From 07346145e50203cc9e30347657cf8026a0fc6503 Mon Sep 17 00:00:00 2001 From: Marc Bevand Date: Mon, 16 Nov 2020 14:01:56 -0800 Subject: [PATCH] update COVID IFR from Levin paper v7 --- README.md | 420 ++++++++++++++++++++++++------------------------ apply_ifr.py | 14 +- covid_vs_flu.py | 14 +- 3 files changed, 224 insertions(+), 224 deletions(-) diff --git a/README.md b/README.md index a544e02..5d6b007 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -*Updated: 21 Oct 2020* +*Updated: 16 Nov 2020* Author: Marc Bevand @@ -27,7 +27,7 @@ The COVID-19 IFR curves represent these estimates: 1. [US CDC COVID-19 Pandemic Planning Scenarios](https://web.archive.org/web/20200911222029/https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html) (table 1); which is based on [Estimation of SARS-CoV-2 mortality during the early stages of an epidemic: A modeling study in Hubei, China, and six regions in Europe](https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003189) 1. [Verity et al.: Estimates of the severity of coronavirus disease 2019: a model-based analysis](https://www.thelancet.com/journals/laninf/article/PIIS1473-3099%2820%2930243-7/fulltext) (table 1) -1. [Levin et al.: Assessing the age specificity of infection fatality rates for COVID-19: systematic review, meta-analysis, and public policy implications](https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v5) (table 3) +1. [Levin et al.: Assessing the age specificity of infection fatality rates for COVID-19: systematic review, meta-analysis, and public policy implications](https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v7) (table 3) 1. [Perez-Saez et al.: Serology-informed estimates of SARS-CoV-2 infection fatality risk in Geneva, Switzerland](https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30584-3/fulltext) 1. [Poletti et al.: Age-specific SARS-CoV-2 infection fatality ratio and associated risk factors, Italy, February to April 2020](https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.31.2001383) (table 1, column "Any time") 1. [Picon et al.: Coronavirus Disease 2019 Population-based Prevalence, Risk Factors, Hospitalization, and Fatality Rates in Southern Brazil](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493765/) (table 2) @@ -98,214 +98,214 @@ ENE-COVID column): | ENE-COVID | COVID: US CDC | COVID: Verity | COVID: Levin | Flu: US CDC | Region | | ------------- | ------------- | ------------- | ------------- | ------------- | ------ | -| 1.274 | 1.311 | 1.605 | 2.247 | 0.125 | Japan | -| 1.065 | 1.092 | 1.382 | 1.847 | 0.106 | Italy | -| 1.041 | 1.043 | 1.339 | 1.806 | 0.102 | Greece | -| 0.993 | 1.012 | 1.305 | 1.702 | 0.100 | Germany | -| 0.984 | 1.045 | 1.320 | 1.726 | 0.104 | Portugal | -| 0.931 | 0.985 | 1.270 | 1.648 | 0.100 | Martinique | -| 0.919 | 0.933 | 1.221 | 1.658 | 0.095 | Lithuania | -| 0.916 | 0.942 | 1.207 | 1.648 | 0.093 | Spain | -| 0.914 | 0.941 | 1.201 | 1.606 | 0.095 | France | -| 0.899 | 1.008 | 1.248 | 1.556 | 0.102 | Finland | -| 0.881 | 0.919 | 1.192 | 1.624 | 0.095 | Latvia | -| 0.875 | 0.957 | 1.205 | 1.528 | 0.096 | Puerto Rico | -| 0.868 | 0.892 | 1.171 | 1.516 | 0.093 | Estonia | -| 0.865 | 0.932 | 1.209 | 1.487 | 0.098 | Croatia | -| 0.855 | 0.965 | 1.205 | 1.471 | 0.099 | Malta | -| 0.846 | 0.881 | 1.137 | 1.478 | 0.089 | Belgium | -| 0.843 | 0.905 | 1.181 | 1.489 | 0.095 | Slovenia | -| 0.840 | 0.943 | 1.154 | 1.471 | 0.093 | Sweden | -| 0.836 | 0.910 | 1.149 | 1.462 | 0.090 | Austria | -| 0.825 | 0.897 | 1.132 | 1.447 | 0.089 | Switzerland | -| 0.810 | 0.861 | 1.117 | 1.396 | 0.089 | Europe | -| 0.802 | 0.909 | 1.141 | 1.394 | 0.093 | Netherlands | -| 0.801 | 0.949 | 1.181 | 1.377 | 0.098 | Bulgaria | -| 0.798 | 0.864 | 1.113 | 1.399 | 0.090 | Guadeloupe | -| 0.797 | 0.935 | 1.136 | 1.370 | 0.093 | Denmark | -| 0.794 | 0.868 | 1.089 | 1.384 | 0.087 | United Kingdom | -| 0.791 | 0.811 | 1.102 | 1.367 | 0.087 | China, Hong Kong SAR | -| 0.759 | 0.830 | 1.090 | 1.285 | 0.089 | Romania | -| 0.753 | 0.854 | 1.101 | 1.323 | 0.093 | Hungary | -| 0.745 | 0.800 | 1.064 | 1.285 | 0.087 | Poland | -| 0.739 | 0.828 | 1.059 | 1.315 | 0.084 | Channel Islands | -| 0.738 | 0.878 | 1.092 | 1.302 | 0.092 | Czechia | -| 0.734 | 0.810 | 1.047 | 1.288 | 0.085 | Canada | -| 0.719 | 0.756 | 0.998 | 1.259 | 0.079 | Barbados | -| 0.713 | 0.808 | 1.038 | 1.210 | 0.084 | Curaçao | -| 0.709 | 0.802 | 1.007 | 1.239 | 0.082 | Norway | -| 0.680 | 0.800 | 1.029 | 1.160 | 0.088 | Serbia | -| 0.676 | 0.694 | 0.904 | 1.193 | 0.071 | Uruguay | -| 0.675 | 0.745 | 0.967 | 1.181 | 0.079 | Northern America | -| 0.671 | 0.736 | 0.944 | 1.174 | 0.076 | Australia | -| 0.671 | 0.733 | 0.983 | 1.103 | 0.080 | Ukraine | -| 0.669 | 0.738 | 0.958 | 1.169 | 0.078 | United States of America | -| 0.659 | 0.757 | 1.011 | 1.088 | 0.085 | Bosnia and Herzegovina | -| 0.654 | 0.742 | 0.945 | 1.137 | 0.077 | New Zealand | -| 0.644 | 0.735 | 0.941 | 1.131 | 0.077 | Cuba | -| 0.641 | 0.877 | 1.059 | 1.152 | 0.094 | United States Virgin Islands | -| 0.633 | 0.725 | 0.963 | 1.090 | 0.077 | Republic of Korea | -| 0.628 | 0.686 | 0.938 | 1.100 | 0.077 | China, Taiwan Province of China | -| 0.624 | 0.663 | 0.916 | 1.030 | 0.074 | Russian Federation | -| 0.624 | 0.657 | 0.921 | 1.082 | 0.075 | Belarus | -| 0.615 | 0.668 | 0.881 | 1.078 | 0.070 | Luxembourg | -| 0.607 | 0.670 | 0.896 | 1.002 | 0.073 | Georgia | -| 0.605 | 0.683 | 0.888 | 1.061 | 0.073 | Iceland | -| 0.604 | 0.709 | 0.935 | 1.059 | 0.079 | Slovakia | -| 0.582 | 0.667 | 0.891 | 0.989 | 0.075 | Montenegro | -| 0.563 | 0.653 | 0.838 | 0.972 | 0.070 | Ireland | -| 0.561 | 0.649 | 0.839 | 0.957 | 0.069 | Cyprus | -| 0.548 | 0.659 | 0.857 | 0.941 | 0.071 | Albania | -| 0.531 | 0.652 | 0.874 | 0.920 | 0.072 | Aruba | -| 0.518 | 0.580 | 0.754 | 0.902 | 0.062 | Oceania | -| 0.510 | 0.588 | 0.795 | 0.881 | 0.065 | Thailand | -| 0.500 | 0.569 | 0.763 | 0.880 | 0.063 | Réunion | -| 0.499 | 0.545 | 0.710 | 0.872 | 0.060 | Israel | -| 0.497 | 0.522 | 0.748 | 0.794 | 0.059 | Armenia | -| 0.497 | 0.616 | 0.816 | 0.851 | 0.070 | North Macedonia | -| 0.493 | 0.550 | 0.736 | 0.861 | 0.061 | Chile | -| 0.479 | 0.550 | 0.796 | 0.829 | 0.067 | Singapore | -| 0.454 | 0.515 | 0.671 | 0.790 | 0.056 | Argentina | -| 0.449 | 0.514 | 0.738 | 0.770 | 0.062 | China, Macao SAR | -| 0.447 | 0.544 | 0.732 | 0.772 | 0.063 | Mauritius | -| 0.435 | 0.501 | 0.721 | 0.766 | 0.062 | Republic of Moldova | -| 0.415 | 0.511 | 0.681 | 0.717 | 0.058 | Trinidad and Tobago | -| 0.413 | 0.475 | 0.638 | 0.712 | 0.053 | Costa Rica | -| 0.413 | 0.468 | 0.626 | 0.704 | 0.051 | Saint Lucia | -| 0.409 | 0.507 | 0.695 | 0.707 | 0.061 | China | -| 0.394 | 0.497 | 0.648 | 0.712 | 0.052 | Antigua and Barbuda | -| 0.387 | 0.495 | 0.651 | 0.668 | 0.056 | Sri Lanka | -| 0.377 | 0.487 | 0.635 | 0.622 | 0.050 | Dem. People's Republic of Korea | -| 0.376 | 0.437 | 0.594 | 0.645 | 0.050 | Brazil | -| 0.365 | 0.464 | 0.611 | 0.618 | 0.052 | Guam | -| 0.364 | 0.425 | 0.569 | 0.627 | 0.047 | Jamaica | -| 0.361 | 0.454 | 0.605 | 0.663 | 0.051 | Saint Vincent and the Grenadines | -| 0.359 | 0.399 | 0.540 | 0.623 | 0.045 | Panama | -| 0.358 | 0.418 | 0.566 | 0.615 | 0.048 | WORLD | -| 0.356 | 0.410 | 0.555 | 0.614 | 0.047 | Latin America and the Caribbean | -| 0.355 | 0.412 | 0.560 | 0.613 | 0.047 | Colombia | -| 0.354 | 0.438 | 0.595 | 0.642 | 0.050 | Grenada | -| 0.347 | 0.399 | 0.528 | 0.595 | 0.045 | El Salvador | -| 0.343 | 0.363 | 0.528 | 0.602 | 0.043 | Viet Nam | -| 0.342 | 0.408 | 0.552 | 0.588 | 0.047 | Turkey | -| 0.339 | 0.397 | 0.537 | 0.583 | 0.045 | Peru | -| 0.336 | 0.394 | 0.553 | 0.579 | 0.047 | Tunisia | -| 0.327 | 0.432 | 0.573 | 0.547 | 0.049 | New Caledonia | -| 0.325 | 0.394 | 0.541 | 0.559 | 0.047 | Asia | -| 0.310 | 0.350 | 0.463 | 0.535 | 0.039 | Bolivia (Plurinational State of) | -| 0.309 | 0.348 | 0.480 | 0.532 | 0.040 | Dominican Republic | -| 0.307 | 0.348 | 0.503 | 0.505 | 0.042 | Kazakhstan | -| 0.306 | 0.352 | 0.485 | 0.532 | 0.041 | Mexico | -| 0.305 | 0.365 | 0.502 | 0.526 | 0.042 | Venezuela (Bolivarian Republic of) | -| 0.303 | 0.347 | 0.474 | 0.525 | 0.040 | Ecuador | -| 0.295 | 0.346 | 0.482 | 0.501 | 0.041 | Lebanon | -| 0.293 | 0.400 | 0.542 | 0.477 | 0.045 | Seychelles | -| 0.287 | 0.384 | 0.527 | 0.513 | 0.046 | French Polynesia | -| 0.282 | 0.326 | 0.456 | 0.456 | 0.038 | Guyana | -| 0.280 | 0.335 | 0.463 | 0.469 | 0.039 | Suriname | -| 0.273 | 0.313 | 0.474 | 0.452 | 0.039 | Azerbaijan | -| 0.272 | 0.337 | 0.474 | 0.462 | 0.041 | Morocco | -| 0.269 | 0.358 | 0.495 | 0.460 | 0.042 | Bahamas | -| 0.263 | 0.325 | 0.453 | 0.442 | 0.039 | Malaysia | -| 0.260 | 0.305 | 0.426 | 0.446 | 0.037 | Algeria | -| 0.257 | 0.307 | 0.418 | 0.436 | 0.037 | Paraguay | -| 0.251 | 0.297 | 0.403 | 0.423 | 0.035 | Bhutan | -| 0.246 | 0.301 | 0.431 | 0.418 | 0.037 | Iran (Islamic Republic of) | -| 0.234 | 0.293 | 0.414 | 0.398 | 0.037 | India | -| 0.229 | 0.293 | 0.416 | 0.387 | 0.036 | Indonesia | -| 0.228 | 0.259 | 0.373 | 0.393 | 0.032 | Nicaragua | -| 0.221 | 0.269 | 0.368 | 0.374 | 0.031 | Bangladesh | -| 0.221 | 0.232 | 0.349 | 0.374 | 0.029 | Cabo Verde | -| 0.217 | 0.284 | 0.375 | 0.310 | 0.032 | Tonga | -| 0.215 | 0.277 | 0.401 | 0.366 | 0.036 | Myanmar | -| 0.208 | 0.235 | 0.334 | 0.351 | 0.029 | Belize | -| 0.206 | 0.235 | 0.331 | 0.353 | 0.029 | Honduras | -| 0.204 | 0.233 | 0.323 | 0.349 | 0.029 | Guatemala | -| 0.204 | 0.255 | 0.360 | 0.342 | 0.032 | Philippines | -| 0.202 | 0.267 | 0.360 | 0.344 | 0.033 | Nepal | -| 0.197 | 0.249 | 0.381 | 0.331 | 0.032 | Brunei Darussalam | -| 0.194 | 0.237 | 0.331 | 0.330 | 0.030 | Haiti | -| 0.193 | 0.251 | 0.355 | 0.325 | 0.032 | South Africa | -| 0.193 | 0.222 | 0.339 | 0.316 | 0.029 | Turkmenistan | -| 0.192 | 0.247 | 0.343 | 0.321 | 0.031 | Egypt | -| 0.192 | 0.262 | 0.376 | 0.318 | 0.033 | Fiji | -| 0.188 | 0.220 | 0.335 | 0.310 | 0.029 | Kyrgyzstan | -| 0.188 | 0.245 | 0.353 | 0.344 | 0.031 | French Guiana | -| 0.187 | 0.219 | 0.340 | 0.317 | 0.029 | Uzbekistan | -| 0.185 | 0.224 | 0.323 | 0.317 | 0.029 | Syrian Arab Republic | -| 0.182 | 0.226 | 0.324 | 0.307 | 0.028 | Libya | -| 0.181 | 0.229 | 0.319 | 0.308 | 0.029 | Lesotho | -| 0.173 | 0.216 | 0.320 | 0.294 | 0.027 | Mongolia | -| 0.170 | 0.225 | 0.317 | 0.287 | 0.028 | Djibouti | -| 0.170 | 0.238 | 0.325 | 0.271 | 0.029 | Samoa | -| 0.168 | 0.221 | 0.314 | 0.288 | 0.029 | Cambodia | -| 0.164 | 0.210 | 0.292 | 0.274 | 0.026 | Pakistan | -| 0.158 | 0.204 | 0.273 | 0.268 | 0.026 | Eritrea | -| 0.157 | 0.183 | 0.277 | 0.252 | 0.024 | Maldives | -| 0.157 | 0.194 | 0.268 | 0.281 | 0.024 | Mayotte | -| 0.156 | 0.199 | 0.279 | 0.260 | 0.025 | Jordan | -| 0.155 | 0.203 | 0.289 | 0.263 | 0.027 | Botswana | -| 0.154 | 0.199 | 0.287 | 0.257 | 0.026 | Lao People's Democratic Republic | -| 0.152 | 0.209 | 0.279 | 0.253 | 0.025 | Timor-Leste | -| 0.146 | 0.180 | 0.282 | 0.248 | 0.024 | Saudi Arabia | -| 0.145 | 0.187 | 0.254 | 0.239 | 0.024 | Eswatini | -| 0.139 | 0.173 | 0.248 | 0.234 | 0.023 | Namibia | -| 0.135 | 0.176 | 0.302 | 0.222 | 0.024 | Kuwait | -| 0.134 | 0.173 | 0.244 | 0.224 | 0.023 | Sudan | -| 0.133 | 0.173 | 0.245 | 0.221 | 0.023 | Gabon | -| 0.130 | 0.167 | 0.231 | 0.216 | 0.022 | Ethiopia | -| 0.130 | 0.174 | 0.242 | 0.224 | 0.023 | Solomon Islands | -| 0.128 | 0.158 | 0.245 | 0.207 | 0.022 | Tajikistan | -| 0.127 | 0.165 | 0.236 | 0.212 | 0.022 | Africa | -| 0.125 | 0.157 | 0.229 | 0.212 | 0.022 | Iraq | -| 0.125 | 0.150 | 0.253 | 0.199 | 0.021 | Bahrain | -| 0.124 | 0.163 | 0.225 | 0.204 | 0.021 | South Sudan | -| 0.123 | 0.168 | 0.244 | 0.196 | 0.023 | Vanuatu | -| 0.122 | 0.165 | 0.247 | 0.204 | 0.023 | Papua New Guinea | -| 0.121 | 0.157 | 0.226 | 0.203 | 0.021 | Liberia | -| 0.121 | 0.157 | 0.222 | 0.203 | 0.021 | Benin | -| 0.120 | 0.155 | 0.224 | 0.199 | 0.021 | Mauritania | -| 0.120 | 0.157 | 0.222 | 0.196 | 0.021 | State of Palestine | -| 0.119 | 0.150 | 0.219 | 0.173 | 0.020 | Sao Tome and Principe | -| 0.118 | 0.178 | 0.278 | 0.228 | 0.027 | Micronesia (Fed. States of) | -| 0.118 | 0.138 | 0.222 | 0.195 | 0.020 | Oman | -| 0.118 | 0.160 | 0.260 | 0.195 | 0.024 | Western Sahara | -| 0.116 | 0.157 | 0.230 | 0.190 | 0.021 | Ghana | -| 0.116 | 0.146 | 0.216 | 0.193 | 0.020 | Madagascar | -| 0.113 | 0.149 | 0.220 | 0.193 | 0.021 | Comoros | -| 0.112 | 0.142 | 0.205 | 0.188 | 0.020 | Zimbabwe | -| 0.112 | 0.146 | 0.216 | 0.193 | 0.021 | Rwanda | -| 0.111 | 0.146 | 0.208 | 0.184 | 0.020 | Senegal | -| 0.110 | 0.144 | 0.203 | 0.182 | 0.019 | Democratic Republic of the Congo | -| 0.107 | 0.139 | 0.202 | 0.175 | 0.020 | Yemen | -| 0.106 | 0.141 | 0.203 | 0.174 | 0.019 | Sierra Leone | -| 0.103 | 0.165 | 0.239 | 0.197 | 0.023 | Kiribati | -| 0.103 | 0.136 | 0.192 | 0.168 | 0.019 | Mozambique | -| 0.102 | 0.135 | 0.192 | 0.168 | 0.019 | Somalia | -| 0.102 | 0.139 | 0.202 | 0.168 | 0.019 | Togo | -| 0.101 | 0.137 | 0.201 | 0.166 | 0.019 | Congo | -| 0.101 | 0.133 | 0.191 | 0.166 | 0.019 | Central African Republic | -| 0.100 | 0.134 | 0.194 | 0.166 | 0.019 | Guinea | -| 0.100 | 0.135 | 0.197 | 0.165 | 0.019 | Côte d'Ivoire | -| 0.098 | 0.130 | 0.189 | 0.160 | 0.018 | Cameroon | -| 0.097 | 0.130 | 0.192 | 0.160 | 0.019 | Guinea-Bissau | -| 0.097 | 0.129 | 0.183 | 0.157 | 0.018 | Malawi | -| 0.096 | 0.129 | 0.186 | 0.157 | 0.018 | United Republic of Tanzania | -| 0.096 | 0.128 | 0.184 | 0.156 | 0.018 | Afghanistan | -| 0.094 | 0.122 | 0.186 | 0.153 | 0.018 | Kenya | -| 0.094 | 0.130 | 0.190 | 0.154 | 0.019 | Nigeria | -| 0.092 | 0.118 | 0.179 | 0.149 | 0.018 | Equatorial Guinea | -| 0.091 | 0.126 | 0.177 | 0.146 | 0.017 | Gambia | -| 0.091 | 0.116 | 0.170 | 0.150 | 0.017 | Chad | -| 0.090 | 0.112 | 0.203 | 0.141 | 0.018 | Qatar | -| 0.088 | 0.121 | 0.172 | 0.146 | 0.017 | Niger | -| 0.088 | 0.118 | 0.173 | 0.144 | 0.017 | Burkina Faso | -| 0.088 | 0.109 | 0.169 | 0.144 | 0.017 | Burundi | -| 0.087 | 0.117 | 0.169 | 0.145 | 0.017 | Mali | -| 0.085 | 0.111 | 0.164 | 0.139 | 0.016 | Angola | -| 0.083 | 0.104 | 0.190 | 0.130 | 0.016 | United Arab Emirates | -| 0.083 | 0.107 | 0.158 | 0.134 | 0.016 | Zambia | -| 0.074 | 0.099 | 0.147 | 0.121 | 0.015 | Uganda | +| 1.274 | 1.311 | 1.605 | 2.660 | 0.125 | Japan | +| 1.065 | 1.092 | 1.382 | 2.177 | 0.106 | Italy | +| 1.041 | 1.043 | 1.339 | 2.135 | 0.102 | Greece | +| 0.993 | 1.012 | 1.305 | 1.997 | 0.100 | Germany | +| 0.984 | 1.045 | 1.320 | 2.027 | 0.104 | Portugal | +| 0.931 | 0.985 | 1.270 | 1.938 | 0.100 | Martinique | +| 0.919 | 0.933 | 1.221 | 1.953 | 0.095 | Lithuania | +| 0.916 | 0.942 | 1.207 | 1.950 | 0.093 | Spain | +| 0.914 | 0.941 | 1.201 | 1.899 | 0.095 | France | +| 0.899 | 1.008 | 1.248 | 1.819 | 0.102 | Finland | +| 0.881 | 0.919 | 1.192 | 1.910 | 0.095 | Latvia | +| 0.875 | 0.957 | 1.205 | 1.789 | 0.096 | Puerto Rico | +| 0.868 | 0.892 | 1.171 | 1.773 | 0.093 | Estonia | +| 0.865 | 0.932 | 1.209 | 1.733 | 0.098 | Croatia | +| 0.855 | 0.965 | 1.205 | 1.716 | 0.099 | Malta | +| 0.846 | 0.881 | 1.137 | 1.740 | 0.089 | Belgium | +| 0.843 | 0.905 | 1.181 | 1.740 | 0.095 | Slovenia | +| 0.840 | 0.943 | 1.154 | 1.722 | 0.093 | Sweden | +| 0.836 | 0.910 | 1.149 | 1.709 | 0.090 | Austria | +| 0.825 | 0.897 | 1.132 | 1.697 | 0.089 | Switzerland | +| 0.810 | 0.861 | 1.117 | 1.633 | 0.089 | Europe | +| 0.802 | 0.909 | 1.141 | 1.625 | 0.093 | Netherlands | +| 0.801 | 0.949 | 1.181 | 1.592 | 0.098 | Bulgaria | +| 0.798 | 0.864 | 1.113 | 1.637 | 0.090 | Guadeloupe | +| 0.797 | 0.935 | 1.136 | 1.593 | 0.093 | Denmark | +| 0.794 | 0.868 | 1.089 | 1.622 | 0.087 | United Kingdom | +| 0.791 | 0.811 | 1.102 | 1.607 | 0.087 | China, Hong Kong SAR | +| 0.759 | 0.830 | 1.090 | 1.494 | 0.089 | Romania | +| 0.753 | 0.854 | 1.101 | 1.534 | 0.093 | Hungary | +| 0.745 | 0.800 | 1.064 | 1.502 | 0.087 | Poland | +| 0.739 | 0.828 | 1.059 | 1.538 | 0.084 | Channel Islands | +| 0.738 | 0.878 | 1.092 | 1.510 | 0.092 | Czechia | +| 0.734 | 0.810 | 1.047 | 1.505 | 0.085 | Canada | +| 0.719 | 0.756 | 0.998 | 1.480 | 0.079 | Barbados | +| 0.713 | 0.808 | 1.038 | 1.403 | 0.084 | Curaçao | +| 0.709 | 0.802 | 1.007 | 1.447 | 0.082 | Norway | +| 0.680 | 0.800 | 1.029 | 1.337 | 0.088 | Serbia | +| 0.676 | 0.694 | 0.904 | 1.407 | 0.071 | Uruguay | +| 0.675 | 0.745 | 0.967 | 1.379 | 0.079 | Northern America | +| 0.671 | 0.736 | 0.944 | 1.374 | 0.076 | Australia | +| 0.671 | 0.733 | 0.983 | 1.271 | 0.080 | Ukraine | +| 0.669 | 0.738 | 0.958 | 1.365 | 0.078 | United States of America | +| 0.659 | 0.757 | 1.011 | 1.243 | 0.085 | Bosnia and Herzegovina | +| 0.654 | 0.742 | 0.945 | 1.323 | 0.077 | New Zealand | +| 0.644 | 0.735 | 0.941 | 1.314 | 0.077 | Cuba | +| 0.641 | 0.877 | 1.059 | 1.308 | 0.094 | United States Virgin Islands | +| 0.633 | 0.725 | 0.963 | 1.259 | 0.077 | Republic of Korea | +| 0.628 | 0.686 | 0.938 | 1.280 | 0.077 | China, Taiwan Province of China | +| 0.624 | 0.663 | 0.916 | 1.191 | 0.074 | Russian Federation | +| 0.624 | 0.657 | 0.921 | 1.252 | 