voila

data/QALY_model/interim/long_COVID/average_QALY_losses_per_age_group_SMR100.csv

@@ -1,41 +1,41 @@
 hospitalisation,age_group,mean,sd,lower,upper
-Non-hospitalised,"[0, 12)",0.7007124662772034,0.2676912904450194,0.1446688395996455,1.2374509097821997
-Non-hospitalised,"[12, 18)",0.609550025791266,0.2307455402974724,0.13015702617116243,1.0711273600608555
-Non-hospitalised,"[18, 25)",0.5472661243309876,0.20545721591422927,0.12030042947052276,0.9576558295055875
-Non-hospitalised,"[25, 35)",0.47465585736838384,0.17591197706866557,0.10888503109152997,0.8255804945064931
-Non-hospitalised,"[35, 45)",0.3977512473373117,0.14453627828744953,0.09688757296976598,0.6859527881533536
-Non-hospitalised,"[45, 55)",0.32682507723255017,0.11554034596386943,0.08588718156447123,0.5573644862611579
-Non-hospitalised,"[55, 65)",0.2624121785837585,0.08920200449110868,0.07590138445487413,0.4406110423625363
-Non-hospitalised,"[65, 75)",0.20023682318940064,0.06382021086756653,0.0662144076375496,0.32780289613229696
-Non-hospitalised,"[75, 85)",0.141685422937724,0.03998552576581599,0.05701776661961077,0.22139184019910954
-Non-hospitalised,"[85, 120)",0.09445396182231887,0.020845220226073012,0.04962486217670849,0.135414209316056
-Hospitalised (no IC),"[0, 12)",1.9225870437049741,0.7822975992767989,0.4872214309311447,3.486041636906913
-Hospitalised (no IC),"[12, 18)",1.6763918112374891,0.6816772305432514,0.42834977958554127,3.0355564582089087
-Hospitalised (no IC),"[18, 25)",1.5047472849323487,0.6107415832980412,0.38792585125095397,2.7206365332176645
-Hospitalised (no IC),"[25, 35)",1.300234964504839,0.5251968407343157,0.340542022810944,2.3443486641289497
-Hospitalised (no IC),"[35, 45)",1.0781736449561836,0.4310396407916119,0.2900368440295111,1.934483990845256
-Hospitalised (no IC),"[45, 55)",0.8695128091498024,0.34167870526612704,0.24323044729902252,1.5484648158099321
-Hospitalised (no IC),"[55, 65)",0.6795415010815067,0.2602229631293996,0.200636153319262,1.1969179352299937
-Hospitalised (no IC),"[65, 75)",0.4986331658305124,0.1832095200625048,0.15964356047215597,0.8627041997756654
-Hospitalised (no IC),"[75, 85)",0.3321890686706806,0.11324870373713247,0.12367913078022028,0.5561158458241988
-Hospitalised (no IC),"[85, 120)",0.20126536006528772,0.059126432818673406,0.09491924095022707,0.31575781459724483
-Hospitalised (IC),"[0, 12)",3.024719489978397,1.0265548261377537,1.1975394639057406,5.077234121740847
-Hospitalised (IC),"[12, 18)",2.631690667216445,0.8949009906302372,1.0401437579925896,4.427929652353256
-Hospitalised (IC),"[18, 25)",2.3575421238665304,0.8019216326839035,0.9319236000199507,3.970603305357227
-Hospitalised (IC),"[25, 35)",2.0307290374024936,0.6895877818528608,0.8048830149924033,3.4198755188631735
-Hospitalised (IC),"[35, 45)",1.6756689154984816,0.5657026367693686,0.6692431871735698,2.814837650229509
-Hospitalised (IC),"[45, 55)",1.3418966725132067,0.4479726602066601,0.5433797098745519,2.2414408005705626
-Hospitalised (IC),"[55, 65)",1.0380081617077674,0.34065155397873,0.42898254727283214,1.7188213642104697
