] 10229989.96 0.14 10229990.00 10229989.74 10229990.14 2.72 2.21\n", " auxiliary[0,1] 10229979.62 0.79 10229979.83 10229978.39 10229980.67 2.64 2.33\n", " auxiliary[0,2] 10229967.07 2.25 10229967.56 10229963.65 10229970.21 2.61 2.39\n", " auxiliary[0,3] 10229951.98 4.50 10229952.82 10229945.21 10229958.62 2.59 2.42\n", " auxiliary[0,4] 10229934.37 7.51 10229935.62 10229923.24 10229945.76 2.59 2.43\n", " auxiliary[0,5] 10229914.37 11.10 10229916.05 10229898.05 10229931.60 2.59 2.44\n", " auxiliary[0,6] 10229892.23 15.11 10229894.30 10229870.20 10229916.25 2.59 2.44\n", " auxiliary[0,7] 10229868.19 19.43 10229870.60 10229838.49 10229897.88 2.59 2.45\n", " auxiliary[0,8] 10229842.47 23.94 10229845.08 10229806.09 10229879.55 2.59 2.45\n", " auxiliary[0,9] 10229815.32 28.57 10229818.10 10229772.23 10229860.08 2.59 2.45\n", "auxiliary[0,10] 10229786.88 33.24 10229789.94 10229737.01 10229839.44 2.59 2.45\n", "auxiliary[0,11] 10229757.35 37.89 10229760.59 10229700.74 10229817.88 2.59 2.45\n", "auxiliary[0,12] 10229726.86 42.49 10229730.19 10229663.64 10229795.26 2.59 2.45\n", "auxiliary[0,13] 10229695.52 47.01 10229699.04 10229625.76 10229771.73 2.59 2.44\n", "auxiliary[0,14] 10229663.40 51.46 10229667.01 10229587.38 10229747.25 2.59 2.44\n", "auxiliary[0,15] 10229630.60 55.81 10229634.16 10229548.47 10229721.98 2.60 2.44\n", "auxiliary[0,16] 10229597.20 60.06 10229600.82 10229508.92 10229695.84 2.60 2.43\n", "auxiliary[0,17] 10229563.23 64.20 10229566.99 10229469.21 10229669.09 2.60 2.43\n", "auxiliary[0,18] 10229528.74 68.24 10229532.61 10229429.10 10229641.58 2.60 2.43\n", "auxiliary[0,19] 10229493.78 72.17 10229497.61 10229388.75 10229613.39 2.60 2.43\n", "auxiliary[0,20] 10229458.39 76.01 10229462.32 10229347.78 10229584.65 2.60 2.43\n", "auxiliary[0,21] 10229422.60 79.76 10229426.71 10229306.35 10229555.08 2.60 2.43\n", "auxiliary[0,22] 10229386.42 83.42 10229390.71 10229265.16 10229525.33 2.60 2.43\n", "auxiliary[0,23] 10229349.95 86.95 10229354.43 10229223.62 10229494.83 2.60 2.43\n", "auxiliary[0,24] 10229313.07 90.42 10229317.62 10229181.75 10229463.72 2.60 2.42\n", "auxiliary[0,25] 10229275.89 93.79 10229280.73 10229139.52 10229432.18 2.60 2.42\n", "auxiliary[0,26] 10229238.37 97.07 10229243.43 10229096.97 10229400.27 2.60 2.43\n", "auxiliary[0,27] 10229200.59 100.27 10229205.82 10229054.50 10229367.80 2.60 2.43\n", "auxiliary[0,28] 10229162.49 103.39 10229168.11 10229011.61 10229334.73 2.60 2.43\n", "auxiliary[0,29] 10229124.09 106.44 10229130.07 10228968.56 10229301.28 2.60 2.43\n", "auxiliary[0,30] 10229085.42 109.40 10229091.81 10228925.61 10229267.31 2.60 2.43\n", "auxiliary[0,31] 10229046.47 112.28 10229053.24 10228882.23 10229232.88 2.60 2.43\n", "auxiliary[0,32] 10229007.25 115.09 10229014.49 10228838.78 10229197.73 2.60 2.43\n", "auxiliary[0,33] 10228967.74 117.82 10228975.58 10228795.03 10229162.49 2.60 2.43\n", "auxiliary[0,34] 10228927.97 120.47 10228936.26 10228750.97 10229126.72 2.60 2.43\n", "auxiliary[0,35] 10228887.91 123.03 10228896.68 10228706.93 10229090.12 2.60 2.43\n", "auxiliary[0,36] 10228847.69 125.64 10228856.90 10228662.80 10229053.63 2.60 2.43\n", "auxiliary[0,37] 10228807.05 128.04 10228816.65 10228618.40 10229016.42 2.60 2.43\n", "auxiliary[0,38] 10228766.19 130.27 10228776.40 10228573.64 10228978.04 2.59 2.44\n", "auxiliary[0,39] 10228724.91 132.49 10228735.54 10228528.68 10228939.56 2.59 2.44\n", "auxiliary[0,40] 10228683.18 134.21 10228695.05 10228483.36 10228899.05 2.59 2.44\n", "auxiliary[0,41] 10228641.16 136.24 10228653.51 10228437.73 10228859.37 2.59 2.45\n", "auxiliary[0,42] 10228598.62 138.15 10228611.25 10228392.15 10228818.93 2.59 2.45\n", "auxiliary[0,43] 10228552.98 138.43 10228566.36 10228345.44 10228772.47 2.58 2.45\n", "auxiliary[0,44] 10228504.57 138.05 10228518.50 10228297.07 10228722.60 2.58 2.45\n", "auxiliary[0,45] 10228454.00 137.60 10228468.14 10228246.76 10228670.69 2.58 2.45\n", "auxiliary[0,46] 10228402.03 137.50 10228416.36 10228194.67 10228618.22 2.59 2.45\n", "auxiliary[0,47] 10228348.83 137.78 10228362.98 10228141.04 10228565.24 2.58 2.45\n", "auxiliary[0,48] 10228293.68 137.93 10228307.96 10228085.94 10228510.63 2.58 2.46\n", "auxiliary[0,49] 10228235.42 136.91 10228249.90 10228028.83 10228449.78 2.58 2.46\n", "auxiliary[0,50] 10228173.83 134.65 10228188.83 10227970.06 10228383.59 2.58 2.46\n", "auxiliary[0,51] 10228109.30 131.43 10228125.35 10227909.02 10228311.74 2.58 2.46\n", "auxiliary[0,52] 10228042.55 128.32 10228059.27 10227856.38 10228243.10 2.58 2.46\n", "auxiliary[0,53] 10227971.29 122.45 10227991.10 10227790.08 10228144.82 2.55 2.50\n", "auxiliary[0,54] 10227892.55 112.56 10227919.72 10227719.68 10228035.12 2.56 2.46\n", "auxiliary[0,55] 10227802.55 99.43 10227836.06 10227643.36 10227915.04 2.63 2.33\n", "auxiliary[0,56] 10227698.94 83.99 10227735.36 10227560.05 10227785.80 2.73 2.15\n", "auxiliary[0,57] 10227582.14 64.74 10227612.69 10227472.66 10227644.94 2.90 1.97\n", "auxiliary[0,58] 10227447.91 46.52 10227468.80 10227368.59 10227495.46 3.09 1.85\n", "auxiliary[0,59] 10227294.58 31.45 10227305.59 10227242.45 10227330.36 3.12 1.87\n", "auxiliary[0,60] 10227092.27 28.69 10227101.25 10227045.00 10227127.34 3.05 1.92\n", " auxiliary[1,0] 9.91 0.01 9.91 9.90 9.92 2.44 2.97\n", " auxiliary[1,1] 13.97 0.00 13.98 13.97 13.98 7.33 1.57\n", " auxiliary[1,2] 19.54 0.01 19.54 19.53 19.55 5.28 1.33\n", " auxiliary[1,3] 24.94 0.01 24.93 24.92 24.96 3.36 1.68\n", " auxiliary[1,4] 26.76 0.01 26.76 26.73 26.78 3.56 1.72\n", " auxiliary[1,5] 30.54 0.01 30.54 30.52 30.55 3.52 1.89\n", " auxiliary[1,6] 30.12 0.01 30.11 30.10 30.14 4.80 1.29\n", " auxiliary[1,7] 31.42 0.02 31.43 31.38 31.44 3.00 1.83\n", " auxiliary[1,8] 31.21 0.01 31.21 31.20 31.23 3.39 1.90\n", " auxiliary[1,9] 31.56 0.02 31.57 31.53 31.59 2.68 2.29\n", "auxiliary[1,10] 39.43 0.03 39.42 39.38 39.47 2.75 2.35\n", "auxiliary[1,11] 40.57 0.01 40.57 40.56 40.59 6.53 1.21\n", "auxiliary[1,12] 37.14 0.02 37.13 37.12 37.17 3.34 1.59\n", "auxiliary[1,13] 40.47 0.01 40.47 40.46 40.49 4.91 1.46\n", "auxiliary[1,14] 41.93 0.01 41.93 41.91 41.93 6.87 1.25\n", "auxiliary[1,15] 44.13 0.02 44.13 44.11 44.16 2.88 2.29\n", "auxiliary[1,16] 45.02 0.01 45.02 45.01 45.05 4.19 1.49\n", "auxiliary[1,17] 44.79 0.01 44.79 44.78 44.81 12.60 1.00\n", "auxiliary[1,18] 52.28 0.02 52.27 52.25 52.32 2.97 1.79\n", "auxiliary[1,19] 51.54 0.02 51.54 51.49 51.57 3.95 1.30\n", "auxiliary[1,20] 50.71 0.01 50.71 50.69 50.73 2.76 2.27\n", "auxiliary[1,21] 48.86 0.02 48.87 48.83 48.89 5.30 1.20\n", "auxiliary[1,22] 49.64 0.01 49.64 49.62 49.66 4.92 1.66\n", "auxiliary[1,23] 39.02 0.01 39.02 39.01 39.04 6.54 1.08\n", "auxiliary[1,24] 46.94 0.01 46.94 46.92 46.95 7.55 1.00\n", "auxiliary[1,25] 48.14 0.03 48.14 48.11 48.19 3.05 1.64\n", "auxiliary[1,26] 57.80 0.02 57.81 57.77 57.83 8.74 1.02\n", "auxiliary[1,27] 52.49 0.01 52.49 52.47 52.51 5.06 1.32\n", "auxiliary[1,28] 53.47 0.01 53.46 53.44 53.49 7.48 1.26\n", "auxiliary[1,29] 60.60 0.01 60.60 60.58 60.63 4.73 1.56\n", "auxiliary[1,30] 65.99 0.02 65.99 65.96 66.01 5.23 1.02\n", "auxiliary[1,31] 74.57 0.02 74.57 74.55 74.60 7.05 1.05\n", "auxiliary[1,32] 78.51 0.03 78.50 78.48 78.56 5.56 1.23\n", "auxiliary[1,33] 94.40 0.02 94.40 94.37 94.42 11.92 1.05\n", "auxiliary[1,34] 94.89 0.03 94.90 94.84 94.93 4.63 1.37\n", "auxiliary[1,35] 114.01 0.04 114.01 113.96 114.07 4.79 1.05\n", "auxiliary[1,36] 126.00 0.03 125.99 125.95 126.05 7.89 1.02\n", "auxiliary[1,37] 140.80 0.05 140.82 140.69 140.86 3.54 1.82\n", "auxiliary[1,38] 156.55 0.05 156.56 156.47 156.63 4.00 1.13\n", "auxiliary[1,39] 169.05 0.09 169.05 168.92 169.16 3.19 1.60\n", "auxiliary[1,40] 186.00 0.13 185.98 185.85 186.21 3.68 1.35\n", "auxiliary[1,41] 204.18 0.10 204.17 204.03 204.31 2.92 2.18\n", "auxiliary[1,42] 213.68 0.93 213.77 212.03 214.80 2.71 2.27\n", "auxiliary[1,43] 224.86 0.72 224.80 223.75 225.90 2.57 2.47\n", "auxiliary[1,44] 231.00 0.43 230.82 230.55 231.73 2.78 2.08\n", "auxiliary[1,45] 243.89 0.17 243.84 243.67 244.18 3.33 1.52\n", "auxiliary[1,46] 262.45 0.18 262.43 262.19 262.71 4.37 1.00\n", "auxiliary[1,47] 291.15 0.11 291.16 290.97 291.30 6.69 1.00\n", "auxiliary[1,48] 316.21 0.11 316.16 316.08 316.38 3.11 1.81\n", "auxiliary[1,49] 341.23 0.27 341.26 340.80 341.64 2.95 1.97\n", "auxiliary[1,50] 366.81 0.84 366.69 365.72 368.31 2.61 2.42\n", "auxiliary[1,51] 373.56 1.55 373.37 371.40 376.13 2.67 2.32\n", "auxiliary[1,52] 399.10 1.85 399.02 396.63 401.84 2.50 2.58\n", "auxiliary[1,53] 416.83 1.06 417.41 415.23 417.95 2.44 2.83\n", "auxiliary[1,54] 460.58 0.56 460.86 459.65 461.11 3.31 1.55\n", "auxiliary[1,55] 463.03 0.25 462.99 462.73 463.49 3.94 1.42\n", "auxiliary[1,56] 