0.075 | Belarus | +| 0.615 | 0.668 | 0.881 | 1.261 | 0.070 | Luxembourg | +| 0.607 | 0.670 | 0.896 | 1.155 | 0.073 | Georgia | +| 0.605 | 0.683 | 0.888 | 1.236 | 0.073 | Iceland | +| 0.604 | 0.709 | 0.935 | 1.222 | 0.079 | Slovakia | +| 0.582 | 0.667 | 0.891 | 1.138 | 0.075 | Montenegro | +| 0.563 | 0.653 | 0.838 | 1.126 | 0.070 | Ireland | +| 0.561 | 0.649 | 0.839 | 1.106 | 0.069 | Cyprus | +| 0.548 | 0.659 | 0.857 | 1.079 | 0.071 | Albania | +| 0.531 | 0.652 | 0.874 | 1.049 | 0.072 | Aruba | +| 0.518 | 0.580 | 0.754 | 1.052 | 0.062 | Oceania | +| 0.510 | 0.588 | 0.795 | 1.017 | 0.065 | Thailand | +| 0.500 | 0.569 | 0.763 | 1.020 | 0.063 | Réunion | +| 0.499 | 0.545 | 0.710 | 1.021 | 0.060 | Israel | +| 0.497 | 0.522 | 0.748 | 0.915 | 0.059 | Armenia | +| 0.497 | 0.616 | 0.816 | 0.968 | 0.070 | North Macedonia | +| 0.493 | 0.550 | 0.736 | 1.001 | 0.061 | Chile | +| 0.479 | 0.550 | 0.796 | 0.952 | 0.067 | Singapore | +| 0.454 | 0.515 | 0.671 | 0.917 | 0.056 | Argentina | +| 0.449 | 0.514 | 0.738 | 0.887 | 0.062 | China, Macao SAR | +| 0.447 | 0.544 | 0.732 | 0.885 | 0.063 | Mauritius | +| 0.435 | 0.501 | 0.721 | 0.876 | 0.062 | Republic of Moldova | +| 0.415 | 0.511 | 0.681 | 0.820 | 0.058 | Trinidad and Tobago | +| 0.413 | 0.475 | 0.638 | 0.823 | 0.053 | Costa Rica | +| 0.413 | 0.468 | 0.626 | 0.818 | 0.051 | Saint Lucia | +| 0.409 | 0.507 | 0.695 | 0.806 | 0.061 | China | +| 0.394 | 0.497 | 0.648 | 0.822 | 0.052 | Antigua and Barbuda | +| 0.387 | 0.495 | 0.651 | 0.762 | 0.056 | Sri Lanka | +| 0.377 | 0.487 | 0.635 | 0.706 | 0.050 | Dem. People's Republic of Korea | +| 0.376 | 0.437 | 0.594 | 0.743 | 0.050 | Brazil | +| 0.365 | 0.464 | 0.611 | 0.703 | 0.052 | Guam | +| 0.364 | 0.425 | 0.569 | 0.725 | 0.047 | Jamaica | +| 0.361 | 0.454 | 0.605 | 0.764 | 0.051 | Saint Vincent and the Grenadines | +| 0.359 | 0.399 | 0.540 | 0.724 | 0.045 | Panama | +| 0.358 | 0.418 | 0.566 | 0.709 | 0.048 | WORLD | +| 0.356 | 0.410 | 0.555 | 0.710 | 0.047 | Latin America and the Caribbean | +| 0.355 | 0.412 | 0.560 | 0.707 | 0.047 | Colombia | +| 0.354 | 0.438 | 0.595 | 0.740 | 0.050 | Grenada | +| 0.347 | 0.399 | 0.528 | 0.687 | 0.045 | El Salvador | +| 0.343 | 0.363 | 0.528 | 0.701 | 0.043 | Viet Nam | +| 0.342 | 0.408 | 0.552 | 0.675 | 0.047 | Turkey | +| 0.339 | 0.397 | 0.537 | 0.671 | 0.045 | Peru | +| 0.336 | 0.394 | 0.553 | 0.664 | 0.047 | Tunisia | +| 0.327 | 0.432 | 0.573 | 0.616 | 0.049 | New Caledonia | +| 0.325 | 0.394 | 0.541 | 0.640 | 0.047 | Asia | +| 0.310 | 0.350 | 0.463 | 0.622 | 0.039 | Bolivia (Plurinational State of) | +| 0.309 | 0.348 | 0.480 | 0.616 | 0.040 | Dominican Republic | +| 0.307 | 0.348 | 0.503 | 0.574 | 0.042 | Kazakhstan | +| 0.306 | 0.352 | 0.485 | 0.615 | 0.041 | Mexico | +| 0.305 | 0.365 | 0.502 | 0.604 | 0.042 | Venezuela (Bolivarian Republic of) | +| 0.303 | 0.347 | 0.474 | 0.607 | 0.040 | Ecuador | +| 0.295 | 0.346 | 0.482 | 0.576 | 0.041 | Lebanon | +| 0.293 | 0.400 | 0.542 | 0.527 | 0.045 | Seychelles | +| 0.287 | 0.384 | 0.527 | 0.579 | 0.046 | French Polynesia | +| 0.282 | 0.326 | 0.456 | 0.521 | 0.038 | Guyana | +| 0.280 | 0.335 | 0.463 | 0.536 | 0.039 | Suriname | +| 0.273 | 0.313 | 0.474 | 0.515 | 0.039 | Azerbaijan | +| 0.272 | 0.337 | 0.474 | 0.522 | 0.041 | Morocco | +| 0.269 | 0.358 | 0.495 | 0.517 | 0.042 | Bahamas | +| 0.263 | 0.325 | 0.453 | 0.504 | 0.039 | Malaysia | +| 0.260 | 0.305 | 