-Hospitalised (IC),"[65, 75)",0.7487133941045105,0.2392868131804628,0.3190531699034124,1.2241831892977466
-Hospitalised (IC),"[75, 85)",0.4827007436300753,0.1473242397457434,0.21656875487067243,0.7740071717211945
-Hospitalised (IC),"[85, 120)",0.27360665752397645,0.07614177654185664,0.1359744985210216,0.4242051228165759
-Non-hospitalised (no AD),"[0, 12)",0.06022375220009922,0.0029368162500658934,0.05411813168099017,0.06586791859253233
-Non-hospitalised (no AD),"[12, 18)",0.06019953136034096,0.002936816250065892,0.05409391084123191,0.06584369775277407
-Non-hospitalised (no AD),"[18, 25)",0.06017475524798904,0.0029368162500658943,0.054069134728879996,0.06581892164042216
-Non-hospitalised (no AD),"[25, 35)",0.06013712087633692,0.0029368162500658917,0.05403150035722789,0.06578128726877004
-Non-hospitalised (no AD),"[35, 45)",0.0600861321108908,0.0029368162500658934,0.05398051159178175,0.0657302985033239
-Non-hospitalised (no AD),"[45, 55)",0.06002785731596969,0.0029368162500658926,0.05392223679686064,0.0656720237084028
-Non-hospitalised (no AD),"[55, 65)",0.05996583279069703,0.0029368162500658934,0.05386021227158799,0.06560999918313015
-Non-hospitalised (no AD),"[65, 75)",0.05989757960355838,0.0029368162500658934,0.053791959084449344,0.06554174599599151
-Non-hospitalised (no AD),"[75, 85)",0.059824835301914,0.002936816250026131,0.05371921478288762,0.06546900169427071
-Non-hospitalised (no AD),"[85, 120)",0.059734550320283034,0.002936085041335324,0.05363044997902952,0.06537731142774374
+Non-hospitalised,"[0, 12)",,,,
+Non-hospitalised,"[12, 18)",,,,
+Non-hospitalised,"[18, 25)",,,,
+Non-hospitalised,"[25, 35)",,,,
+Non-hospitalised,"[35, 45)",,,,
+Non-hospitalised,"[45, 55)",,,,
+Non-hospitalised,"[55, 65)",,,,
+Non-hospitalised,"[65, 75)",,,,
+Non-hospitalised,"[75, 85)",,,,
+Non-hospitalised,"[85, 120)",,,,
+Hospitalised (no IC),"[0, 12)",,,,
+Hospitalised (no IC),"[12, 18)",,,,
+Hospitalised (no IC),"[18, 25)",,,,
+Hospitalised (no IC),"[25, 35)",,,,
+Hospitalised (no IC),"[35, 45)",,,,
+Hospitalised (no IC),"[45, 55)",,,,
+Hospitalised (no IC),"[55, 65)",,,,
+Hospitalised (no IC),"[65, 75)",,,,
+Hospitalised (no IC),"[75, 85)",,,,
+Hospitalised (no IC),"[85, 120)",,,,
+Hospitalised (IC),"[0, 12)",,,,
+Hospitalised (IC),"[12, 18)",,,,
+Hospitalised (IC),"[18, 25)",,,,
+Hospitalised (IC),"[25, 35)",,,,
+Hospitalised (IC),"[35, 45)",,,,
+Hospitalised (IC),"[45, 55)",,,,
+Hospitalised (IC),"[55, 65)",,,,
+Hospitalised (IC),"[65, 75)",,,,
+Hospitalised (IC),"[75, 85)",,,,
+Hospitalised (IC),"[85, 120)",,,,
+Non-hospitalised (no AD),"[0, 12)",,,,
+Non-hospitalised (no AD),"[12, 18)",,,,
+Non-hospitalised (no AD),"[18, 25)",,,,
+Non-hospitalised (no AD),"[25, 35)",,,,
+Non-hospitalised (no AD),"[35, 45)",,,,
+Non-hospitalised (no AD),"[45, 55)",,,,
+Non-hospitalised (no AD),"[55, 65)",,,,
+Non-hospitalised (no AD),"[65, 75)",,,,
+Non-hospitalised (no AD),"[75, 85)",,,,
+Non-hospitalised (no AD),"[85, 120)",,,,

