fix: run severe_outcomes scripts again after removing the deaths not …

…caused by covid-19 from the death incidence.

severe_outcomes/outputs/percentages.csv

@@ -1,13 +1,13 @@
 wave,age_group,HOSP-%,HOSP-%_lower,HOSP-%_upper,ICU-%,ICU-%_lower,ICU-%_upper,DEATH-%,DEATH-%_lower,DEATH-%_upper
 1.0,0-9,2.702,2.696,2.708,1.323,1.316,1.33,0.11,0.107,0.112
 1.0,10-19,1.426,1.421,1.43,1.397,1.39,1.404,0.082,0.08,0.084
-1.0,20-29,5.291,5.283,5.3,4.987,4.973,5.0,0.905,0.898,0.912
-1.0,30-39,9.916,9.906,9.927,9.455,9.437,9.473,2.604,2.592,2.616
-1.0,40-49,13.05,13.037,13.062,12.906,12.886,12.926,6.058,6.041,6.076
-1.0,50-59,20.294,20.279,20.308,20.52,20.496,20.544,14.227,14.201,14.253
-1.0,60-69,20.523,20.508,20.537,23.712,23.686,23.737,23.41,23.379,23.441
-1.0,70-79,15.231,15.218,15.244,17.31,17.287,17.332,25.302,25.27,25.333
-1.0,80+,11.568,11.556,11.579,8.391,8.374,8.408,27.303,27.27,27.335
+1.0,20-29,5.292,5.284,5.3,4.987,4.974,5.0,0.905,0.898,0.912
+1.0,30-39,9.917,9.906,9.928,9.456,9.438,9.474,2.604,2.592,2.616
+1.0,40-49,13.05,13.038,13.062,12.907,12.887,12.927,6.058,6.041,6.076
+1.0,50-59,20.294,20.28,20.309,20.522,20.497,20.546,14.227,14.201,14.253
+1.0,60-69,20.523,20.509,20.538,23.714,23.688,23.74,23.41,23.379,23.441
+1.0,70-79,15.228,15.215,15.241,17.302,17.279,17.325,25.302,25.27,25.333
+1.0,80+,11.568,11.556,11.579,8.392,8.375,8.409,27.303,27.27,27.335
 2.0,0-9,2.064,2.058,2.07,1.109,1.102,1.116,0.066,0.064,0.068
 2.0,10-19,1.168,1.164,1.173,0.661,0.655,0.666,0.066,0.064,0.068
 2.0,20-29,3.908,3.9,3.916,2.088,2.079,2.098,0.544,0.538,0.55

severe_outcomes/outputs/proportions_60p.csv

@@ -1,5 +1,5 @@
 wave,cases,hosp,hosp_lower,hosp_upper,icu,icu_lower,icu_upper,death,death_lower,death_upper
-1.0,38313.0,0.37253673687782213,0.36769552916902,0.37737794458662427,0.13940437971445724,0.1359361106182817,0.14287264881063277,0.14475504397985017,0.14123184537928662,0.14827824258041372
+1.0,38312.0,0.3725203591564001,0.3676791315051317,0.37736158680766846,0.13938191689287951,0.135913836716777,0.14284999706898202,0.1447588223011067,0.14123553952248283,0.14828210507973058
 2.0,50244.0,0.2707586975559271,0.2668733235998882,0.27464407151196596,0.10413183663721041,0.10146116924818613,0.1068025040262347,0.09919592389140992,0.09658214965875855,0.10180969812406129
 3.0,91330.0,0.20720464250520093,0.20457605976312207,0.2098332252472798,0.07665608233877148,0.07493065601883288,0.07838150865871009,0.09348516369210555,0.09159717161809769,0.09537315576611341
 4.0,52176.0,0.09816773995706839,0.09561468607909081,0.10072079383504597,0.01803511192885618,0.016893232889995044,0.019176990967717314,0.029668813247470102,0.028212942624744254,0.03112468387019595

severe_outcomes/outputs/proportions_all.csv

@@ -1,5 +1,5 @@
 wave,cases,hosp,hosp_lower,hosp_upper,icu,icu_lower,icu_upper,death,death_lower,death_upper
-1.0,270931.0,0.1113272383005267,0.110142860132388,0.11251161646866539,0.03989576681885794,0.03915881118762448,0.0406327224500914,0.02692936577947891,0.02631982328653463,0.02753890827242319
+1.0,270929.0,0.11132436911515563,0.11013999992591676,0.11250873830439449,0.039892370325804914,0.03915544204182121,0.04062929860978862,0.02692956457226801,0.026320017641939766,0.027539111502596254
 2.0,331060.0,0.07419803056847701,0.07330523921651491,0.07509082192043912,0.025602609798828006,0.02506458175843908,0.02614063783921693,0.018329003805956624,0.017872076464215562,0.018785931147697686
 3.0,781860.0,0.05437802164070294,0.053875385081387166,0.054880658200018716,0.020038114240401094,0.01972750339907906,0.02034872508172313,0.01687642288900826,0.0165909085994992,0.01716193717851732
 4.0,305481.0,0.028119588452309635,0.02753336001227751,0.02870581689234176,0.004458542429807418,0.004222286827175201,0.004694798032439635,0.005614097112422704,0.005349141313547686,0.005879052911297722