488.86 0.99 489.39 487.02 489.66 3.63 1.47\n", "auxiliary[1,57] 513.68 0.17 513.68 513.39 513.97 4.19 1.30\n", "auxiliary[1,58] 532.40 0.30 532.49 531.90 532.74 3.18 1.51\n", "auxiliary[1,59] 560.68 0.77 560.35 559.91 561.80 3.13 1.78\n", "auxiliary[1,60] 611.78 0.56 611.94 610.93 612.55 2.59 2.38\n", " auxiliary[2,0] 1.91 0.00 1.91 1.90 1.91 2.97 2.45\n", " auxiliary[2,1] 3.28 0.00 3.28 3.28 3.29 2.54 3.84\n", " auxiliary[2,2] 6.36 0.00 6.36 6.35 6.36 7.28 1.28\n", " auxiliary[2,3] 9.72 0.00 9.72 9.72 9.72 8.31 1.01\n", " auxiliary[2,4] 16.22 0.01 16.22 16.20 16.23 2.99 1.97\n", " auxiliary[2,5] 17.26 0.00 17.26 17.25 17.26 3.57 1.91\n", " auxiliary[2,6] 21.50 0.01 21.50 21.49 21.52 4.11 1.03\n", " auxiliary[2,7] 28.23 0.01 28.23 28.22 28.24 4.77 1.44\n", " auxiliary[2,8] 37.40 0.02 37.40 37.38 37.43 2.63 2.48\n", " auxiliary[2,9] 41.72 0.01 41.72 41.70 41.73 2.70 2.44\n", "auxiliary[2,10] 43.12 0.02 43.12 43.09 43.14 6.54 1.15\n", "auxiliary[2,11] 51.54 0.02 51.54 51.51 51.55 3.65 1.96\n", "auxiliary[2,12] 58.60 0.01 58.60 58.58 58.62 7.65 1.03\n", "auxiliary[2,13] 60.94 0.02 60.94 60.92 60.97 8.09 1.24\n", "auxiliary[2,14] 66.58 0.02 66.58 66.56 66.61 4.45 1.64\n", "auxiliary[2,15] 69.62 0.01 69.62 69.61 69.65 5.76 1.15\n", "auxiliary[2,16] 79.41 0.02 79.42 79.37 79.44 4.63 1.32\n", "auxiliary[2,17] 86.08 0.03 86.08 86.05 86.12 9.09 1.07\n", "auxiliary[2,18] 88.39 0.02 88.39 88.36 88.43 4.80 1.05\n", "auxiliary[2,19] 92.18 0.02 92.18 92.14 92.21 3.23 2.09\n", "auxiliary[2,20] 99.58 0.03 99.58 99.54 99.62 4.70 1.10\n", "auxiliary[2,21] 104.76 0.02 104.76 104.73 104.79 14.69 1.12\n", "auxiliary[2,22] 108.30 0.03 108.31 108.26 108.35 4.33 1.42\n", "auxiliary[2,23] 102.53 0.03 102.54 102.50 102.58 11.13 1.00\n", "auxiliary[2,24] 107.65 0.02 107.65 107.63 107.68 12.63 1.03\n", "auxiliary[2,25] 115.83 0.04 115.82 115.76 115.88 5.22 1.18\n", "auxiliary[2,26] 119.52 0.06 119.51 119.43 119.62 3.64 1.76\n", "auxiliary[2,27] 130.23 0.05 130.24 130.16 130.30 3.58 1.39\n", "auxiliary[2,28] 139.36 0.05 139.36 139.29 139.44 2.86 2.34\n", "auxiliary[2,29] 144.00 0.03 144.00 143.94 144.03 6.01 1.03\n", "auxiliary[2,30] 151.02 0.06 151.02 150.93 151.12 4.26 1.62\n", "auxiliary[2,31] 156.20 0.06 156.20 156.11 156.27 2.82 2.50\n", "auxiliary[2,32] 167.98 0.04 167.99 167.91 168.05 5.18 1.73\n", "auxiliary[2,33] 178.06 0.04 178.06 178.00 178.13 5.03 1.32\n", "auxiliary[2,34] 195.33 0.16 195.28 195.14 195.60 2.58 2.51\n", "auxiliary[2,35] 205.45 0.07 205.44 205.36 205.56 4.02 1.75\n", "auxiliary[2,36] 229.82 0.09 229.79 229.73 229.98 3.04 2.17\n", "auxiliary[2,37] 247.46 0.15 247.43 247.24 247.69 2.82 2.55\n", "auxiliary[2,38] 270.68 0.18 270.69 270.45 270.97 2.74 2.30\n", "auxiliary[2,39] 287.20 0.18 287.27 286.90 287.43 4.62 1.07\n", "auxiliary[2,40] 310.94 0.37 310.86 310.44 311.46 2.56 2.44\n", "auxiliary[2,41] 328.16 0.28 328.18 327.72 328.51 2.50 2.56\n", "auxiliary[2,42] 359.69 2.42 360.15 355.57 362.82 2.68 2.30\n", "auxiliary[2,43] 394.06 2.23 393.88 390.46 397.21 2.52 2.59\n", "auxiliary[2,44] 437.38 1.48 436.76 435.63 439.61 2.56 2.44\n", "auxiliary[2,45] 475.48 0.83 475.07 474.71 477.07 3.14 1.61\n", "auxiliary[2,46] 509.78 0.54 509.61 509.16 510.61 3.99 1.12\n", "auxiliary[2,47] 535.68 0.43 535.55 535.10 536.36 4.02 1.36\n", "auxiliary[2,48] 566.52 0.22 566.49 566.11 566.80 2.80 2.44\n", "auxiliary[2,49] 600.90 0.64 600.90 599.92 601.96 2.84 2.19\n", "auxiliary[2,50] 638.27 2.46 638.21 634.58 642.10 2.63 2.38\n", "auxiliary[2,51] 696.22 5.05 695.53 689.61 705.12 2.67 2.33\n", "auxiliary[2,52] 735.71 5.88 735.57 728.24 744.30 2.45 2.71\n", "auxiliary[2,53] 781.93 4.52 784.25 775.03 786.38 2.48 2.64\n", "auxiliary[2,54] 802.01 1.17 802.56 799.75 803.15 3.73 1.39\n", "auxiliary[2,55] 872.02 0.73 872.03 871.14 872.94 7.61 1.07\n", "auxiliary[2,56] 935.24 3.49 937.27 928.85 937.71 3.60 1.48\n", "auxiliary[2,57] 983.49 0.22 983.48 983.16 983.85 4.67 1.68\n", "auxiliary[2,58] 1044.23 0.26 1044.16 1043.86 1044.63 4.19 1.66\n", "auxiliary[2,59] 1120.15 4.43 1119.05 1113.83 1127.05 2.74 2.24\n", "auxiliary[2,60] 1267.76 2.42 1268.02 1263.90 1270.99 2.59 2.49\n", " auxiliary[3,0] 0.50 0.00 0.50 0.50 0.50 3.22 2.11\n", " auxiliary[3,1] 0.50 0.00 0.50 0.50 0.50 6.03 1.16\n", " auxiliary[3,2] 0.50 0.00 0.50 0.50 0.50 4.85 1.78\n", " auxiliary[3,3] 0.50 0.00 0.50 0.50 0.50 2.79 2.07\n", " auxiliary[3,4] 0.50 0.00 0.50 0.50 0.50 6.81 1.32\n", " auxiliary[3,5] 0.50 0.00 0.50 0.50 0.50 9.27 1.10\n", " auxiliary[3,6] 0.50 0.00 0.50 0.50 0.50 6.97 1.34\n", " auxiliary[3,7] 0.50 0.00 0.50 0.50 0.50 7.25 1.04\n", " auxiliary[3,8] 0.50 0.00 0.50 0.50 0.50 4.81 1.37\n", " auxiliary[3,9] 0.50 0.00 0.50 0.50 0.50 2.58 2.45\n", "auxiliary[3,10] 0.50 0.00 0.50 0.50 0.50 4.85 1.48\n", "auxiliary[3,11] 0.50 0.00 0.50 0.50 0.50 4.11 1.48\n", "auxiliary[3,12] 0.50 0.00 0.50 0.50 0.50 3.10 1.93\n", "auxiliary[3,13] 0.50 0.00 0.50 0.50 0.50 7.16 1.14\n", "auxiliary[3,14] 0.50 0.00 0.50 0.50 0.50 4.02 1.59\n", "auxiliary[3,15] 0.67 0.00 0.67 0.67 0.67 6.61 1.00\n", "auxiliary[3,16] 0.99 0.00 0.99 0.99 0.99 5.24 1.44\n", "auxiliary[3,17] 0.82 0.00 0.82 0.81 0.82 5.22 1.01\n", "auxiliary[3,18] 0.96 0.00 0.96 0.96 0.96 4.60 1.68\n", "auxiliary[3,19] 1.05 0.00 1.05 1.05 1.05 6.89 1.21\n", "auxiliary[3,20] 0.93 0.00 0.93 0.93 0.93 8.92 1.48\n", "auxiliary[3,21] 1.09 0.00 1.09 1.09 1.09 4.21 1.12\n", "auxiliary[3,22] 1.15 0.00 1.15 1.15 1.15 9.93 1.01\n", "auxiliary[3,23] 1.17 0.00 1.17 1.17 1.17 2.88 2.19\n", "auxiliary[3,24] 1.03 0.00 1.03 1.03 1.03 3.78 1.55\n", "auxiliary[3,25] 1.59 0.00 1.59 1.59 1.59 9.67 1.21\n", "auxiliary[3,26] 1.99 0.00 1.99 1.98 1.99 2.97 2.02\n", "auxiliary[3,27] 2.08 0.00 2.08 2.07 2.08 2.61 2.52\n", "auxiliary[3,28] 2.37 0.00 2.37 2.37 2.37 7.86 1.02\n", "auxiliary[3,29] 2.52 0.00 2.52 2.52 2.52 3.58 1.70\n", "auxiliary[3,30] 2.77 0.00 2.77 2.76 2.77 8.74 1.00\n", "auxiliary[3,31] 2.97 0.00 2.97 2.97 2.97 6.45 1.02\n", "auxiliary[3,32] 3.23 0.00 3.23 3.23 3.23 7.62 1.19\n", "auxiliary[3,33] 3.22 0.00 3.22 3.22 3.22 3.20 1.96\n", "auxiliary[3,34] 3.68 0.00 3.68 3.67 3.68 2.75 2.20\n", "auxiliary[3,35] 4.03 0.00 4.03 4.03 4.03 7.79 1.00\n", "auxiliary[3,36] 3.81 0.00 3.81 3.81 3.81 3.24 2.13\n", "auxiliary[3,37] 3.73 0.00 3.73 3.73 3.73 10.02 1.08\n", "auxiliary[3,38] 3.60 0.00 3.60 3.60 3.60 3.46 1.40\n", "auxiliary[3,39] 3.79 0.00 3.79 3.78 3.79 5.58 1.08\n", "auxiliary[3,40] 3.80 0.00 3.80 3.80 3.81 3.68 1.78\n", "auxiliary[3,41] 4.05 0.00 4.05 4.05 4.05 8.28 1.09\n", "auxiliary[3,42] 4.68 0.00 4.68 4.68 4.68 3.01 1.96\n", "auxiliary[3,43] 5.55 0.00 5.55 5.54 5.55 2.73 2.48\n", "auxiliary[3,44] 5.91 0.00 5.91 5.91 5.92 3.14 1.93\n", "auxiliary[3,45] 7.20 0.00 7.20 7.19 7.20 5.40 1.43\n", "auxiliary[3,46] 8.09 0.00 8.09 8.09 8.10 11.02 1.02\n", "auxiliary[3,47] 8.39 0.00 8.39 8.38 8.39 4.65 1.17\n", "auxiliary[3,48] 9.32 0.00 9.33 9.32 9.33 3.05 1.80\n", "auxiliary[3,49] 9.90 0.00 9.90 9.90 9.91 7.20 1.03\n", "auxiliary[3,50] 10.14 0.01 10.14 10.13 10.15 4.24 1.60\n", "auxiliary[3,51] 11.23 0.00 11.23 11.22 11.23 8.46 1.01\n", "auxiliary[3,52] 12.60 0.00 12.60 12.60 12.61 3.82 1.81\n", "auxiliary[3,53] 14.15 0.00 14.15 14.14 14.16 3.04 2.06\n", "auxiliary[3,54] 15.71 0.00 15.71 15.71 15.72 5.95 1.00\n", "auxiliary[3,55] 17.63 0.01 17.64 17.62 17.65 3.29 1.91\n", "auxiliary[3,56] 19.45 0.02 19.45 19.42 19.49 2.77 2.24\n", "auxiliary[3,57] 22.05 0.02 22.05 22.03 22.08 2.72 2.12\n", "auxiliary[3,58] 24.81 0.02 24.81 24.79 24.84 2.79 2.20\n", "auxiliary[3,59] 27.92 0.02 27.92 27.88 27.93 3.54 1.70\n", "auxiliary[3,60] 31.45 0.04 31.44 31.41 31.52 3.19 1.82\n", " incub_time 4.76 0.00 4.76 4.76 4.76 4.21 1.07\n", " mort_rate 0.01 0.00 0.01 0.01 0.01 3.54 1.59\n", " rec_rate 0.61 0.00 0.61 0.61 0.61 7.14 1.11\n", " rec_time 22.24 0.00 22.24 22.24 22.24 4.05 1.39\n", " rho 0.52 0.00 0.52 0.52 0.52 2.55 2.49\n", "\n", "Number of divergences: 0\n", "CPU times: user 1min 50s, sys: 768 ms, total: 1min 51s\n", "Wall time: 1min 51s\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "wD7d7ySrCxwt", "outputId": "2734eb73-5e5c-4ccf-f494-66aaadc2c219" }, "source": [ "%%time\n", "Sweden_model = CovidModel(10230000, Sweden[\"new_cases\"], Sweden[\"new_recovered\"], Sweden[\"new_deaths\"] )\n", "Sweden_mcmc = Sweden_model.fit_mcmc(num_samples=500, warmup_steps = 200)\n", "Sweden_mcmc.summary()" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "INFO \t Running inference...