0.426 | 0.512 | 0.037 | Algeria | +| 0.257 | 0.307 | 0.418 | 0.500 | 0.037 | Paraguay | +| 0.251 | 0.297 | 0.403 | 0.486 | 0.035 | Bhutan | +| 0.246 | 0.301 | 0.431 | 0.476 | 0.037 | Iran (Islamic Republic of) | +| 0.234 | 0.293 | 0.414 | 0.452 | 0.037 | India | +| 0.229 | 0.293 | 0.416 | 0.437 | 0.036 | Indonesia | +| 0.228 | 0.259 | 0.373 | 0.452 | 0.032 | Nicaragua | +| 0.221 | 0.269 | 0.368 | 0.428 | 0.031 | Bangladesh | +| 0.221 | 0.232 | 0.349 | 0.432 | 0.029 | Cabo Verde | +| 0.217 | 0.284 | 0.375 | 0.342 | 0.032 | Tonga | +| 0.215 | 0.277 | 0.401 | 0.412 | 0.036 | Myanmar | +| 0.208 | 0.235 | 0.334 | 0.406 | 0.029 | Belize | +| 0.206 | 0.235 | 0.331 | 0.407 | 0.029 | Honduras | +| 0.204 | 0.233 | 0.323 | 0.403 | 0.029 | Guatemala | +| 0.204 | 0.255 | 0.360 | 0.388 | 0.032 | Philippines | +| 0.202 | 0.267 | 0.360 | 0.388 | 0.033 | Nepal | +| 0.197 | 0.249 | 0.381 | 0.373 | 0.032 | Brunei Darussalam | +| 0.194 | 0.237 | 0.331 | 0.376 | 0.030 | Haiti | +| 0.193 | 0.251 | 0.355 | 0.366 | 0.032 | South Africa | +| 0.193 | 0.222 | 0.339 | 0.360 | 0.029 | Turkmenistan | +| 0.192 | 0.247 | 0.343 | 0.363 | 0.031 | Egypt | +| 0.192 | 0.262 | 0.376 | 0.354 | 0.033 | Fiji | +| 0.188 | 0.220 | 0.335 | 0.353 | 0.029 | Kyrgyzstan | +| 0.188 | 0.245 | 0.353 | 0.392 | 0.031 | French Guiana | +| 0.187 | 0.219 | 0.340 | 0.359 | 0.029 | Uzbekistan | +| 0.185 | 0.224 | 0.323 | 0.361 | 0.029 | Syrian Arab Republic | +| 0.182 | 0.226 | 0.324 | 0.349 | 0.028 | Libya | +| 0.181 | 0.229 | 0.319 | 0.350 | 0.029 | Lesotho | +| 0.173 | 0.216 | 0.320 | 0.333 | 0.027 | Mongolia | +| 0.170 | 0.225 | 0.317 | 0.324 | 0.028 | Djibouti | +| 0.170 | 0.238 | 0.325 | 0.299 | 0.029 | Samoa | +| 0.168 | 0.221 | 0.314 | 0.325 | 0.029 | Cambodia | +| 0.164 | 0.210 | 0.292 | 0.310 | 0.026 | Pakistan | +| 0.158 | 0.204 | 0.273 | 0.303 | 0.026 | Eritrea | +| 0.157 | 0.183 | 0.277 | 0.285 | 0.024 | Maldives | +| 0.157 | 0.194 | 0.268 | 0.324 | 0.024 | Mayotte | +| 0.156 | 0.199 | 0.279 | 0.294 | 0.025 | Jordan | +| 0.155 | 0.203 | 0.289 | 0.296 | 0.027 | Botswana | +| 0.154 | 0.199 | 0.287 | 0.289 | 0.026 | Lao People's Democratic Republic | +| 0.152 | 0.209 | 0.279 | 0.285 | 0.025 | Timor-Leste | +| 0.146 | 0.180 | 0.282 | 0.281 | 0.024 | Saudi Arabia | +| 0.145 | 0.187 | 0.254 | 0.271 | 0.024 | Eswatini | +| 0.139 | 0.173 | 0.248 | 0.265 | 0.023 | Namibia | +| 0.135 | 0.176 | 0.302 | 0.246 | 0.024 | Kuwait | +| 0.134 | 0.173 | 0.244 | 0.254 | 0.023 | Sudan | +| 0.133 | 0.173 | 0.245 | 0.248 | 0.023 | Gabon | +| 0.130 | 0.167 | 0.231 | 0.244 | 0.022 | Ethiopia | +| 0.130 | 0.174 | 0.242 | 0.252 | 0.023 | Solomon Islands | +| 0.128 | 0.158 | 0.245 | 0.233 | 0.022 | Tajikistan | +| 0.127 | 0.165 | 0.236 | 0.239 | 0.022 | Africa | +| 0.125 | 0.157 | 0.229 | 0.240 | 0.022 | Iraq | +| 0.125 | 0.150 | 0.253 | 0.224 | 0.021 | Bahrain | +| 0.124 | 0.163 | 0.225 | 0.230 | 0.021 | South Sudan | +| 0.123 | 0.168 | 0.244 | 0.216 | 0.023 | Vanuatu | +| 0.122 | 0.165 | 0.247 | 0.227 | 0.023 | Papua New Guinea | +| 0.121 | 0.157 | 0.226 | 0.228 | 0.021 | Liberia | +| 0.121 | 0.157 | 0.222 | 0.229 | 0.021 | Benin | +| 0.120 | 0.155 | 0.224 | 0.224 | 0.021 | Mauritania | +| 0.120 | 0.157 | 0.222 | 0.220 | 0.021 | State of Palestine | +| 0.119 | 0.150 | 0.219 | 0.191 | 0.020 | Sao Tome and Principe | +| 0.118 | 0.178 | 0.278 | 0.250 | 0.027 | Micronesia (Fed. States of) | +| 