QALY calculation scripts and results (#382)

data/QALY_model/interim/life_table_model/Life_table_Belgium_2019.csv

@@ -0,0 +1,107 @@
+x,mu_x
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data/QALY_model/interim/life_table_model/QoL_scores_Belgium_2018_v3.csv

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+age_group;group_limit;QoL_score
+0-9;9;0.99
+10-19;19;0.921419167
+20-29;29;0.85
+30-39;39;0.834838126
+40-49;49;0.79937981
+50-59;59;0.78
+60-69;69;0.78
+70-79;89;0.730646696
+80-110;110;0.66

data/QALY_model/interim/long_COVID/average_QALY_losses_per_age_group.csv

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+hospitalisation,age_group,mean,sd,lower,upper
+Non-hospitalised,"[0, 12)",0.7549139354806483,0.2694793460593751,0.26033009381509126,1.2654616489762913
+Non-hospitalised,"[12, 18)",0.6557682465121549,0.2319941046629199,0.23045372285893342,1.0953384536860604
+Non-hospitalised,"[18, 25)",0.5880445016279974,0.2063723398223531,0.20999398363634544,0.9790782480476492
+Non-hospitalised,"[25, 35)",0.5091859479830138,0.1765102746143206,0.186103734244279,0.8436328969220431
+Non-hospitalised,"[35, 45)",0.42584808226184356,0.1449126549567518,0.1604649496836378,0.7004064743683598
+Non-hospitalised,"[45, 55)",0.3491923396383036,0.11581944544988457,0.1368567772399197,0.5686024656989533
+Non-hospitalised,"[55, 65)",0.27969699686034233,0.08944193486207846,0.1154619020140246,0.44910453369341524
+Non-hospitalised,"[65, 75)",0.2126266394094571,0.06400609633358172,0.09476051283649502,0.3338201724504505
+Non-hospitalised,"[75, 85)",0.14939012711229085,0.04005908402606354,0.07515845558458831,0.22519449849936593
+Non-hospitalised,"[85, 120)",0.09828109776916907,0.020763278513057953,0.05923471330586266,0.13746974820739163
+Cohort,"[0, 12)",1.947344085248101,0.8829639350355141,0.5412114592110516,3.604281750091514
+Cohort,"[12, 18)",1.6987183071446816,0.7690716896261184,0.4783040910288788,3.1482470035334598
+Cohort,"[18, 25)",1.5249729878066711,0.6887680123577957,0.434387154298585,2.8264323232466313
+Cohort,"[25, 35)",1.3175888898488481,0.5919806641239077,0.38202444758207266,2.438351224528888
+Cohort,"[35, 45)",1.0920935043268636,0.4855752793860406,0.3251580085312155,2.01155621562992
+Cohort,"[45, 55)",0.8801245695316176,0.3847321499777779,0.2717491661845526,1.6069922740029907
+Cohort,"[55, 65)",0.687311735355322,0.29289620531534105,0.2229126837437332,1.238524417668631
+Cohort,"[65, 75)",0.504013524458945,0.20608777240492873,0.17585731883702357,0.8902525649839934
+Cohort,"[75, 85)",0.33570615664482356,0.1271930468929509,0.1322131364633784,0.5737736324455484
+Cohort,"[85, 120)",0.2035409329616504,0.06606929554916093,0.09746170546937125,0.3283851787805579
+ICU,"[0, 12)",3.0458057335864352,1.1556055055051586,0.9479553850387902,5.033795329043032
+ICU,"[12, 18)",2.6483296474992724,1.0077417622788762,0.8292613202990119,4.389522587765419
+ICU,"[18, 25)",2.3712176184520075,0.9031283363394529,0.7465306849634975,3.935484401607709
+ICU,"[25, 35)",2.041279732573488,0.7765853791756424,0.6480557113435373,3.3887197036126837
+ICU,"[35, 45)",1.6835328129672527,0.6369160143929701,0.5413132363211832,2.788335483444341
+ICU,"[45, 55)",1.3479507354630411,0.5041738109373548,0.4412056820786608,2.219865106898985
+ICU,"[55, 65)",1.0427993720331827,0.3832494824727844,0.3501759277790381,1.7022073769061836
+ICU,"[65, 75)",0.752297215384547,0.2691716929942119,0.2634972701683917,1.2125534296753606
+ICU,"[75, 85)",0.484877070693285,0.16581782726261002,0.1836767039998967,0.7669847660173886
+ICU,"[85, 120)",0.2743083448199896,0.08590104372637732,0.12078862220202156,0.4206731519138677
+Non-hospitalised (no AD),"[0, 12)",0.060282821089509275,0.0031930620711356746,0.05333806424954111,0.06667994760964666
+Non-hospitalised (no AD),"[12, 18)",0.060258956115156394,0.0031930620711356768,0.05331419927518823,0.06665608263529377
+Non-hospitalised (no AD),"[18, 25)",0.06023431230082882,0.003193062071135676,0.05328955546086065,0.0666314388209662
+Non-hospitalised (no AD),"[25, 35)",0.06019667198670331,0.003193062071135676,0.05325191514673514,0.06659379850684069
+Non-hospitalised (no AD),"[35, 45)",0.06014543739797787,0.003193062071135674,0.05320068055800971,0.06654256391811524
+Non-hospitalised (no AD),"[45, 55)",0.060086650014045964,0.0031930620711356763,0.05314189317407779,0.06648377653418333
+Non-hospitalised (no AD),"[55, 65)",0.06002388450843266,0.003193062071135675,0.05307912766846448,0.06642101102857004
+Non-hospitalised (no AD),"[65, 75)",0.05995463758703485,0.003193062071135675,0.05300988074706668,0.06635176410717222
+Non-hospitalised (no AD),"[75, 85)",0.05988066945971605,0.0031930620710924457,0.05293591261984191,0.06627779597976682
+Non-hospitalised (no AD),"[85, 120)",0.05978895111949516,0.003192267062301329,0.05284592338560672,0.06618448488259096