data/QALY_model/interim/long_COVID/average_QALY_losses_per_age_group_SMR150.csv

@@ -0,0 +1,41 @@
+hospitalisation,age_group,mean,sd,lower,upper
+Non-hospitalised,"[0, 12)",0.668462419110261,0.2582313828457331,0.2036324547925269,1.2266842634252282
+Non-hospitalised,"[12, 18)",0.5798944237428355,0.22187795956279144,0.18094233731503914,1.0596337319588378
+Non-hospitalised,"[18, 25)",0.5190581364867876,0.1968431158317833,0.16537131828772747,0.9447050484446313
+Non-hospitalised,"[25, 35)",0.44763489426351,0.16736730072686784,0.1471094089416646,0.8092417221722648
+Non-hospitalised,"[35, 45)",0.37120795187222455,0.13572307883109985,0.12759033988719307,0.6642768756212402
+Non-hospitalised,"[45, 55)",0.3002411506332599,0.10627491577506192,0.10947793400313126,0.5297938114190412
+Non-hospitalised,"[55, 65)",0.23622082675172743,0.07971458883081076,0.0929959256939798,0.4084045703816341
+Non-hospitalised,"[65, 75)",0.17618743525018343,0.05486694992256693,0.07783840424384207,0.29459863667090785
+Non-hospitalised,"[75, 85)",0.12206526711280687,0.03255206915706073,0.06381993641723875,0.1920038620032939
+Non-hospitalised,"[85, 120)",0.08103127670002823,0.015751336483312568,0.05284996746867399,0.1150524706145426
+Hospitalised (no IC),"[0, 12)",1.8980894392621346,0.7267827620017653,0.6207356011360611,3.4240096409038068
+Hospitalised (no IC),"[12, 18)",1.6478459932072107,0.6300813814747115,0.546874783644301,2.9726944049100523
+Hospitalised (no IC),"[18, 25)",1.472820461853593,0.5617587044599202,0.49489406166793193,2.654800869057853
+Hospitalised (no IC),"[25, 35)",1.2634184870428975,0.47914425110921366,0.4321870750253125,2.272532748393311
+Hospitalised (no IC),"[35, 45)",1.0346805795675365,0.3878601694223998,0.3623500214659087,1.8514667391139488
+Hospitalised (no IC),"[45, 55)",0.8193694351258769,0.30129304663868833,0.2966104797693478,1.4529560947554594
+Hospitalised (no IC),"[55, 65)",0.6252626513069367,0.22328391548470894,0.23728421113389478,1.0937858217247964
+Hospitalised (no IC),"[65, 75)",0.44562604115188553,0.15161325700772058,0.18080980173221772,0.7631334746039069
+Hospitalised (no IC),"[75, 85)",0.28685503228783793,0.08900307321463005,0.13044941001272536,0.4732435233307565
+Hospitalised (no IC),"[85, 120)",0.16891493919738063,0.04328019853546922,0.09158887797754195,0.2612073485364238
+Hospitalised (IC),"[0, 12)",2.9237322020738303,0.9793705841671974,1.2107236313271368,4.999388921316399
+Hospitalised (IC),"[12, 18)",2.531638312858393,0.8497821429058505,1.0519529833728634,4.331883645375432
+Hospitalised (IC),"[18, 25)",2.257562381291156,0.757962284073033,0.9411960051611258,3.8628058096578908
+Hospitalised (IC),"[25, 35)",1.9298543316512762,0.6466155391861154,0.8090419079356348,3.2987897263962442
+Hospitalised (IC),"[35, 45)",1.5721185906351458,0.5232154765316691,0.6651014247066298,2.679412531598891
+Hospitalised (IC),"[45, 55)",1.2355267693612049,0.40597563326945363,0.5298650819811873,2.094388339582217
+Hospitalised (IC),"[55, 65)",0.9320835477121102,0.3003429071567427,0.40793600939386565,1.56709365027751
+Hospitalised (IC),"[65, 75)",0.6511568673099988,0.2034594772850809,0.2948885959200651,1.0807438310262218
+Hospitalised (IC),"[75, 85)",0.4027184979804148,0.1189921363368849,0.1936167990895866,0.6530541829319151
+Hospitalised (IC),"[85, 120)",0.21808592502322638,0.057238589088626377,0.11680411982667387,0.33711143404710353
+Non-hospitalised (no AD),"[0, 12)",0.06014137527980275,0.002961992425985527,0.05453426633193338,0.06582908835826626
+Non-hospitalised (no AD),"[12, 18)",0.06011715444004468,0.002961992425985527,0.054510045492175314,0.0658048675185082
+Non-hospitalised (no AD),"[18, 25)",0.06009237832769276,0.0029619924259855273,0.05448526937982339,0.06578009140615626
+Non-hospitalised (no AD),"[25, 35)",0.06005474395604065,0.0029619924259855278,0.054447635008171284,0.06574245703450415
+Non-hospitalised (no AD),"[35, 45)",0.06000375519059451,0.002961992425985528,0.054396646242725145,0.06569146826905803
+Non-hospitalised (no AD),"[45, 55)",0.059945480395673406,0.002961992425985528,0.05433837144780404,0.06563319347413692
+Non-hospitalised (no AD),"[55, 65)",0.05988345587040076,0.002961992425985525,0.054276346922531395,0.06557116894886428
+Non-hospitalised (no AD),"[65, 75)",0.05981520268326211,0.0029619924259855247,0.054208093735392746,0.06550291576172562
+Non-hospitalised (no AD),"[75, 85)",0.05974245826449364,0.0029619924191818985,0.05413534932950368,0.06543017132989262
+Non-hospitalised (no AD),"[85, 120)",0.05963967771162379,0.0029605970042578026,0.05403521032407272,0.06532471125642572