\n", "Warmup: 0%| | 0/700 [00:00, ?it/s]INFO \t Heuristic init: R0=2.49, incub_time=5.56, mort_rate=0.0429, rec_rate=0.673, rec_time=15.5, rho=0.18\n", "Sample: 100%|██████████| 700/700 [01:20, 8.70it/s, step size=1.74e-03, acc. prob=0.597]\n" ], "name": "stderr" }, { "output_type": "stream", "text": [ "\n", " mean std median 5.0% 95.0% n_eff r_hat\n", " R0 2.49 0.00 2.49 2.49 2.49 6.33 1.32\n", " auxiliary[0,0] 10229991.15 0.59 10229991.11 10229990.07 10229991.94 2.73 2.25\n", " auxiliary[0,1] 10229981.86 1.44 10229981.75 10229979.25 10229983.84 2.73 2.26\n", " auxiliary[0,2] 10229971.31 2.52 10229971.10 10229966.86 10229974.77 2.71 2.27\n", " auxiliary[0,3] 10229959.59 3.78 10229959.26 10229952.94 10229964.80 2.72 2.26\n", " auxiliary[0,4] 10229946.74 5.22 10229946.28 10229937.59 10229953.90 2.72 2.26\n", " auxiliary[0,5] 10229932.85 6.82 10229932.21 10229920.95 10229942.20 2.73 2.25\n", " auxiliary[0,6] 10229917.93 8.56 10229917.14 10229903.07 10229929.66 2.73 2.25\n", " auxiliary[0,7] 10229902.02 10.44 10229901.01 10229883.94 10229916.37 2.73 2.25\n", " auxiliary[0,8] 10229885.12 12.44 10229883.88 10229863.63 10229902.22 2.73 2.24\n", " auxiliary[0,9] 10229867.27 14.54 10229865.81 10229842.20 10229887.23 2.74 2.24\n", "auxiliary[0,10] 10229848.48 16.76 10229846.78 10229819.66 10229871.52 2.74 2.23\n", "auxiliary[0,11] 10229828.79 19.05 10229826.84 10229796.23 10229855.01 2.75 2.23\n", "auxiliary[0,12] 10229808.19 21.43 10229806.04 10229771.59 10229837.65 2.75 2.23\n", "auxiliary[0,13] 10229786.73 23.90 10229784.28 10229745.98 10229819.61 2.75 2.22\n", "auxiliary[0,14] 10229764.40 26.43 10229761.62 10229719.46 10229800.76 2.75 2.22\n", "auxiliary[0,15] 10229741.21 29.03 10229738.09 10229691.89 10229781.17 2.75 2.22\n", "auxiliary[0,16] 10229717.19 31.66 10229713.80 10229663.51 10229760.82 2.76 2.22\n", "auxiliary[0,17] 10229692.34 34.34 10229688.64 10229634.20 10229739.72 2.76 2.21\n", "auxiliary[0,18] 10229666.65 37.06 10229662.55 10229604.16 10229717.75 2.76 2.21\n", "auxiliary[0,19] 10229640.16 39.81 10229635.56 10229573.10 10229695.10 2.76 2.21\n", "auxiliary[0,20] 10229612.85 42.60 10229607.81 10229541.21 10229671.65 2.76 2.21\n", "auxiliary[0,21] 10229584.73 45.38 10229579.33 10229508.59 10229647.46 2.77 2.21\n", "auxiliary[0,22] 10229555.80 48.18 10229550.10 10229474.83 10229622.36 2.77 2.20\n", "auxiliary[0,23] 10229526.08 50.98 10229519.94 10229440.38 10229596.60 2.77 2.20\n", "auxiliary[0,24] 10229495.56 53.79 10229488.96 10229405.07 10229569.95 2.77 2.20\n", "auxiliary[0,25] 10229464.23 56.59 10229457.24 10229369.30 10229542.51 2.77 2.20\n", "auxiliary[0,26] 10229432.06 59.39 10229424.77 10229332.49 10229514.23 2.77 2.20\n", "auxiliary[0,27] 10229399.08 62.17 10229391.41 10229294.96 10229485.09 2.77 2.20\n", "auxiliary[0,28] 10229365.23 64.93 10229357.17 10229256.51 10229455.05 2.77 2.20\n", "auxiliary[0,29] 10229330.49 67.68 10229322.04 10229217.26 10229424.05 2.77 2.20\n", "auxiliary[0,30] 10229294.88 70.35 10229286.01 10229177.41 10229392.24 2.77 2.20\n", "auxiliary[0,31] 10229258.29 72.99 10229249.17 10229136.57 10229359.37 2.77 2.20\n", "auxiliary[0,32] 10229220.74 75.59 10229211.40 10229094.73 10229325.48 2.77 2.20\n", "auxiliary[0,33] 10229182.15 78.12 10229172.58 10229051.73 10229290.42 2.77 2.20\n", "auxiliary[0,34] 10229142.46 80.57 10229132.68 10229007.72 10229254.13 2.77 2.21\n", "auxiliary[0,35] 10229102.07 82.81 10229092.09 10228963.68 10229216.85 2.76 2.21\n", "auxiliary[0,36] 10229059.90 85.00 10229049.84 10228917.62 10229177.52 2.76 2.21\n", "auxiliary[0,37] 10229016.66 87.00 10229006.51 10228870.57 10229137.30 2.76 2.21\n", "auxiliary[0,38] 10228971.38 88.88 10228961.18 10228821.74 10229094.54 2.76 2.21\n", "auxiliary[0,39] 10228924.56 90.37 10228914.56 10228771.62 10229049.96 2.75 2.22\n", "auxiliary[0,40] 10228875.40 91.64 10228865.94 10228719.14 10229002.09 2.74 2.24\n", "auxiliary[0,41] 10228823.85 92.41 10228814.97 10228665.46 10228951.14 2.73 2.25\n", "auxiliary[0,42] 10228769.10 92.72 10228760.69 10228608.90 10228896.72 2.72 2.26\n", "auxiliary[0,43] 10228709.86 92.36 10228701.65 10228548.67 10228836.66 2.72 2.26\n", "auxiliary[0,44] 10228646.14 91.08 10228638.49 10228485.95 10228772.32 2.71 2.28\n", "auxiliary[0,45] 10228577.12 88.61 10228570.13 10228418.73 10228699.36 2.70 2.29\n", "auxiliary[0,46] 10228501.68 85.34 10228497.34 10228346.21 10228618.95 2.68 2.31\n", "auxiliary[0,47] 10228418.20 80.95 10228416.06 10228323.33 10228578.74 2.67 2.32\n", "auxiliary[0,48] 10228326.83 76.22 10228325.53 10228235.30 10228470.42 2.65 2.35\n", "auxiliary[0,49] 10228227.10 69.73 10228227.36 10228143.15 10228354.91 2.65 2.36\n", "auxiliary[0,50] 10228117.59 62.61 10228119.31 10228042.96 10228231.05 2.67 2.34\n", "auxiliary[0,51] 10227998.15 55.42 10227999.71 10227930.48 10228098.27 2.69 2.30\n", "auxiliary[0,52] 10227869.05 48.39 10227870.31 10227811.68 10227958.18 2.70 2.29\n", "auxiliary[0,53] 10227729.96 42.15 10227730.96 10227680.97 10227808.62 2.72 2.26\n", "auxiliary[0,54] 10227581.27 36.58 10227580.88 10227539.15 10227652.29 2.75 2.24\n", "auxiliary[0,55] 10227423.73 31.88 10227422.67 10227377.08 10227477.75 2.80 2.18\n", "auxiliary[0,56] 10227258.38 27.06 10227257.57 10227227.53 10227313.51 2.82 2.15\n", "auxiliary[0,57] 10227085.10 23.09 10227086.22 10227052.36 10227126.00 2.85 2.14\n", "auxiliary[0,58] 10226905.70 20.47 10226906.44 10226881.30 10226947.37 2.82 2.16\n", "auxiliary[0,59] 10226709.37 24.28 10226709.01 10226681.56 10226758.18 2.73 2.26\n", "auxiliary[0,60] 10226481.02 25.52 10226480.71 10226452.43 10226530.86 2.72 2.27\n", " auxiliary[1,0] 6.66 0.01 6.66 6.65 6.67 3.57 1.64\n", " auxiliary[1,1] 10.23 0.01 10.22 10.22 10.25 3.16 1.84\n", " auxiliary[1,2] 15.89 0.01 15.89 15.88 15.90 8.67 1.04\n", " auxiliary[1,3] 19.91 0.01 19.91 19.89 19.92 4.29 1.23\n", " auxiliary[1,4] 23.70 0.01 23.70 23.69 23.72 9.07 1.19\n", " auxiliary[1,5] 28.29 0.02 28.29 28.27 28.31 8.87 1.00\n", " auxiliary[1,6] 33.87 0.01 33.87 33.84 33.89 9.43 1.00\n", " auxiliary[1,7] 29.92 0.03 29.92 29.88 29.95 5.49 1.36\n", " auxiliary[1,8] 40.04 0.02 40.04 40.01 40.07 4.06 1.45\n", " auxiliary[1,9] 40.80 0.04 40.80 40.75 40.85 2.57 2.70\n", "auxiliary[1,10] 43.06 0.05 43.07 42.98 43.12 2.57 2.31\n", "auxiliary[1,11] 33.68 0.01 33.67 33.66 33.70 8.90 1.02\n", "auxiliary[1,12] 34.75 0.02 34.75 34.72 34.78 3.27 2.16\n", "auxiliary[1,13] 34.80 0.03 34.81 34.76 34.84 2.87 2.21\n", "auxiliary[1,14] 36.97 0.03 36.97 36.93 37.02 3.58 1.69\n", "auxiliary[1,15] 42.01 0.03 42.00 41.98 42.04 6.88 1.15\n", "auxiliary[1,16] 43.07 0.03 43.08 43.02 43.10 4.06 1.70\n", "auxiliary[1,17] 41.62 0.03 41.61 41.56 41.66 5.47 1.00\n", "auxiliary[1,18] 49.07 0.06 49.08 48.98 49.14 2.57 2.75\n", "auxiliary[1,19] 44.54 0.05 44.57 44.47 44.60 3.35 1.62\n", "auxiliary[1,20] 53.25 0.02 53.24 53.22 53.27 9.30 1.15\n", "auxiliary[1,21] 47.51 0.05 47.52 47.45 47.57 2.95 2.07\n", "auxiliary[1,22] 46.80 0.06 46.82 46.70 46.85 2.86 2.25\n", "auxiliary[1,23] 47.34 0.05 47.32 47.28 47.43 3.46 1.63\n", "auxiliary[1,24] 42.41 0.03 42.41 42.35 42.45 2.63 2.98\n", "auxiliary[1,25] 40.67 0.02 40.67 40.64 40.70 10.47 1.03\n", "auxiliary[1,26] 53.37 0.09 53.32 53.25 53.50 2.52 2.78\n", "auxiliary[1,27] 54.84 0.05 54.82 54.77 54.92 3.89 1.31\n", "auxiliary[1,28] 66.33 0.07 66.37 66.22 66.40 3.48 1.54\n", "auxiliary[1,29] 70.65 0.04 70.65 70.57 70.70 7.31 1.00\n", "auxiliary[1,30] 60.40 0.04 60.40 60.31 60.44 8.10 1.08\n", "auxiliary[1,31] 75.65 0.06 75.64 75.57 75.76 3.39 2.03\n", "auxiliary[1,32] 93.04 0.04 93.04 92.97 93.10 16.86 1.10\n", "auxiliary[1,33] 116.31 0.07 116.31 116.23 116.42 5.04 1.29\n", "auxiliary[1,34] 123.28 0.36 123.26 122.71 123.77 2.57 2.55\n", "auxiliary[1,35] 148.64 0.42 148.61 148.17 149.38 2.97 2.03\n", "auxiliary[1,36] 166.57 0.48 166.52 166.08 167.65 2.91 2.06\n", "auxiliary[1,37] 186.14 0.45 186.16 185.48 186.67 2.67 2.26\n", "auxiliary[1,38] 200.84 0.52 200.81 200.22 201.60 2.63 2.41\n", "auxiliary[1,39] 216.42 0.24 216.34 216.09 216.81 4.00 1.22\n", "auxiliary[1,40] 242.89 0.17 242.89 242.63 243.14 5.06 1.41\n", "auxiliary[1,41] 269.64 0.28 269.58 269.26 270.07 2.87 2.25\n", "auxiliary[1,42] 289.27 0.86 289.26 288.20 290.79 2.64 2.33\n", "auxiliary[1,43] 306.87 0.38 307.04 306.21 307.28 2.72 2.04\n", "auxiliary[1,44] 344.20 0.65 344.25 343.43 345.21 2.71 2.36\n", "auxiliary[1,45] 384.44 0.55 384.22 383.77 385.15 4.69 1.21\n", "auxiliary[1,46] 408.56 1.21 408.70 406.65 410.09 2.55 2.63\n", "auxiliary[1,47] 427.39 0.69 427.07 426.62 428.55 3.18 1.56\n", "auxiliary[1,48] 476.65 0.43 476.63 476.07 477.31 4.55 1.21\n", "auxiliary[1,49] 509.23 0.39 509.12 508.67 509.80 3.10 1.83\n", "auxiliary[1,50] 550.91 0.39 550.92 550.30 551.49 3.01 1.92\n", "auxiliary[1,51] 584.26 0.48 584.44 583.46 584.81 3.43 2.03\n", "auxiliary[1,52] 632.77 0.41 632.70 632.23 633.33 12.27 1.00\n", "auxiliary[1,53] 655.03 0.47 654.97 654.38 