data/QALY_model/interim/postponed_healthcare/hospital_yearly_QALYs.csv

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+MDC,disease_group,yearly_QALYs_mean,yearly_QALYs_lower,yearly_QALYs_upper
+16,Diseases of the blood,5591.36,1473.02,/
+05,Diseases of the circulatory system,96017.05,57073.49,306294.39
+06,Diseases of the digestive system,45442.18,35149.98,64727.40
+11,Diseases of the genitourinary system,22424.97,17534.55,31036.16
+12,Diseases of the genitourinary system,5919.74,4628.77,8192.92
+13,Diseases of the genitourinary system,6009.09,4698.63,8316.57
+08,Diseases of the musculoskeletal system,93206.00,73809.07,127020.27
+01,Diseases of the nervous system,66838.16,42246.76,159934.17
+04,Diseases of the respiratory system,82861.50,53679.84,176376.61
+02,Diseases of the eyes and ears,8218.67,6156.79,12533.47
+03,Diseases of the eyes and ears,49823.69,37324.07,75981.13
+09,Diseases of the skin,44437.40,30014.74,85542.00
+10,Endocrine diseases,23213.11,15148.55,48812.00
+18,Infectious diseases,30538.13,21783.86,51055.93
+19,Mental disorders,19483.23,14332.49,30412.84
+20,Mental disorders,6932.35,5099.66,10821.23
+AA,Mental disorders,/,/,/
+17,Neoplasms,21151.73,13253.79,51595.11
+14,"Pregnancy,  childbirth and perinatal period",19029.06,13161.77,34220.59
+15,"Pregnancy,  childbirth and perinatal period",4646.28,3213.68,8355.56
+00,Symptoms not elsewhere classified,33468.71,25528.79,47994.12
+07,Symptoms not elsewhere classified,36953.67,28187.00,52991.57
+21,Symptoms not elsewhere classified,12225.60,9325.27,17531.51
+22,Symptoms not elsewhere classified,1799.11,1372.30,2579.93
+23,Symptoms not elsewhere classified,29677.34,22636.87,42557.31
+24,Symptoms not elsewhere classified,1013.70,773.21,1453.64
+25,Symptoms not elsewhere classified,5681.47,4333.63,8147.23
+PP,Symptoms not elsewhere classified,22283.89,16997.39,31955.10

data/QALY_model/raw/life_table_model/QoL_scores_Belgium_2018.csv

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+age_group;group_limit;QoL_score
+0-14;14;0.99
+15-24;24;0.85
+25-34;34;0.85
+35-44;44;0.82
+45-54;54;0.78
+55-64;64;0.78
+65-74;74;0.78
+75+;110;0.66

data/QALY_model/raw/long_COVID/Long_COVID_prevalence.csv

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+Severity group,Months,Prevalence
+Mild,0,1
+Mild,0.918032787,0.623655914
+Mild,1.836065574,0.451612903
+Mild,2.754098361,0.247311828
+Mild,3.672131148,0.193548387
+Mild,4.590163934,0.139784946
+Mild,5.508196721,0.096774194
+Mild,6.426229508,0.075268817
+Mild,7.344262295,0.075268817
+Mild,8.262295082,0.064516129
+Mild,9.180327869,0.064516129
+Mild,10.09836066,0.053763441
+Mild,11.01639344,0.043010753
+Mild,11.93442623,0.021505376
+Moderate,0,1
+Moderate,0.918032787,0.85915493
+Moderate,1.836065574,0.669014085
+Moderate,2.754098361,0.485915493
+Moderate,3.672131148,0.401408451
+Moderate,4.590163934,0.345070423
+Moderate,5.508196721,0.309859155
+Moderate,6.426229508,0.246478873
+Moderate,7.344262295,0.211267606
+Moderate,8.262295082,0.183098592
+Moderate,9.180327869,0.147887324
+Moderate,10.09836066,0.126760563
+Moderate,11.01639344,0.112676056
+Moderate,11.93442623,0.105633803
+Severe-Critical,0,1
+Severe-Critical,0.918032787,0.9
+Severe-Critical,1.836065574,0.733333333
+Severe-Critical,2.754098361,0.555555556
+Severe-Critical,3.672131148,0.433333333
+Severe-Critical,4.590163934,0.322222222
+Severe-Critical,5.508196721,0.288888889
+Severe-Critical,6.426229508,0.277777778
+Severe-Critical,7.344262295,0.244444444
+Severe-Critical,8.262295082,0.244444444
+Severe-Critical,9.180327869,0.233333333
+Severe-Critical,10.09836066,0.233333333
+Severe-Critical,11.01639344,0.233333333
+Severe-Critical,11.93442623,0.211111111