notebooks/analysis/woldmuyn_long_COVID.py

@@ -202,6 +202,6 @@
         lower = np.quantile(total,0.025)
         upper = np.quantile(total,0.975)
 
-        QALY_table[total_label]['Total'] = f'{mean:.0f}\n({lower:.0f};{upper:.0f})'
+        QALY_table[total_label]['Total'] = f'{mean:.0f}\n({lower:.0f}; {upper:.0f})'
 
     QALY_table.to_csv(os.path.join(result_folder,f'Long_COVID_summary_SMR{SMR*100:.0f}.csv'))

notebooks/preprocessing/woldmuyn_long_covid_average_QALY_loss.py

@@ -317,7 +317,7 @@ def QALY_loss_func(t,tau,p_AD,age,QoL_after):
     beta = QoL_Belgium_func(age+t/12)-QoL_after
     return prevalence_func(t,tau,p_AD) * max(0,beta)
 
-draws = 300
+draws = 500
 
 # Pre-allocate new multi index series with index=hospitalisation,age,draw
 multi_index = pd.MultiIndex.from_product([hospitalisation_groups+['Non-hospitalised (no AD)'],np.arange(draws),LE_table.index.values],names=['hospitalisation','draw','age'])
@@ -346,7 +346,7 @@ def QALY_loss_func(t,tau,p_AD,age,QoL_after):
     # integrate QALY_loss_func from 0 to LE (OPM: kan ook discreet) 
     QALY_loss = quad(QALY_loss_func,0,LE,args=(tau,p_AD,age,QoL_after))[0]/12 
     average_QALY_losses_per_age.iloc[idx] = QALY_loss
-    
+
 print('\n(4.2) Bin average QALY loss per age to age groups\n')
 
 # bin data

results/QALY_model/direct_QALYs/analysis/Long_COVID_summary_SMR150.csv

@@ -0,0 +1,89 @@
+,Non-hospitalised (no AD),Non-hospitalised (AD),Cohort,ICU,Deaths,Total (no AD),Total (AD)
+0-12,"8270
+(7280;9352)","90236
+(14582;157711)","1794
+(432;3082)","73
+(20;140)","0
+(0;0)","10136
+(8429;11889)","92079
+(16423;159442)"
+12-18,"4599
+(4054;5177)","43563
+(7403;75963)","792
+(191;1351)","158
+(43;277)","254
+(125;416)","5804
+(4968;6680)","44756
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+18-25,"3739
+(3248;4278)","31716
+(5667;54786)","861
+(209;1480)","147
+(40;256)","0
+(0;0)","4748
+(3934;5613)","32712
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+25-35,"6593
+(5730;7541)","48277
+(9210;82875)","2210
+(539;3785)","319
+(83;546)","1358
+(841;1959)","10480
+(8406;12473)","52132
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+35-45,"8483
+(7444;9686)","51582
+(10766;87745)","2620
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+(10026;14919)","21277
+(17736;24985)","35015
+(21034;48394)"
+65-75,"1786
+(1486;2126)","5186
+(1670;8394)","3366
+(1100;5565)","1738
+(575;2832)","24676
+(22406;27343)","31566
+(27673;35399)","34910
+(29820;40108)"
+75-85,"507
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+(764;3156)","610
+(223;993)","22990
+(20883;25499)","26084
+(23459;28960)","26575
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+85+,"278
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+(206;556)","621
+(301;956)","41
+(18;71)","7839
+(7043;8729)","8779
+(7932;9755)","8870
+(7957;9836)"
+Total,"47225
+(41067;54111)","330853
+(64709;566318)","21113
+(6043;35368)","6321
+(1913;10391)","78909
+(72366;85375)","153568
+(134389; 173180)","436876
+(166479; 673679)"