655.97 4.23 1.62\n", "auxiliary[1,54] 694.68 0.66 694.88 693.82 695.67 2.75 2.28\n", "auxiliary[1,55] 698.19 0.57 698.06 697.35 699.00 2.76 2.16\n", "auxiliary[1,56] 768.29 0.70 768.37 767.15 768.88 5.52 1.53\n", "auxiliary[1,57] 823.90 0.39 824.00 823.17 824.36 9.17 1.15\n", "auxiliary[1,58] 850.59 3.89 850.75 844.69 855.16 2.68 2.34\n", "auxiliary[1,59] 942.18 6.18 943.26 933.54 951.90 2.74 2.26\n", "auxiliary[1,60] 1026.96 6.99 1028.46 1016.67 1037.38 2.74 2.21\n", " auxiliary[2,0] 1.03 0.00 1.04 1.03 1.04 4.67 1.76\n", " auxiliary[2,1] 0.50 0.00 0.50 0.50 0.50 3.20 1.73\n", " auxiliary[2,2] 3.30 0.00 3.30 3.29 3.30 6.10 1.00\n", " auxiliary[2,3] 7.02 0.00 7.02 7.02 7.03 8.67 1.12\n", " auxiliary[2,4] 6.35 0.00 6.35 6.34 6.35 11.67 1.14\n", " auxiliary[2,5] 9.23 0.01 9.23 9.22 9.24 6.83 1.04\n", " auxiliary[2,6] 11.01 0.01 11.01 11.00 11.02 9.04 1.11\n", " auxiliary[2,7] 16.87 0.01 16.87 16.85 16.89 2.84 2.36\n", " auxiliary[2,8] 16.07 0.02 16.06 16.04 16.09 3.63 1.72\n", " auxiliary[2,9] 21.25 0.01 21.25 21.24 21.27 10.24 1.42\n", "auxiliary[2,10] 25.24 0.02 25.24 25.21 25.27 4.79 1.35\n", "auxiliary[2,11] 33.07 0.02 33.07 33.04 33.11 6.04 1.05\n", "auxiliary[2,12] 40.58 0.02 40.58 40.54 40.60 8.50 1.10\n", "auxiliary[2,13] 45.15 0.02 45.15 45.10 45.17 12.16 1.20\n", "auxiliary[2,14] 46.26 0.03 46.25 46.23 46.33 8.42 1.09\n", "auxiliary[2,15] 45.21 0.02 45.21 45.18 45.25 5.36 1.06\n", "auxiliary[2,16] 49.21 0.02 49.21 49.17 49.24 7.08 1.15\n", "auxiliary[2,17] 57.22 0.04 57.22 57.18 57.30 3.62 1.85\n", "auxiliary[2,18] 58.95 0.03 58.95 58.91 59.00 4.01 1.46\n", "auxiliary[2,19] 64.50 0.08 64.51 64.41 64.62 3.37 1.75\n", "auxiliary[2,20] 64.44 0.04 64.45 64.38 64.50 6.64 1.12\n", "auxiliary[2,21] 69.62 0.03 69.62 69.58 69.68 7.35 1.03\n", "auxiliary[2,22] 78.71 0.05 78.71 78.62 78.78 7.26 1.19\n", "auxiliary[2,23] 85.40 0.06 85.40 85.31 85.50 5.63 1.13\n", "auxiliary[2,24] 92.38 0.07 92.39 92.27 92.44 8.57 1.03\n", "auxiliary[2,25] 100.82 0.07 100.81 100.73 100.97 4.87 1.01\n", "auxiliary[2,26] 96.65 0.05 96.65 96.58 96.73 4.65 1.46\n", "auxiliary[2,27] 105.91 0.06 105.91 105.83 105.98 9.31 1.26\n", "auxiliary[2,28] 110.33 0.08 110.33 110.20 110.43 11.02 1.10\n", "auxiliary[2,29] 121.10 0.11 121.07 120.96 121.29 2.84 2.30\n", "auxiliary[2,30] 138.69 0.11 138.72 138.55 138.87 3.16 1.89\n", "auxiliary[2,31] 144.41 0.16 144.44 144.17 144.64 3.13 1.93\n", "auxiliary[2,32] 153.74 0.09 153.70 153.64 153.89 6.07 1.12\n", "auxiliary[2,33] 159.49 0.17 159.42 159.30 159.78 2.61 2.38\n", "auxiliary[2,34] 172.89 0.69 172.72 171.87 173.86 2.67 2.32\n", "auxiliary[2,35] 186.35 0.79 186.41 185.22 187.74 2.67 2.30\n", "auxiliary[2,36] 192.99 0.65 193.02 192.03 194.00 2.57 2.43\n", "auxiliary[2,37] 216.13 0.47 216.23 215.03 216.58 3.81 1.65\n", "auxiliary[2,38] 238.02 0.73 238.13 237.02 239.13 2.44 2.95\n", "auxiliary[2,39] 269.18 0.41 269.29 268.58 269.78 3.02 1.96\n", "auxiliary[2,40] 289.13 0.36 289.14 288.64 289.53 5.59 1.13\n", "auxiliary[2,41] 313.80 0.45 313.94 313.06 314.36 3.05 2.21\n", "auxiliary[2,42] 347.44 0.91 347.36 346.06 348.51 2.62 2.37\n", "auxiliary[2,43] 378.13 0.39 378.15 377.64 378.77 3.82 1.67\n", "auxiliary[2,44] 402.48 0.14 402.49 402.26 402.68 6.76 1.21\n", "auxiliary[2,45] 423.38 0.61 423.51 422.38 424.11 4.39 1.00\n", "auxiliary[2,46] 467.70 1.18 467.68 465.44 468.98 2.54 2.59\n", "auxiliary[2,47] 529.78 1.12 529.12 528.67 531.63 3.13 1.62\n", "auxiliary[2,48] 565.59 0.74 565.78 564.58 566.66 4.02 1.33\n", "auxiliary[2,49] 605.86 0.38 605.80 605.34 606.65 10.06 1.02\n", "auxiliary[2,50] 645.31 0.46 645.29 644.91 646.03 6.58 1.24\n", "auxiliary[2,51] 697.50 0.57 697.49 696.66 698.39 3.06 1.96\n", "auxiliary[2,52] 751.77 0.58 751.75 750.84 752.56 6.95 1.26\n", "auxiliary[2,53] 803.75 0.45 803.59 803.24 804.56 6.60 1.24\n", "auxiliary[2,54] 865.17 0.66 865.16 863.98 865.97 5.27 1.55\n", "auxiliary[2,55] 953.04 0.96 953.30 951.62 954.53 5.12 1.25\n", "auxiliary[2,56] 1025.98 0.64 1025.78 1024.96 1026.92 5.35 1.03\n", "auxiliary[2,57] 1098.97 1.20 1099.05 1096.88 1100.58 2.98 1.96\n", "auxiliary[2,58] 1178.61 6.52 1178.03 1170.90 1187.41 2.56 2.51\n", "auxiliary[2,59] 1276.74 11.33 1278.14 1260.73 1294.78 2.87 2.11\n", "auxiliary[2,60] 1415.96 11.75 1416.86 1400.48 1435.96 2.81 2.18\n", " auxiliary[3,0] 0.49 0.00 0.49 0.49 0.49 8.16 1.20\n", " auxiliary[3,1] 0.50 0.00 0.50 0.50 0.50 2.80 2.29\n", " auxiliary[3,2] 0.50 0.00 0.50 0.50 0.50 3.30 1.74\n", " auxiliary[3,3] 0.50 0.00 0.50 0.50 0.50 5.88 1.36\n", " auxiliary[3,4] 0.50 0.00 0.50 0.50 0.50 13.89 1.02\n", " auxiliary[3,5] 0.50 0.00 0.50 0.50 0.50 6.51 1.00\n", " auxiliary[3,6] 0.50 0.00 0.50 0.50 0.50 3.90 1.26\n", " auxiliary[3,7] 0.50 0.00 0.50 0.50 0.50 10.16 1.03\n", " auxiliary[3,8] 0.50 0.00 0.50 0.50 0.50 7.01 1.41\n", " auxiliary[3,9] 0.50 0.00 0.50 0.50 0.50 10.54 1.16\n", "auxiliary[3,10] 0.59 0.00 0.59 0.59 0.59 14.70 1.13\n", "auxiliary[3,11] 1.05 0.00 1.05 1.05 1.05 4.17 1.25\n", "auxiliary[3,12] 1.37 0.00 1.37 1.37 1.38 2.69 2.71\n", "auxiliary[3,13] 1.38 0.00 1.38 1.37 1.38 4.80 1.44\n", "auxiliary[3,14] 1.38 0.00 1.38 1.37 1.38 4.79 1.01\n", "auxiliary[3,15] 1.60 0.00 1.60 1.60 1.61 3.27 1.90\n", "auxiliary[3,16] 1.67 0.00 1.67 1.67 1.67 3.16 1.91\n", "auxiliary[3,17] 1.68 0.00 1.68 1.68 1.68 4.31 1.62\n", "auxiliary[3,18] 2.17 0.00 2.17 2.17 2.17 17.44 1.00\n", "auxiliary[3,19] 2.55 0.00 2.55 2.55 2.55 3.41 1.87\n", "auxiliary[3,20] 2.32 0.00 2.32 2.31 2.32 2.83 2.07\n", "auxiliary[3,21] 2.49 0.00 2.49 2.49 2.50 10.17 1.15\n", "auxiliary[3,22] 2.74 0.00 2.74 2.74 2.74 5.73 1.29\n", "auxiliary[3,23] 2.74 0.00 2.74 2.73 2.74 6.88 1.22\n", "auxiliary[3,24] 3.15 0.00 3.15 3.14 3.15 4.69 1.37\n", "auxiliary[3,25] 2.77 0.00 2.77 2.76 2.77 4.47 1.00\n", "auxiliary[3,26] 2.90 0.00 2.90 2.90 2.91 2.72 2.17\n", "auxiliary[3,27] 3.48 0.00 3.48 3.47 3.49 4.08 1.58\n", "auxiliary[3,28] 3.74 0.01 3.74 3.73 3.75 3.79 1.25\n", "auxiliary[3,29] 4.32 0.01 4.32 4.31 4.33 3.16 2.01\n", "auxiliary[3,30] 3.98 0.01 3.98 3.97 3.99 3.11 1.96\n", "auxiliary[3,31] 3.97 0.00 3.96 3.96 3.97 4.34 1.39\n", "auxiliary[3,32] 3.66 0.00 3.66 3.65 3.66 5.86 1.31\n", "auxiliary[3,33] 3.42 0.00 3.42 3.41 3.43 2.86 2.15\n", "auxiliary[3,34] 3.73 0.00 3.73 3.73 3.74 4.28 1.56\n", "auxiliary[3,35] 4.93 0.01 4.92 4.92 4.94 2.94 1.97\n", "auxiliary[3,36] 5.46 0.00 5.46 5.45 5.47 5.39 1.23\n", "auxiliary[3,37] 5.63 0.00 5.64 5.63 5.64 5.65 1.08\n", "auxiliary[3,38] 5.64 0.01 5.64 5.63 5.65 2.80 2.17\n", "auxiliary[3,39] 5.39 0.00 5.39 5.39 5.40 7.40 1.38\n", "auxiliary[3,40] 6.12 0.02 6.12 6.09 6.15 2.75 2.23\n", "auxiliary[3,41] 5.86 0.01 5.86 5.84 5.87 2.52 2.71\n", "auxiliary[3,42] 6.54 0.00 6.54 6.54 6.55 8.75 1.03\n", "auxiliary[3,43] 7.31 0.01 7.31 7.30 7.32 3.77 1.60\n", "auxiliary[3,44] 8.74 0.01 8.73 8.73 8.75 3.76 1.71\n", "auxiliary[3,45] 10.35 0.02 10.35 10.33 10.38 2.85 2.28\n", "auxiliary[3,46] 12.88 0.01 12.88 12.85 12.90 6.86 1.31\n", "auxiliary[3,47] 14.97 0.02 14.97 14.95 15.01 3.12 1.84\n", "auxiliary[3,48] 16.92 0.02 16.92 16.89 16.96 2.77 2.48\n", "auxiliary[3,49] 18.87 0.04 18.87 18.81 18.91 2.69 2.34\n", "auxiliary[3,50] 20.98 0.16 21.01 20.75 21.24 2.87 2.10\n", "auxiliary[3,51] 24.33 0.23 24.35 24.01 24.72 2.80 2.17\n", "auxiliary[3,52] 29.00 0.22 29.04 28.70 29.38 2.86 2.11\n", "auxiliary[3,53] 34.44 0.10 34.45 34.24 34.54 2.83 2.12\n", "auxiliary[3,54] 40.16 0.03 40.17 40.11 40.20 3.68 1.43\n", "auxiliary[3,55] 45.94 0.06 45.94 45.87 46.02 3.42 1.72\n", "auxiliary[3,56] 51.52 0.18 51.52 51.31 51.88 2.71 2.22\n", "auxiliary[3,57] 56.86 0.31 56.84 56.37 57.30 2.66 2.38\n", "auxiliary[3,58] 61.88 0.42 61.89 61.18 62.46 2.75 2.26\n", "auxiliary[3,59] 66.55 0.51 66.48 65.75 67.27 2.81 2.17\n", "auxiliary[3,60] 70.82 0.55 70.75 69.96 71.60 2.88 2.09\n", " incub_time 5.56 0.00 5.56 5.56 5.56 7.23 1.05\n", " mort_rate 0.04 0.00 0.04 0.04 0.04 2.88 2.24\n", " rec_rate 0.67 0.00 0.67 0.67 0.67 4.72 1.38\n", " rec_time 15.47 0.00 15.47 15.47 15.48 6.55 1.10\n", " rho 0.52 0.00 0.52 0.51 0.52 2.81 2.17\n", "\n", "Number of divergences: 0\n", "CPU times: user 1min 20s, sys: 573 ms, total: 1min 20s\n", "Wall time: 1min 20s\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "pFItIVvUGTRs", "outputId": "7db163f1-67e8-4f59-ba87-af4393153a3d" }, "source": [ "%%time\n", "Sweden_model = CovidModel(10230000, Sweden[\"new_cases\"], Sweden[\"new_recovered\"], Sweden[\"new_deaths\"] )\n", "Sweden_mcmc = Sweden_model.fit_mcmc(num_samples=500, warmup_steps = 200)\n", "Sweden_mcmc.summary()" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "INFO \t Running inference...