0.118 | 0.138 | 0.222 | 0.222 | 0.020 | Oman | +| 0.118 | 0.160 | 0.260 | 0.214 | 0.024 | Western Sahara | +| 0.116 | 0.157 | 0.230 | 0.212 | 0.021 | Ghana | +| 0.116 | 0.146 | 0.216 | 0.218 | 0.020 | Madagascar | +| 0.113 | 0.149 | 0.220 | 0.217 | 0.021 | Comoros | +| 0.112 | 0.142 | 0.205 | 0.211 | 0.020 | Zimbabwe | +| 0.112 | 0.146 | 0.216 | 0.218 | 0.021 | Rwanda | +| 0.111 | 0.146 | 0.208 | 0.206 | 0.020 | Senegal | +| 0.110 | 0.144 | 0.203 | 0.205 | 0.019 | Democratic Republic of the Congo | +| 0.107 | 0.139 | 0.202 | 0.196 | 0.020 | Yemen | +| 0.106 | 0.141 | 0.203 | 0.195 | 0.019 | Sierra Leone | +| 0.103 | 0.165 | 0.239 | 0.217 | 0.023 | Kiribati | +| 0.103 | 0.136 | 0.192 | 0.189 | 0.019 | Mozambique | +| 0.102 | 0.135 | 0.192 | 0.189 | 0.019 | Somalia | +| 0.102 | 0.139 | 0.202 | 0.187 | 0.019 | Togo | +| 0.101 | 0.137 | 0.201 | 0.185 | 0.019 | Congo | +| 0.101 | 0.133 | 0.191 | 0.186 | 0.019 | Central African Republic | +| 0.100 | 0.134 | 0.194 | 0.185 | 0.019 | Guinea | +| 0.100 | 0.135 | 0.197 | 0.184 | 0.019 | Côte d'Ivoire | +| 0.098 | 0.130 | 0.189 | 0.178 | 0.018 | Cameroon | +| 0.097 | 0.130 | 0.192 | 0.178 | 0.019 | Guinea-Bissau | +| 0.097 | 0.129 | 0.183 | 0.176 | 0.018 | Malawi | +| 0.096 | 0.129 | 0.186 | 0.175 | 0.018 | United Republic of Tanzania | +| 0.096 | 0.128 | 0.184 | 0.175 | 0.018 | Afghanistan | +| 0.094 | 0.122 | 0.186 | 0.172 | 0.018 | Kenya | +| 0.094 | 0.130 | 0.190 | 0.171 | 0.019 | Nigeria | +| 0.092 | 0.118 | 0.179 | 0.167 | 0.018 | Equatorial Guinea | +| 0.091 | 0.126 | 0.177 | 0.162 | 0.017 | Gambia | +| 0.091 | 0.116 | 0.170 | 0.168 | 0.017 | Chad | +| 0.090 | 0.112 | 0.203 | 0.158 | 0.018 | Qatar | +| 0.088 | 0.121 | 0.172 | 0.162 | 0.017 | Niger | +| 0.088 | 0.118 | 0.173 | 0.160 | 0.017 | Burkina Faso | +| 0.088 | 0.109 | 0.169 | 0.161 | 0.017 | Burundi | +| 0.087 | 0.117 | 0.169 | 0.162 | 0.017 | Mali | +| 0.085 | 0.111 | 0.164 | 0.155 | 0.016 | Angola | +| 0.083 | 0.104 | 0.190 | 0.146 | 0.016 | United Arab Emirates | +| 0.083 | 0.107 | 0.158 | 0.150 | 0.016 | Zambia | +| 0.074 | 0.099 | 0.147 | 0.136 | 0.015 | Uganda | Note that in addition to countries, there are rows for each continent and for the world. diff --git a/apply_ifr.py b/apply_ifr.py index 8b321fd..9c574b2 100755 --- a/apply_ifr.py +++ b/apply_ifr.py @@ -69,16 +69,16 @@ ifrs = [ }), # Levin et al. - # https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v5 + # https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v7 # (table 3) ('COVID: Levin', { (0,34): 0.004, - (35,44): 0.06, - (45,54): 0.2, - (55,64): 0.7, - (65,74): 2.3, - (75,84): 7.6, - (85,maxage): 22.3, + (35,44): 0.068, + (45,54): 0.23, + (55,64): 0.75, + (65,74): 2.5, + (75,84): 8.5, + (85,maxage): 28.3, }), # IFR for seasonal influenza diff --git a/covid_vs_flu.py b/covid_vs_flu.py index c614bae..e607307 100755 --- a/covid_vs_flu.py +++ b/covid_vs_flu.py @@ -55,16 +55,16 @@ ifrs_covid = [ }), # Levin et al. - # https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v5 + # https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v7 # (table 3) ('Levin', { (0,34): 0.004, - (35,44): 0.06, - (45,54): 0.2, - (55,64): 0.7, - (65,74): 2.3, - (75,84): 7.6, - (85,maxage): 22.3, + (35,44): 0.068, + (45,54): 0.23, + (55,64): 0.75, + (65,74): 2.5, + (75,84): 8.5, + (85,maxage): 28.3, }), # Salje et al.: Estimating the burden of SARS-CoV-2 in France