severe_outcomes/outputs/ratios.csv

@@ -1,13 +1,13 @@
 wave,age_group,cases,hosp,icu,hosp_death,icu_death,deaths,CFR,CFR_lower,CFR_upper,HCR,HCR_lower,HCR_upper,ICU-CR,ICU-CR_lower,ICU-CR_upper,HFR,HFR_lower,HFR_upper,ICU-FR,ICU-FR_lower,ICU-FR_upper
-1.0,all,270931,30162,10809,7220,3958.0,7296,0.0269,0.0263,0.0275,0.1113,0.1101,0.1125,0.0399,0.0392,0.0406,0.2394,0.2346,0.2442,0.3662,0.3571,0.3753
+1.0,all,270929,30161,10808,7220,3958.0,7296,0.0269,0.0263,0.0275,0.1113,0.1101,0.1125,0.0399,0.0392,0.0406,0.2394,0.2346,0.2442,0.3662,0.3571,0.3753
 1.0,0-9,11489,815,143,8,6.0,8,0.0007,0.0002,0.0012,0.0709,0.0662,0.0756,0.0124,0.0104,0.0145,0.0098,0.003,0.0166,0.042,0.0091,0.0748
-1.0,10-19,19202,430,151,6,3.0,6,0.0003,0.0001,0.0006,0.0224,0.0203,0.0245,0.0079,0.0066,0.0091,0.014,0.0029,0.025,0.0199,0.0,0.0421
+1.0,10-19,19201,430,151,6,3.0,6,0.0003,0.0001,0.0006,0.0224,0.0203,0.0245,0.0079,0.0066,0.0091,0.014,0.0029,0.025,0.0199,0.0,0.0421
 1.0,20-29,59732,1596,539,66,44.0,66,0.0011,0.0008,0.0014,0.0267,0.0254,0.028,0.009,0.0083,0.0098,0.0414,0.0316,0.0511,0.0816,0.0585,0.1047
 1.0,30-39,60465,2991,1022,190,120.0,190,0.0031,0.0027,0.0036,0.0495,0.0477,0.0512,0.0169,0.0159,0.0179,0.0635,0.0548,0.0723,0.1174,0.0977,0.1372
 1.0,40-49,44209,3936,1395,439,297.0,442,0.01,0.0091,0.0109,0.089,0.0864,0.0917,0.0316,0.0299,0.0332,0.1115,0.1017,0.1214,0.2129,0.1914,0.2344
 1.0,50-59,37521,6121,2218,1030,680.0,1038,0.0277,0.026,0.0293,0.1631,0.1594,0.1669,0.0591,0.0567,0.0615,0.1683,0.1589,0.1776,0.3066,0.2874,0.3258
 1.0,60-69,21338,6190,2563,1691,1091.0,1708,0.08,0.0764,0.0837,0.2901,0.284,0.2962,0.1201,0.1158,0.1245,0.2732,0.2621,0.2843,0.4257,0.4065,0.4448
-1.0,70-79,10610,4594,1871,1830,1106.0,1846,0.174,0.1668,0.1812,0.433,0.4236,0.4424,0.1763,0.1691,0.1836,0.3983,0.3842,0.4125,0.5911,0.5689,0.6134
+1.0,70-79,10609,4593,1870,1830,1106.0,1846,0.174,0.1668,0.1812,0.4329,0.4235,0.4424,0.1763,0.169,0.1835,0.3984,0.3843,0.4126,0.5914,0.5692,0.6137
 1.0,80+,6365,3489,907,1960,611.0,1992,0.313,0.3016,0.3244,0.5482,0.5359,0.5604,0.1425,0.1339,0.1511,0.5618,0.5453,0.5782,0.6736,0.6431,0.7042
 2.0,all,331060,24564,8476,5979,3517.0,6068,0.0183,0.0179,0.0188,0.0742,0.0733,0.0751,0.0256,0.0251,0.0261,0.2434,0.238,0.2488,0.4149,0.4044,0.4254
 2.0,0-9,10584,507,94,4,2.0,4,0.0004,0.0,0.0007,0.0479,0.0438,0.052,0.0089,0.0071,0.0107,0.0079,0.0002,0.0156,0.0213,0.0,0.0504

tables/outputs/table_s1.csv

@@ -1,5 +1,5 @@
 wave,Start,End,Confirmed cases,Hospitalizations,ICU,Deaths,R(t)
-1,2020-02-26,2020-09-25,270929,28610,9339,7084,"2.44(2.06, 2.86)"
+1,2020-02-26,2020-09-25,270929,30161,10808,7296,"2.44(2.06, 2.86)"
 2,2020-11-01,2021-03-01,331060,24564,8476,6068,"1.22(1.21, 1.23)"
 3,2021-03-01,2021-09-14,781860,42516,15667,13195,"1.46(1.44, 1.47)"
-4,2021-11-20,2022-03-24,305481,8584,1361,1697,"2.27(2.25, 2.28)"
+4,2021-11-20,2022-03-24,305481,8590,1362,1715,"2.27(2.25, 2.28)"