\n", "Warmup: 0%| | 0/700 [00:00, ?it/s]INFO \t Heuristic init: R0=2.82, incub_time=4.09, mort_rate=0.0318, rec_rate=0.316, rec_time=13.7, rho=0.178\n", "Sample: 100%|██████████| 700/700 [02:08, 5.44it/s, step size=7.26e-04, acc. prob=0.898]\n" ], "name": "stderr" }, { "output_type": "stream", "text": [ "\n", " mean std median 5.0% 95.0% n_eff r_hat\n", " R0 2.82 0.00 2.83 2.82 2.83 5.96 1.04\n", " auxiliary[0,0] 10229991.30 0.24 10229991.31 10229990.95 10229991.65 2.46 2.73\n", " auxiliary[0,1] 10229982.96 0.50 10229982.92 10229982.26 10229983.75 2.50 2.62\n", " auxiliary[0,2] 10229974.33 0.69 10229974.30 10229973.38 10229975.40 2.48 2.66\n", " auxiliary[0,3] 10229965.47 0.82 10229965.45 10229964.33 10229966.73 2.46 2.71\n", " auxiliary[0,4] 10229956.42 0.93 10229956.42 10229955.09 10229957.80 2.46 2.71\n", " auxiliary[0,5] 10229947.20 1.03 10229947.22 10229945.74 10229948.71 2.47 2.70\n", " auxiliary[0,6] 10229969.94 1.89 10229970.59 10229966.75 10229971.87 2.66 2.27\n", " auxiliary[0,7] 10229959.88 2.38 10229960.50 10229956.00 10229962.59 2.59 2.41\n", " auxiliary[0,8] 10229949.13 3.24 10229949.72 10229944.03 10229953.13 2.53 2.53\n", " auxiliary[0,9] 10229937.68 4.39 10229938.29 10229930.94 10229943.44 2.50 2.61\n", "auxiliary[0,10] 10229925.52 5.83 10229926.14 10229916.64 10229933.39 2.49 2.64\n", "auxiliary[0,11] 10229912.62 7.52 10229913.21 10229901.35 10229922.99 2.48 2.66\n", "auxiliary[0,12] 10229898.94 9.44 10229899.50 10229884.96 10229912.20 2.48 2.67\n", "auxiliary[0,13] 10229884.48 11.59 10229885.00 10229867.45 10229900.99 2.47 2.68\n", "auxiliary[0,14] 10229869.19 13.96 10229869.70 10229848.85 10229889.31 2.47 2.69\n", "auxiliary[0,15] 10229853.07 16.52 10229853.53 10229829.16 10229877.11 2.47 2.69\n", "auxiliary[0,16] 10229836.10 19.26 10229836.49 10229808.22 10229864.36 2.47 2.69\n", "auxiliary[0,17] 10229818.26 22.17 10229818.59 10229786.32 10229851.02 2.47 2.69\n", "auxiliary[0,18] 10229799.51 25.25 10229799.72 10229763.25 10229837.09 2.47 2.69\n", "auxiliary[0,19] 10229779.82 28.47 10229779.87 10229739.08 10229822.46 2.47 2.69\n", "auxiliary[0,20] 10229759.19 31.83 10229759.05 10229713.76 10229807.08 2.47 2.69\n", "auxiliary[0,21] 10229737.59 35.31 10229737.28 10229687.38 10229790.94 2.47 2.69\n", "auxiliary[0,22] 10229714.98 38.88 10229714.56 10229659.87 10229774.01 2.47 2.69\n", "auxiliary[0,23] 10229691.34 42.54 10229690.67 10229631.17 10229756.15 2.47 2.69\n", "auxiliary[0,24] 10229666.64 46.24 10229665.66 10229601.46 10229737.35 2.47 2.68\n", "auxiliary[0,25] 10229640.81 49.99 10229639.59 10229570.41 10229717.46 2.47 2.68\n", "auxiliary[0,26] 10229613.82 53.75 10229612.48 10229538.26 10229696.42 2.47 2.68\n", "auxiliary[0,27] 10229585.62 57.49 10229584.05 10229504.93 10229674.20 2.47 2.68\n", "auxiliary[0,28] 10229556.16 61.17 10229554.52 10229470.37 10229650.58 2.47 2.68\n", "auxiliary[0,29] 10229525.36 64.76 10229523.56 10229434.69 10229625.43 2.47 2.68\n", "auxiliary[0,30] 10229493.13 68.21 10229491.24 10229397.41 10229598.23 2.47 2.68\n", "auxiliary[0,31] 10229459.37 71.46 10229457.57 10229358.89 10229569.26 2.47 2.68\n", "auxiliary[0,32] 10229423.92 74.31 10229422.56 10229319.27 10229537.58 2.47 2.69\n", "auxiliary[0,33] 10229386.04 76.24 10229385.22 10229278.02 10229501.89 2.47 2.68\n", "auxiliary[0,34] 10229344.98 77.13 10229344.53 10229235.32 10229461.57 2.47 2.68\n", "auxiliary[0,35] 10229299.64 77.12 10229299.84 10229189.63 10229415.52 2.47 2.68\n", "auxiliary[0,36] 10229249.48 75.91 10229250.52 10229140.21 10229361.77 2.47 2.69\n", "auxiliary[0,37] 10229194.72 75.02 10229196.26 10229086.50 10229304.74 2.47 2.68\n", "auxiliary[0,38] 10229133.07 72.70 10229136.11 10229026.71 10229234.99 2.47 2.70\n", "auxiliary[0,39] 10229062.15 68.43 10229067.84 10228960.49 10229151.32 2.45 2.74\n", "auxiliary[0,40] 10228979.68 62.27 10228989.48 10228884.43 10229055.13 2.45 2.73\n", "auxiliary[0,41] 10228884.86 54.72 10228898.95 10228798.36 10228947.34 2.49 2.64\n", "auxiliary[0,42] 10228777.39 46.18 10228792.63 10228701.14 10228828.57 2.60 2.38\n", "auxiliary[0,43] 10228655.80 36.88 10228667.34 10228593.87 10228697.10 2.69 2.25\n", "auxiliary[0,44] 10228518.11 28.82 10228525.03 10228471.31 10228553.53 2.67 2.30\n", "auxiliary[0,45] 10228363.09 24.16 10228367.21 10228324.19 10228395.17 2.59 2.44\n", "auxiliary[0,46] 10228191.88 22.36 10228193.76 10228158.15 10228221.72 2.49 2.64\n", "auxiliary[0,47] 10228003.05 21.28 10228004.80 10227971.03 10228031.88 2.50 2.63\n", "auxiliary[0,48] 10227796.41 21.26 10227798.20 10227763.45 10227824.29 2.50 2.58\n", "auxiliary[0,49] 10227571.55 20.21 10227572.43 10227540.66 10227599.54 2.52 2.54\n", "auxiliary[0,50] 10227326.27 18.79 10227327.93 10227298.53 10227353.91 2.54 2.52\n", "auxiliary[0,51] 10227061.61 17.90 10227062.19 10227035.55 10227088.14 2.56 2.42\n", "auxiliary[0,52] 10226776.98 16.27 10226773.81 10226756.33 10226802.18 2.44 2.73\n", "auxiliary[0,53] 10226474.07 13.76 10226468.02 10226459.90 10226497.47 2.60 2.36\n", "auxiliary[0,54] 10226158.71 8.45 10226159.26 10226146.86 10226171.10 3.76 1.13\n", "auxiliary[0,55] 10225840.03 34.60 10225836.45 10225800.31 10225891.31 2.39 3.07\n", "auxiliary[0,56] 10225498.57 53.74 10225505.41 10225415.98 10225569.39 2.50 2.61\n", "auxiliary[0,57] 10225149.40 60.72 10225159.67 10225050.39 10225234.12 2.56 2.49\n", "auxiliary[0,58] 10224796.09 64.55 10224805.13 10224685.50 10224881.11 2.55 2.51\n", "auxiliary[0,59] 10224445.56 70.25 10224454.23 10224328.84 10224541.42 2.53 2.54\n", "auxiliary[0,60] 10224114.83 74.22 10224125.39 10223985.51 10224211.08 2.54 2.51\n", " auxiliary[1,0] 7.72 0.01 7.72 7.71 7.73 3.86 1.76\n", " auxiliary[1,1] 17.11 0.05 17.11 17.03 17.19 2.48 2.77\n", " auxiliary[1,2] 14.83 0.01 14.83 14.82 14.85 3.29 1.86\n", " auxiliary[1,3] 15.40 0.01 15.40 15.39 15.41 8.98 1.06\n", " auxiliary[1,4] 15.64 0.01 15.64 15.62 15.66 4.60 1.40\n", " auxiliary[1,5] 21.55 0.59 21.54 20.68 22.38 2.45 2.75\n", " auxiliary[1,6] 17.18 0.37 17.16 16.67 17.76 2.48 2.68\n", " auxiliary[1,7] 20.89 0.02 20.90 20.86 20.92 2.62 3.20\n", " auxiliary[1,8] 24.58 0.03 24.58 24.53 24.62 2.92 2.02\n", " auxiliary[1,9] 28.66 0.02 28.66 28.63 28.71 6.43 1.00\n", "auxiliary[1,10] 31.11 0.04 31.12 31.05 31.16 2.54 2.88\n", "auxiliary[1,11] 25.11 0.01 25.11 25.09 25.12 5.49 1.11\n", "auxiliary[1,12] 28.01 0.01 28.01 27.99 28.03 4.61 1.52\n", "auxiliary[1,13] 29.02 0.02 29.03 29.00 29.05 7.85 1.03\n", "auxiliary[1,14] 35.70 0.02 35.70 35.66 35.73 4.60 1.03\n", "auxiliary[1,15] 36.78 0.02 36.78 36.73 36.80 4.32 1.46\n", "auxiliary[1,16] 33.74 0.02 33.74 33.72 33.77 5.95 1.11\n", "auxiliary[1,17] 24.55 0.02 24.55 24.53 24.58 5.69 1.18\n", "auxiliary[1,18] 27.97 0.01 27.97 27.95 27.99 3.95 1.87\n", "auxiliary[1,19] 25.91 0.01 25.91 25.89 25.92 8.68 1.02\n", "auxiliary[1,20] 22.27 0.01 22.28 22.25 22.29 6.09 1.00\n", "auxiliary[1,21] 26.32 0.01 26.32 26.31 26.33 5.81 1.48\n", "auxiliary[1,22] 35.97 0.01 35.98 35.95 35.99 6.47 1.43\n", "auxiliary[1,23] 37.13 0.03 37.11 37.09 37.19 3.61 1.47\n", "auxiliary[1,24] 30.95 0.01 30.95 30.94 30.97 11.99 1.12\n", "auxiliary[1,25] 39.77 0.02 39.78 39.74 39.81 4.78 1.16\n", "auxiliary[1,26] 52.73 0.04 52.73 52.67 52.79 3.25 1.76\n", "auxiliary[1,27] 63.04 0.04 63.05 62.97 63.09 3.47 1.81\n", "auxiliary[1,28] 62.12 0.04 62.11 62.07 62.20 4.84 1.05\n", "auxiliary[1,29] 59.45 0.05 59.47 59.37 59.52 3.97 1.21\n", "auxiliary[1,30] 71.74 0.05 71.75 71.65 71.81 3.72 1.59\n", "auxiliary[1,31] 76.07 0.16 76.10 75.83 76.26 2.38 3.33\n", "auxiliary[1,32] 96.46 0.17 96.54 96.12 96.60 3.26 1.66\n", "auxiliary[1,33] 118.69 0.40 118.74 118.16 119.19 2.32 3.58\n", "auxiliary[1,34] 135.03 0.49 135.11 134.36 135.67 2.36 3.18\n", "auxiliary[1,35] 153.78 0.34 153.64 153.36 154.41 2.95 1.82\n", "auxiliary[1,36] 191.41 0.68 191.17 190.67 192.70 3.28 1.57\n", "auxiliary[1,37] 218.38 0.82 217.96 217.57 219.84 2.61 2.27\n", "auxiliary[1,38] 238.60 1.11 237.92 237.50 240.25 2.52 2.49\n", "auxiliary[1,39] 264.79 0.56 264.94 264.04 265.49 2.37 3.78\n", "auxiliary[1,40] 292.36 0.94 292.60 290.95 293.53 2.37 3.20\n", "auxiliary[1,41] 346.54 1.66 347.48 343.79 348.10 2.59 2.35\n", "auxiliary[1,42] 407.81 0.77 408.16 406.35 408.57 4.40 1.21\n", "auxiliary[1,43] 433.96 0.36 433.83 433.50 434.48 3.84 1.46\n", "auxiliary[1,44] 475.63 0.26 475.68 475.15 475.99 6.73 1.20\n", "auxiliary[1,45] 513.26 0.28 513.29 512.81 513.68 4.64 1.06\n", "auxiliary[1,46] 561.45 0.37 561.31 561.01 562.15 3.23 1.71\n", "auxiliary[1,47] 604.57 0.25 604.55 604.26 605.04 10.25 1.00\n", "auxiliary[1,48] 670.60 0.43 670.52 670.03 671.30 3.08 2.17\n", "auxiliary[1,49] 698.37 0.29 698.41 697.91 698.82 5.03 1.24\n", "auxiliary[1,50] 785.46 0.60 785.31 784.67 786.49 3.07 2.17\n", "auxiliary[1,51] 867.64 0.37 867.79 866.92 868.01 4.23 1.44\n", "auxiliary[1,52] 937.56 0.38 937.52 936.88 938.11 7.78 1.12\n", "auxiliary[1,53] 990.67 0.83 990.70 989.54 991.75 2.43 3.00\n", "auxiliary[1,54] 1074.03 0.42 1074.08 1073.33 1074.66 5.92 1.28\n", "auxiliary[1,55] 1145.20 4.43 1143.15 1141.04 1153.12 2.79 2.05\n", "auxiliary[1,56] 1289.72 6.26 1290.93 1280.85 1297.51 2.39 2.98\n", "auxiliary[1,57] 1441.49 5.69 1441.90 1432.58 1449.28 2.55 2.44\n", "auxiliary[1,58] 1575.48 5.43 1575.72 1567.49 1583.93 2.51 2.68\n", "auxiliary[1,59] 1698.91 3.07 1700.45 1692.91 1701.95 3.29 1.71\n", "auxiliary[1,60] 1841.41 0.69 1841.37 1839.88 1842.35 9.25 1.19\n", " auxiliary[2,0] 0.50 0.00 0.50 0.50 0.50 3.15 2.29\n", " auxiliary[2,1] 1.58 0.00 1.58 1.58 1.58 4.70 1.43\n", " auxiliary[2,2] 4.99 0.00 4.99 4.98 4.99 3.94 1.02\n", " auxiliary[2,3] 8.10 0.00 8.10 8.09 8.10 7.69 1.17\n", " auxiliary[2,4] 12.90 0.02 12.89 12.88 12.92 2.90 2.18\n", " auxiliary[2,5] 13.25 0.21 13.25 12.94 13.54 2.46 2.75\n", " auxiliary[2,6] 11.82 0.18 11.81 11.56 12.08 2.44 2.77\n", " auxiliary[2,7] 14.70 0.02 14.70 14.67 14.72 2.59 2.62\n", " auxiliary[2,8] 13.71 0.01 13.71 13.70 13.73 2.61 2.57\n", " auxiliary[2,9] 20.16 0.02 20.16 20.14 20.19 3.98 1.54\n", "auxiliary[2,10] 24.72 0.02 24.71 24.70 24.76 3.92 1.67\n", "auxiliary[2,11] 31.69 0.02 31.69 31.66 31.73 3.55 1.84\n", "auxiliary[2,12] 35.34 0.03 35.34 35.28 35.37 3.79 1.67\n", "auxiliary[2,13] 39.42 0.02 39.42 39.39 39.45 3.87 1.54\n", "auxiliary[2,14] 38.16 0.03 38.16 38.12 38.21 3.54 1.77\n", "auxiliary[2,15] 43.63 0.06 43.65 43.52 43.70 2.73 2.40\n", "auxiliary[2,16] 49.81 0.05 49.82 49.74 49.89 2.63 2.32\n", "auxiliary[2,17] 59.63 0.03 59.63 59.58 59.67 4.78 1.60\n", "auxiliary[2,18] 62.23 0.03 62.22 62.18 62.29 4.27 1.24\n", "auxiliary[2,19] 62.17 0.04 62.18 62.09 62.22 5.54 1.08\n", "auxiliary[2,20] 64.82 0.05 64.80 64.77 64.91 4.36 1.19\n", "auxiliary[2,21] 64.84 0.07 64.83 64.75 64.96 3.25 1.74\n", "auxiliary[2,22] 60.04 0.04 60.03 59.99 60.12 2.94 2.10\n", "auxiliary[2,23] 66.34 0.03 66.33 66.31 66.39 6.37 1.13\n", "auxiliary[2,24] 74.77 0.03 74.76 74.73 74.82 7.21 1.04\n", "auxiliary[2,25] 79.22 0.04 79.21 79.18 79.30 4.85 1.52\n", "auxiliary[2,26] 83.47 0.05 83.45 83.41 83.59 5.30 1.32\n", "auxiliary[2,27] 86.83 0.11 86.80 86.68 86.99 2.64 2.31\n", "auxiliary[2,28] 100.86 0.10 100.91 100.68 100.98 3.81 1.76\n", "auxiliary[2,29] 119.18 0.06 119.16 119.10 119.29 5.20 1.07\n", "auxiliary[2,30] 128.51 0.04 128.51 128.44 128.57 8.98 1.00\n", "auxiliary[2,31] 140.59 0.10 140.55 140.47 140.76 4.44 1.33\n", "auxiliary[2,32] 153.74 0.59 154.01 152.74 154.38 2.94 1.79\n", "auxiliary[2,33] 169.81 0.94 170.05 168.36 170.89 2.41 2.79\n", "auxiliary[2,34] 194.75 0.96 194.60 193.60 196.13 2.38 3.06\n", "auxiliary[2,35] 221.56 0.49 221.29 221.05 222.44 2.71 2.13\n", "auxiliary[2,36] 234.42 0.76 234.03 233.61 235.90 4.08 1.30\n", "auxiliary[2,37] 262.53 1.20 261.90 261.48 264.76 2.88 1.94\n", "auxiliary[2,38] 302.89 1.58 302.34 301.27 305.18 2.44 2.68\n", "auxiliary[2,39] 343.52 1.30 343.51 341.74 345.11 2.33 3.29\n", "auxiliary[2,40] 393.25 1.98 393.62 390.30 395.40 2.37 3.15\n", "auxiliary[2,41] 426.31 2.36 427.79 422.40 428.55 2.66 2.30\n", "auxiliary[2,42] 458.02 1.02 458.22 456.19 459.22 4.92 1.07\n", "auxiliary[2,43] 535.28 0.22 535.26 534.99 535.65 8.27 1.24\n", "auxiliary[2,44] 592.83 0.25 592.84 592.42 593.19 4.06 1.50\n", "auxiliary[2,45] 665.95 0.32 666.01 665.47 666.39 7.71 1.01\n", "auxiliary[2,46] 742.64 0.36 742.65 742.17 743.24 3.75 1.74\n", "auxiliary[2,47] 837.93 0.76 837.75 836.80 838.97 3.46 1.35\n", "auxiliary[2,48] 914.25 0.52 914.18 913.65 915.32 5.16 1.22\n", "auxiliary[2,49] 1037.67 0.33 1037.64 1037.23 1038.31 6.90 1.21\n", "auxiliary[2,50] 1132.78 0.90 1132.42 1131.67 1134.21 3.45 1.68\n", "auxiliary[2,51] 1247.46 2.61 1247.37 1243.64 1250.75 2.39 3.04\n", "auxiliary[2,52] 1366.39 0.78 1366.48 1365.11 1367.61 3.29 1.71\n", "auxiliary[2,53] 1495.57 1.10 1495.66 1493.97 1497.24 3.63 1.34\n", "auxiliary[2,54] 1612.83 0.71 1612.82 1611.97 1614.06 10.51 1.01\n", "auxiliary[2,55] 1777.40 11.74 1772.51 1764.39 1796.52 2.65 2.32\n", "auxiliary[2,56] 1947.44 13.93 1948.26 1928.45 1967.16 2.45 2.77\n", "auxiliary[2,57] 2134.53 13.21 2136.28 2112.92 2151.51 2.47 2.69\n", "auxiliary[2,58] 2347.65 10.12 2350.79 2330.03 2359.19 2.55 2.47\n", "auxiliary[2,59] 2569.33 7.36 2571.33 2557.96 2578.29 2.50 2.57\n", "auxiliary[2,60] 2752.89 6.43 2753.46 2742.06 2760.25 2.45 2.86\n", " auxiliary[3,0] 0.50 0.00 0.50 0.50 0.50 3.97 1.45\n", " auxiliary[3,1] 0.50 0.00 0.50 0.50 0.50 5.14 1.22\n", " auxiliary[3,2] 0.50 0.00 0.50 0.50 0.50 3.02 2.13\n", " auxiliary[3,3] 0.50 0.00 0.50 0.50 0.50 7.34 1.17\n", " auxiliary[3,4] 0.50 0.00 0.50 0.50 0.50 19.40 1.00\n", " auxiliary[3,5] 0.50 0.00 0.50 0.50 0.50 2.63 2.58\n", " auxiliary[3,6] 0.50 0.00 0.50 0.50 0.50 3.15 1.89\n", " auxiliary[3,7] 0.50 0.00 0.50 0.50 0.50 2.88 2.12\n", " auxiliary[3,8] 0.50 0.00 0.50 0.50 0.50 4.04 1.44\n", " auxiliary[3,9] 0.67 0.00 0.67 0.67 0.68 2.73 2.18\n", "auxiliary[3,10] 0.88 0.00 0.88 0.88 0.88 5.37 1.02\n", "auxiliary[3,11] 0.98 0.00 0.98 0.97 0.98 4.80 1.10\n", "auxiliary[3,12] 1.28 0.00 1.28 1.28 1.28 6.60 1.10\n", "auxiliary[3,13] 1.17 0.00 1.17 1.16 1.17 4.89 1.27\n", "auxiliary[3,14] 1.59 0.00 1.59 1.58 1.59 7.11 1.00\n", "auxiliary[3,15] 1.75 0.00 1.75 1.74 1.75 4.17 1.37\n", "auxiliary[3,16] 1.54 0.00 1.54 1.54 1.55 2.81 2.22\n", "auxiliary[3,17] 1.22 0.00 1.22 1.22 1.22 4.49 1.27\n", "auxiliary[3,18] 1.59 0.00 1.59 1.59 1.59 3.81 1.76\n", "auxiliary[3,19] 1.59 0.00 1.59 1.59 1.59 2.76 2.10\n", "auxiliary[3,20] 1.32 0.00 1.32 1.32 1.33 3.43 2.16\n", "auxiliary[3,21] 1.58 0.00 1.58 1.58 1.58 8.76 1.38\n", "auxiliary[3,22] 1.61 0.00 1.61 1.61 1.61 5.60 1.40\n", "auxiliary[3,23] 1.76 0.00 1.76 1.76 1.76 9.54 1.10\n", "auxiliary[3,24] 1.81 0.00 1.81 1.81 1.81 4.28 1.52\n", "auxiliary[3,25] 1.76 0.00 1.76 1.76 1.76 2.64 2.62\n", "auxiliary[3,26] 2.15 0.00 2.15 2.15 2.16 3.07 1.98\n", "auxiliary[3,27] 2.38 0.00 2.38 2.38 2.39 2.76 2.40\n", "auxiliary[3,28] 1.96 0.00 1.96 1.96 1.96 8.57 1.14\n", "auxiliary[3,29] 2.13 0.00 2.13 2.13 2.14 5.93 1.07\n", "auxiliary[3,30] 2.40 0.00 2.40 2.40 2.40 3.42 1.56\n", "auxiliary[3,31] 2.58 0.00 2.58 2.58 2.58 5.53 1.20\n", "auxiliary[3,32] 2.67 0.00 2.67 2.67 2.68 3.50 1.64\n", "auxiliary[3,33] 2.03 0.00 2.03 2.02 2.03 2.81 2.23\n", "auxiliary[3,34] 2.40 0.00 2.40 2.40 2.40 14.26 1.01\n", "auxiliary[3,35] 3.09 0.00 3.09 3.08 3.09 4.66 1.20\n", "auxiliary[3,36] 3.72 0.00 3.72 3.72 3.73 2.79 2.14\n", "auxiliary[3,37] 4.02 0.00 4.02 4.02 4.02 9.04 1.41\n", "auxiliary[3,38] 4.51 0.00 4.51 4.51 4.51 4.43 1.11\n", "auxiliary[3,39] 5.11 0.01 5.11 5.10 5.12 2.87 2.28\n", "auxiliary[3,40] 6.18 0.01 6.18 6.17 6.20 2.91 1.93\n", "auxiliary[3,41] 7.66 0.01 7.67 7.65 7.67 2.76 2.05\n", "auxiliary[3,42] 8.79 0.02 8.80 8.77 8.82 2.45 2.68\n", "auxiliary[3,43] 9.50 0.06 9.50 9.40 9.58 2.43 2.81\n", "auxiliary[3,44] 12.38 0.07 12.37 12.29 12.48 2.52 2.56\n", "auxiliary[3,45] 13.74 0.07 13.75 13.63 13.85 2.50 2.62\n", "auxiliary[3,46] 16.41 0.01 16.41 16.40 16.42 4.33 1.54\n", "auxiliary[3,47] 18.98 0.02 18.98 18.95 19.00 3.01 2.33\n", "auxiliary[3,48] 21.88 0.05 21.87 21.81 21.95 2.70 2.34\n", "auxiliary[3,49] 25.10 0.04 25.09 25.05 25.18 3.21 1.58\n", "auxiliary[3,50] 28.41 0.30 28.40 27.97 28.86 2.46 2.72\n", "auxiliary[3,51] 33.12 0.52 33.11 32.36 33.85 2.44 2.76\n", "auxiliary[3,52] 39.44 0.44 39.40 38.83 40.09 2.43 2.80\n", "auxiliary[3,53] 46.74 0.23 46.73 46.43 47.08 2.44 2.73\n", "auxiliary[3,54] 54.33 0.04 54.34 54.25 54.37 3.80 1.75\n", "auxiliary[3,55] 61.79 0.31 61.86 61.29 62.18 2.54 2.53\n", "auxiliary[3,56] 69.00 0.63 69.07 68.07 69.86 2.48 2.66\n", "auxiliary[3,57] 75.79 1.01 75.81 74.32 77.23 2.45 2.73\n", "auxiliary[3,58] 81.93 1.40 81.89 79.97 84.03 2.45 2.72\n", "auxiliary[3,59] 87.33 1.68 87.26 85.02 90.00 2.47 2.68\n", "auxiliary[3,60] 91.98 1.81 91.91 89.47 94.84 2.47 2.69\n", " incub_time 4.09 0.00 4.09 4.09 4.09 7.91 1.28\n", " mort_rate 0.03 0.00 0.03 0.03 0.03 10.21 1.06\n", " rec_rate 0.32 0.00 0.32 0.32 0.32 3.39 1.74\n", " rec_time 13.71 0.00 13.72 13.71 13.72 2.90 1.89\n", " rho 0.48 0.00 0.48 0.48 0.48 2.93 1.79\n", "\n", "Number of divergences: 0\n", "CPU times: user 2min 8s, sys: 814 ms, total: 2min 8s\n", "Wall time: 2min 8s\n" ], "name": "stdout" } ] }, { "cell_type": "code", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "cZ4P6ED_LY89", "outputId": "86b9b8d0-e8be-4ebc-8140-541d53dbed17" }, "source": [ "%%time\n", "Sweden_model = CovidModel(10230000, Sweden[\"new_cases\"], Sweden[\"new_recovered\"], Sweden[\"new_deaths\"] )\n", "Sweden_mcmc = Sweden_model.fit_mcmc(num_samples=500, warmup_steps = 200)\n", "Sweden_mcmc.summary()" ], "execution_count": null, "outputs": [ { "output_type": "stream", "text": [ "INFO \t Running inference...\n", "Warmup: 0%| | 0/700 [00:00, ?it/s]INFO \t Heuristic init: R0=2.52, incub_time=5.53, mort_rate=0.047, rec_rate=0.398, rec_time=12.2, rho=0.179\n", "Sample: 100%|██████████| 700/700 [01:53, 6.16it/s, step size=9.15e-04, acc. prob=0.850]\n" ], "name": "stderr" }, { "output_type": "stream", "text": [ "\n", " mean std median 5.0% 95.0% n_eff r_hat\n", " R0 2.52 0.00 2.52 2.52 2.52 4.59 1.25\n", " auxiliary[0,0] 10229990.17 0.13 10229990.20 10229989.96 10229990.34 2.46 2.72\n", " auxiliary[0,1] 10229981.13 0.31 10229981.15 10229980.68 10229981.57 2.47 2.73\n", " auxiliary[0,2] 10229971.85 0.49 10229971.87 10229971.15 10229972.55 2.47 2.71\n", " auxiliary[0,3] 10229962.41 0.67 10229962.44 10229961.42 10229963.35 2.47 2.71\n", " auxiliary[0,4] 10229952.82 0.87 10229952.93 10229951.53 10229954.01 2.46 2.75\n", " auxiliary[0,5] 10229943.01 1.07 10229943.16 10229941.44 10229944.48 2.45 2.77\n", " auxiliary[0,6] 10229951.64 6.38 10229953.10 10229941.04 10229959.63 2.48 2.67\n", " auxiliary[0,7] 10229940.87 6.80 10229942.33 10229929.72 10229949.52 2.47 2.69\n", " auxiliary[0,8] 10229929.20 7.45 10229930.61 10229917.20 10229938.86 2.47 2.71\n", " auxiliary[0,9] 10229916.64 8.35 10229918.00 10229903.45 10229927.74 2.46 2.72\n", "auxiliary[0,10] 10229903.23 9.47 10229904.54 10229888.55 10229916.05 2.46 2.73\n", "auxiliary[0,11] 10229888.98 10.82 10229890.26 10229872.49 10229903.89 2.46 2.73\n", "auxiliary[0,12] 10229873.89 12.37 10229875.12 10229855.32 10229891.19 2.47 2.73\n", "auxiliary[0,13] 10229857.96 14.12 10229859.10 10229837.00 10229877.89 2.47 2.72\n", "auxiliary[0,14] 10229841.17 16.05 10229842.24 10229817.62 10229864.08 2.47 2.71\n", "auxiliary[0,15] 10229823.50 18.15 10229824.52 10229797.04 10229849.58 2.47 2.70\n", "auxiliary[0,16] 10229804.94 20.42 10229805.91 10229775.39 10229834.50 2.48 2.70\n", "auxiliary[0,17] 10229785.50 22.84 10229786.44 10229752.73 10229818.72 2.48 2.69\n", "auxiliary[0,18] 10229765.13 25.39 10229766.04 10229728.93 10229802.26 2.48 2.68\n", "auxiliary[0,19] 10229743.85 28.06 10229744.64 10229703.95 10229785.09 2.48 2.68\n", "auxiliary[0,20] 10229721.61 30.87 10229722.34 10229677.95 10229767.09 2.49 2.67\n", "auxiliary[0,21] 10229698.40 33.77 10229699.00 10229650.82 10229748.31 2.49 2.67\n", "auxiliary[0,22] 10229674.20 36.76 10229674.62 10229622.65 10229728.68 2.49 2.67\n", "auxiliary[0,23] 10229648.96 39.83 10229649.16 10229593.27 10229708.10 2.49 2.66\n", "auxiliary[0,24] 10229622.65 42.99 10229622.76 10229562.71 10229686.63 2.49 2.66\n", "auxiliary[0,25] 10229595.25 46.21 10229595.29 10229530.97 10229664.13 2.49 2.65\n", "auxiliary[0,26] 10229566.72 49.46 10229566.68 10229498.11 10229640.52 2.50 2.65\n", "auxiliary[0,27] 10229537.03 52.71 10229536.92 10229464.12 10229615.78 2.50 2.65\n", "auxiliary[0,28] 10229506.10 55.98 10229505.97 10229428.75 10229589.90 2.50 2.65\n", "auxiliary[0,29] 10229473.86 59.24 10229473.68 10229392.01 10229562.59 2.50 2.64\n", "auxiliary[0,30] 10229440.23 62.45 10229439.92 10229354.08 10229533.73 2.50 2.64\n", "auxiliary[0,31] 10229405.10 65.60 10229404.82 10229314.62 10229503.34 2.50 2.65\n", "auxiliary[0,32] 10229368.38 68.62 10229368.23 10229273.59 10229471.12 2.50 2.64\n", "auxiliary[0,33] 10229330.03 71.58 10229329.95 10229231.07 10229437.42 2.50 2.64\n", "auxiliary[0,34] 10229289.67 74.23 10229289.70 10229186.88 10229400.87 2.50 2.65\n", "auxiliary[0,35] 10229247.24 76.60 10229247.31 10229140.78 10229361.54 2.49 2.65\n", "auxiliary[0,36] 10229202.46 78.48 10229203.36 10229092.81 10229318.61 2.48 2.68\n", "auxiliary[0,37] 10229155.30 79.63 10229156.62 10229043.50 10229272.78 2.48 2.69\n", "auxiliary[0,38] 10229104.31 79.61 10229106.37 10228991.69 10229221.13 2.48 2.70\n", "auxiliary[0,39] 10229048.75 78.44 10229051.80 10228936.98 10229162.98 2.47 2.71\n", "auxiliary[0,40] 10228988.22 76.87 10228992.49 10228877.60 10229098.80 2.46 2.74\n", "auxiliary[0,41] 10228920.74 74.18 10228926.67 10228812.37 10229026.06 2.45 2.76\n", "auxiliary[0,42] 10228845.23 70.09 10228852.33 10228740.74 10228942.37 2.45 2.77\n", "auxiliary[0,43] 10228760.55 64.47 10228769.60 10228661.96 10228847.13 2.44 2.79\n", "auxiliary[0,44] 10228665.60 57.80 10228675.27 10228575.41 10228741.43 2.45 2.77\n", "auxiliary[0,45] 10228559.43 50.69 10228568.88 10228478.61 10228625.65 2.46 2.72\n", "auxiliary[0,46] 10228441.47 44.08 10228450.14 10228370.37 10228498.17 2.47 2.70\n", "auxiliary[0,47] 10228311.66 38.59 10228317.95 10228249.33 10228362.42 2.48 2.67\n", "auxiliary[0,48] 10228169.59 34.40 10228174.43 10228115.43 10228216.20 2.47 2.70\n", "auxiliary[0,49] 10228014.90 31.47 10228018.25 10227966.75 10228058.51 2.49 2.67\n", "auxiliary[0,50] 10227847.64 29.19 10227850.21 10227803.53 10227890.48 2.51 2.63\n", "auxiliary[0,51] 10227667.55 26.92 10227668.40 10227628.24 10227706.92 2.52 2.59\n", "auxiliary[0,52] 10227475.53 23.84 10227476.18 10227441.27 10227510.49 2.50 2.67\n", "auxiliary[0,53] 10227272.82 20.11 10227272.83 10227244.72 10227303.94 2.52 2.64\n", "auxiliary[0,54] 10227060.79 14.61 10227059.40 10227040.80 10227082.27 2.54 2.54\n", "auxiliary[0,55] 10226841.73 6.21 10226840.80 10226834.02 10226852.59 2.62 2.29\n", "auxiliary[0,56] 10226619.94 4.57 10226619.83 10226612.47 10226627.40 3.19 1.89\n", "auxiliary[0,57] 10226398.23 12.90 10226400.90 10226375.53 10226415.86 2.88 2.11\n", "auxiliary[0,58] 10226178.53 17.81 10226182.80 10226147.47 10226195.88 2.84 2.11\n", "auxiliary[0,59] 10225939.34 17.79 10225942.01 10225909.90 10225959.22 2.73 2.20\n", "auxiliary[0,60] 10225673.64 16.04 10225672.65 10225649.99 10225694.70 2.64 2.39\n", " auxiliary[1,0] 11.78 0.06 11.79 11.69 11.88 2.50 2.66\n", " auxiliary[1,1] 12.29 0.02 12.29 12.27 12.31 2.40 3.41\n", " auxiliary[1,2] 15.23 0.01 15.23 15.21 15.25 2.80 2.42\n", " auxiliary[1,3] 14.62 0.02 14.62 14.59 14.65 2.41 2.88\n", " auxiliary[1,4] 22.98 0.20 22.99 22.68 23.25 2.46 2.78\n", " auxiliary[1,5] 33.07 0.17 33.09 32.85 33.29 4.13 1.00\n", " auxiliary[1,6] 24.94 0.26 24.80 24.71 25.40 2.96 1.91\n", " auxiliary[1,7] 24.97 0.01 24.97 24.96 24.99 6.80 1.00\n", " auxiliary[1,8] 28.28 0.02 28.29 28.24 28.31 3.65 1.67\n", " auxiliary[1,9] 35.67 0.05 35.66 35.61 35.75 2.51 2.61\n", "auxiliary[1,10] 42.76 0.02 42.75 42.74 42.79 8.73 1.05\n", "auxiliary[1,11] 44.32 0.03 44.32 44.29 44.37 5.56 1.03\n", "auxiliary[1,12] 42.66 0.07 42.66 42.56 42.76 2.65 2.30\n", "auxiliary[1,13] 36.28 0.03 36.29 36.23 36.33 2.95 2.04\n", "auxiliary[1,14] 31.72 0.02 31.72 31.69 31.76 5.33 1.12\n", "auxiliary[1,15] 31.19 0.02 31.19 31.15 31.22 4.79 1.01\n", "auxiliary[1,16] 38.76 0.03 38.77 38.70 38.79 4.94 1.41\n", "auxiliary[1,17] 36.63 0.02 36.62 36.59 36.67 3.55 1.64\n", "auxiliary[1,18] 41.93 0.03 41.94 41.88 41.97 3.01 2.54\n", "auxiliary[1,19] 42.21 0.03 42.22 42.17 42.25 3.65 1.48\n", "auxiliary[1,20] 42.99 0.02 42.99 42.97 43.02 12.88 1.01\n", "auxiliary[1,21] 41.45 0.05 41.47 41.37 41.50 2.67 2.15\n", "auxiliary[1,22] 35.11 0.03 35.12 35.06 35.16 3.47 1.80\n", "auxiliary[1,23] 42.09 0.03 42.08 42.07 42.14 6.44 1.17\n", "auxiliary[1,24] 45.82 0.04 45.82 45.74 45.87 3.13 2.03\n", "auxiliary[1,25] 59.21 0.03 59.20 59.17 59.25 8.65 1.07\n", "auxiliary[1,26] 68.09 0.06 68.09 68.00 68.18 4.25 1.12\n", "auxiliary[1,27] 67.70 0.05 67.69 67.64 67.79 2.83 2.39\n", "auxiliary[1,28] 77.02 0.07 76.99 76.94 77.16 2.98 1.75\n", "auxiliary[1,29] 80.87 0.03 80.87 80.82 80.93 11.80 1.13\n", "auxiliary[1,30] 78.29 0.10 78.28 78.12 78.43 2.60 2.35\n", "auxiliary[1,31] 88.88 0.05 88.87 88.81 88.94 4.42 1.53\n", "auxiliary[1,32] 106.68 0.12 106.63 106.55 106.91 2.94 1.83\n", "auxiliary[1,33] 129.14 0.06 129.15 129.06 129.23 10.89 1.01\n", "auxiliary[1,34] 138.95 0.25 138.93 138.67 139.33 2.41 3.10\n", "auxiliary[1,35] 156.24 0.23 156.16 155.99 156.58 2.66 2.73\n", "auxiliary[1,36] 174.00 0.39 174.19 173.26 174.35 3.28 1.67\n", "auxiliary[1,37] 209.32 0.46 209.55 208.46 209.80 2.92 1.96\n", "auxiliary[1,38] 230.23 0.19 230.31 229.91 230.46 3.29 1.75\n", "auxiliary[1,39] 259.16 0.57 258.96 258.48 260.20 3.73 1.40\n", "auxiliary[1,40] 292.17 0.42 292.23 291.60 292.84 2.61 2.44\n", "auxiliary[1,41] 323.95 0.29 324.03 323.36 324.25 3.66 1.33\n", "auxiliary[1,42] 341.68 0.20 341.70 341.33 341.92 5.57 1.01\n", "auxiliary[1,43] 392.01 0.41 391.97 391.47 392.82 3.66 1.71\n", "auxiliary[1,44] 426.87 0.33 426.96 426.30 427.26 3.55 1.69\n", "auxiliary[1,45] 476.50 0.32 476.49 475.96 477.07 4.51 1.15\n", "auxiliary[1,46] 523.30 0.41 523.23 522.71 523.94 4.86 1.15\n", "auxiliary[1,47] 563.46 0.33 563.41 562.93 564.02 5.60 1.01\n", "auxiliary[1,48] 611.38 0.31 611.42 610.82 611.84 6.63 1.06\n", "auxiliary[1,49] 654.88 0.49 655.02 654.01 655.55 5.05 1.20\n", "auxiliary[1,50] 679.65 0.43 679.77 678.75 680.17 5.85 1.05\n", "auxiliary[1,51] 740.29 0.32 740.32 739.79 740.88 10.13 1.28\n", "auxiliary[1,52] 800.75 0.69 800.89 799.82 801.91 2.74 2.81\n", "auxiliary[1,53] 839.21 1.00 839.30 837.66 840.50 2.50 3.19\n", "auxiliary[1,54] 896.09 0.47 896.16 895.25 896.68 7.20 1.07\n", "auxiliary[1,55] 954.54 0.69 954.51 953.54 955.51 3.53 1.51\n", "auxiliary[1,56] 1051.90 1.73 1052.71 1049.49 1054.14 2.54 2.83\n", "auxiliary[1,57] 1165.19 0.91 1165.41 1163.71 1166.41 7.56 1.02\n", "auxiliary[1,58] 1232.88 10.08 1231.91 1219.33 1247.63 2.47 2.68\n", "auxiliary[1,59] 1315.44 9.38 1315.52 1301.76 1327.71 2.45 2.84\n", "auxiliary[1,60] 1456.07 9.75 1456.29 1440.80 1468.94 2.53 2.61\n", " auxiliary[2,0] 1.86 0.00 1.86 1.85 1.86 2.68 2.47\n", " auxiliary[2,1] 3.56 0.00 3.56 3.56 3.57 3.44 1.48\n", " auxiliary[2,2] 8.10 0.01 8.10 8.09 8.12 2.54 2.61\n", " auxiliary[2,3] 13.44 0.01 13.44 13.43 13.44 6.63 1.07\n", " auxiliary[2,4] 14.25 0.08 14.24 14.14 14.36 2.38 3.05\n", " auxiliary[2,5] 17.66 0.05 17.67 17.57 17.73 4.21 1.01\n", " auxiliary[2,6] 20.30 0.16 20.21 20.18 20.59 3.09 1.81\n", " auxiliary[2,7] 26.04 0.02 26.03 26.01 26.07 4.05 1.23\n", " auxiliary[2,8] 30.62 0.01 30.62 30.60 30.64 9.18 1.09\n", " auxiliary[2,9] 30.84 0.02 30.85 30.82 30.86 5.48 1.08\n", "auxiliary[2,10] 31.48 0.05 31.47 31.42 31.56 2.65 2.79\n", "auxiliary[2,11] 34.69 0.01 34.69 34.67 34.71 11.52 1.10\n", "auxiliary[2,12] 42.68 0.02 42.68 42.65 42.72 5.72 1.07\n", "auxiliary[2,13] 48.09 0.03 48.08 48.05 48.15 5.04 1.01\n", "auxiliary[2,14] 49.37 0.03 49.37 49.33 49.41 4.78 1.03\n", "auxiliary[2,15] 47.42 0.02 47.42 47.39 47.44 6.15 1.22\n", "auxiliary[2,16] 45.79 0.04 45.78 45.74 45.86 4.19 1.26\n", "auxiliary[2,17] 52.09 0.03 52.10 52.06 52.12 11.33 1.05\n", "auxiliary[2,18] 47.51 0.07 47.53 47.39 47.59 2.49 2.90\n", "auxiliary[2,19] 46.23 0.03 46.23 46.18 46.27 4.98 1.16\n", "auxiliary[2,20] 49.78 0.04 49.79 49.70 49.84 3.95 1.10\n", "auxiliary[2,21] 53.78 0.03 53.78 53.72 53.82 4.73 1.06\n", "auxiliary[2,22] 64.18 0.03 64.19 64.11 64.23 6.15 1.14\n", "auxiliary[2,23] 68.44 0.06 68.44 68.35 68.54 4.04 1.33\n", "auxiliary[2,24] 71.77 0.12 71.83 71.59 71.91 2.67 2.26\n", "auxiliary[2,25] 73.91 0.09 73.87 73.83 74.07 3.07 1.73\n", "auxiliary[2,26] 74.72 0.06 74.73 74.61 74.80 3.24 1.75\n", "auxiliary[2,27] 83.39 0.04 83.40 83.33 83.46 3.61 1.98\n", "auxiliary[2,28] 88.95 0.07 88.95 88.86 89.06 5.20 1.06\n", "auxiliary[2,29] 94.38 0.16 94.44 94.12 94.58 2.64 2.49\n", "auxiliary[2,30] 108.89 0.06 108.90 108.78 108.97 3.24 2.24\n", "auxiliary[2,31] 119.59 0.08 119.58 119.49 119.71 2.72 2.33\n", "auxiliary[2,32] 129.23 0.09 129.23 129.05 129.34 5.31 1.36\n", "auxiliary[2,33] 140.19 0.14 140.22 139.92 140.37 5.81 1.02\n", "auxiliary[2,34] 154.61 0.13 154.59 154.47 154.88 2.87 2.10\n", "auxiliary[2,35] 176.43 0.36 176.38 175.89 176.91 2.55 2.79\n", "auxiliary[2,36] 200.95 0.51 201.21 199.98 201.46 2.84 2.15\n", "auxiliary[2,37] 211.59 0.63 211.92 210.43 212.20 3.14 1.77\n", "auxiliary[2,38] 241.33 0.61 241.13 240.59 242.34 2.55 2.50\n", "auxiliary[2,39] 265.92 0.55 265.81 265.09 266.83 4.33 1.03\n", "auxiliary[2,40] 289.21 0.39 289.00 288.81 289.86 2.63 2.19\n", "auxiliary[2,41] 316.90 0.36 316.81 316.42 317.51 2.83 2.04\n", "auxiliary[2,42] 362.72 0.27 362.74 362.31 363.10 2.80 2.46\n", "auxiliary[2,43] 383.50 0.17 383.52 383.22 383.77 9.32 1.00\n", "auxiliary[2,44] 421.17 0.21 421.17 420.77 421.54 6.25 1.02\n", "auxiliary[2,45] 450.70 0.18 450.73 450.41 450.93 9.68 1.29\n", "auxiliary[2,46] 490.77 0.16 490.77 490.55 491.03 7.43 1.30\n", "auxiliary[2,47] 539.34 0.24 539.30 538.98 539.76 9.87 1.00\n", "auxiliary[2,48] 603.26 0.65 602.98 602.38 604.24 2.81 1.88\n", "auxiliary[2,49] 667.07 0.55 667.05 666.33 668.00 2.72 2.35\n", "auxiliary[2,50] 745.72 0.23 745.75 745.36 746.14 11.79 1.17\n", "auxiliary[2,51] 814.44 0.66 814.40 813.47 815.53 3.95 1.59\n", "auxiliary[2,52] 861.99 0.50 861.86 861.26 862.86 4.67 1.42\n", "auxiliary[2,53] 925.26 1.23 924.95 923.57 927.05 3.17 1.86\n", "auxiliary[2,54] 983.46 0.43 983.42 982.88 984.38 8.29 1.28\n", "auxiliary[2,55] 1093.10 1.68 1093.45 1090.38 1095.60 2.86 2.28\n", "auxiliary[2,56] 1160.40 1.28 1160.64 1158.30 1161.98 3.18 2.13\n", "auxiliary[2,57] 1251.76 0.68 1251.73 1250.62 1252.88 9.47 1.00\n", "auxiliary[2,58] 1367.12 11.79 1364.97 1352.12 1384.24 2.40 2.91\n", "auxiliary[2,59] 1518.44 12.27 1516.73 1501.47 1535.70 2.44 2.89\n", "auxiliary[2,60] 1638.92 13.62 1641.21 1617.93 1654.81 2.48 2.67\n", " auxiliary[3,0] 0.50 0.00 0.50 0.50 0.50 6.55 1.00\n", " auxiliary[3,1] 0.50 0.00 0.50 0.50 0.50 3.64 1.52\n", " auxiliary[3,2] 0.50 0.00 0.50 0.50 0.50 7.26 1.21\n", " auxiliary[3,3] 0.50 0.00 0.50 0.50 0.50 3.41 1.60\n", " auxiliary[3,4] 0.50 0.00 0.50 0.50 0.50 2.88 2.95\n", " auxiliary[3,5] 0.50 0.00 0.50 0.50 0.50 7.05 1.11\n", " auxiliary[3,6] 0.50 0.00 0.50 0.50 0.50 4.62 2.30\n", " auxiliary[3,7] 0.50 0.00 0.50 0.49 0.50 3.79 1.61\n", " auxiliary[3,8] 0.50 0.00 0.50 0.50 0.50 3.36 1.70\n", " auxiliary[3,9] 0.50 0.00 0.50 0.50 0.50 6.33 1.02\n", "auxiliary[3,10] 0.50 0.00 0.50 0.50 0.50 3.38 2.47\n", "auxiliary[3,11] 0.50 0.00 0.50 0.50 0.50 5.90 1.20\n", "auxiliary[3,12] 0.50 0.00 0.50 0.50 0.50 5.55 1.03\n", "auxiliary[3,13] 0.50 0.00 0.50 0.50 0.50 2.97 2.89\n", "auxiliary[3,14] 0.50 0.00 0.50 0.50 0.50 3.94 1.48\n", "auxiliary[3,15] 0.50 0.00 0.50 0.49 0.50 2.69 2.76\n", "auxiliary[3,16] 0.50 0.00 0.50 0.50 0.50 3.09 2.30\n", "auxiliary[3,17] 0.50 0.00 0.50 0.50 0.50 7.21 1.32\n", "auxiliary[3,18] 0.50 0.00 0.50 0.50 0.50 3.05 1.88\n", "auxiliary[3,19] 0.50 0.00 0.50 0.50 0.50 4.68 1.46\n", "auxiliary[3,20] 0.50 0.00 0.50 0.50 0.50 3.96 1.48\n", "auxiliary[3,21] 0.50 0.00 0.50 0.50 0.50 4.81 1.25\n", "auxiliary[3,22] 0.51 0.00 0.51 0.50 0.51 13.95 1.00\n", "auxiliary[3,23] 0.50 0.00 0.50 0.50 0.50 7.46 1.69\n", "auxiliary[3,24] 0.50 0.00 0.50 0.50 0.50 2.52 2.89\n", "auxiliary[3,25] 0.50 0.00 0.50 0.50 0.50 12.04 1.03\n", "auxiliary[3,26] 0.50 0.00 0.50 0.50 0.50 3.42 1.91\n", "auxiliary[3,27] 0.50 0.00 0.50 0.50 0.50 2.96 2.13\n", "auxiliary[3,28] 0.50 0.00 0.50 0.50 0.50 4.60 1.02\n", "auxiliary[3,29] 0.50 0.00 0.50 0.50 0.50 2.72 2.55\n", "auxiliary[3,30] 0.73 0.00 0.73 0.73 0.73 2.62 2.46\n", "auxiliary[3,31] 0.67 0.00 0.67 0.67 0.67 9.85 1.11\n", "auxiliary[3,32] 0.50 0.00 0.50 0.50 0.50 9.59 1.01\n", "auxiliary[3,33] 0.50 0.00 0.50 0.50 0.51 2.43 3.44\n", "auxiliary[3,34] 0.50 0.00 0.50 0.50 0.50 3.13 2.21\n", "auxiliary[3,35] 0.56 0.00 0.56 0.56 0.56 3.55 1.74\n", "auxiliary[3,36] 0.77 0.00 0.77 0.77 0.77 7.86 1.19\n", "auxiliary[3,37] 1.15 0.00 1.15 1.15 1.16 3.35 1.91\n", "auxiliary[3,38] 1.17 0.00 1.17 1.17 1.18 2.46 2.73\n", "auxiliary[3,39] 3.01 0.00 3.01 3.01 3.01 3.74 1.42\n", "auxiliary[3,40] 4.72 0.01 4.72 4.70 4.73 2.65 2.32\n", "auxiliary[3,41] 5.61 0.00 5.61 5.60 5.61 6.06 1.44\n", "auxiliary[3,42] 6.34 0.01 6.34 6.32 6.35 2.73 2.20\n", "auxiliary[3,43] 7.88 0.02 7.88 7.85 7.91 2.50 2.55\n", "auxiliary[3,44] 9.84 0.02 9.83 9.80 9.88 2.98 1.97\n", "auxiliary[3,45] 10.91 0.05 10.90 10.83 10.99 2.48 2.74\n", "auxiliary[3,46] 13.52 0.08 13.51 13.42 13.63 2.40 3.07\n", "auxiliary[3,47] 15.10 0.06 15.09 15.01 15.20 2.42 2.86\n", "auxiliary[3,48] 17.24 0.09 17.25 17.09 17.35 2.58 2.36\n", "auxiliary[3,49] 20.33 0.05 20.31 20.27 20.41 2.97 1.73\n", "auxiliary[3,50] 23.65 0.36 23.65 23.12 24.16 2.46 2.74\n", "auxiliary[3,51] 28.77 0.40 28.80 28.14 29.31 2.55 2.54\n", "auxiliary[3,52] 35.31 0.24 35.29 34.97 35.67 2.47 2.76\n", "auxiliary[3,53] 42.48 0.06 42.47 42.40 42.56 2.60 2.67\n", "auxiliary[3,54] 49.69 0.12 49.68 49.52 49.87 2.60 2.35\n", "auxiliary[3,55] 56.74 0.33 56.80 56.24 57.17 2.45 2.75\n", "auxiliary[3,56] 63.48 0.57 63.54 62.63 64.28 2.46 2.73\n", "auxiliary[3,57] 69.82 0.87 69.84 68.59 71.07 2.46 2.70\n", "auxiliary[3,58] 75.62 1.15 75.57 74.04 77.36 2.49 2.65\n", "auxiliary[3,59] 80.80 1.37 80.69 78.99 82.92 2.53 2.57\n", "auxiliary[3,60] 85.33 1.47 85.18 83.41 87.63 2.55 2.53\n", " incub_time 5.54 0.00 5.54 5.53 5.54 6.35 1.00\n", " mort_rate 0.05 0.00 0.05 0.05 0.05 2.78 2.08\n", " rec_rate 0.40 0.00 0.40 0.40 0.40 4.29 1.26\n", " rec_time 12.22 0.00 12.22 12.22 12.22 11.56 1.02\n", " rho 0.50 0.01 0.50 0.49 0.51 2.49 2.62\n", "\n", "Number of divergences: 33\n", "CPU times: user 1min 53s, sys: 772 ms, total: 1min 53s\n", "Wall time: 1min 53s\n" ], "name": "stdout" } ] } ] }