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Results check (TRACE-LAC#33)
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* feat: added update confirmed cases

* run: results waves

* feat: added statsmodels

* run: results severe outomes

* fix: headers in best_model transpose

* style: remove script date

* run: results epidemiological distributions

* fix: start date 1st wave

* rerun table_s1.py

---------

Co-authored-by: ntorresd <[email protected]>
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@davidsantiagoquevedo @ntorresd
davidsantiagoquevedo and ntorresd authored May 29, 2023
1 parent 6708fb8 commit de969cd
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -14,3 +14,6 @@ data/*

# VS Code files
.vscode/*

# Control ou files
nohup*
3 changes: 2 additions & 1 deletion config.yml
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Expand Up @@ -30,4 +30,5 @@ default:
- 13
GAUSSIAN_KERNEL: 10
UPDATE_DATES:
GENOMICS : "20220802"
GENOMICS : "20220802"
CONFIRMED_CASES: "20230515"
80 changes: 40 additions & 40 deletions epidemiological_distributions/outputs/best_fit_summary.csv
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@@ -1,41 +1,41 @@
stat,dist,best,wave_1,wave_2,wave_3,wave_4
mean,hosp_stay,Gen Lognormal,10.76883921474214,8.853216010558954,8.775674693539813,7.853992869337221
q975,hosp_stay,Gen Lognormal,10.910172156715806,8.954060624215765,8.861531694373063,8.022733879587989
q025,hosp_stay,Gen Lognormal,10.630913270206545,8.74987192649207,8.690011552820364,7.703771170710262
observed,hosp_stay,NA,10.655249261179206,8.561534628799203,8.404271789999648,7.3468543046357615
var_mean,hosp_stay,Gen Lognormal,275.1972246400783,153.85900388196077,139.90796420269226,99.63055809961477
var_q975,hosp_stay,Gen Lognormal,276.80134471061774,154.76358101356303,141.32592645555226,103.68124171441131
var_q025,hosp_stay,Gen Lognormal,274.28131759660624,153.01769695601203,138.42425913452746,96.53867615682654
var_observed,hosp_stay,NA,220.32203264254315,117.52526598716223,86.40947010361224,56.15841151899576
mean,icu_stay,Gen Lognormal,16.309026010588127,15.386916952743853,14.43124619416027,12.446364847579147
q975,icu_stay,Gen Lognormal,16.63570598430982,15.683738725182636,14.642089091561846,13.119453697129757
q025,icu_stay,Gen Lognormal,15.985913387037982,15.182387971446536,14.253150948368454,11.983414927733326
observed,icu_stay,NA,14.782096584216726,13.749482972563078,13.25779175401817,11.631620553359683
var_mean,icu_stay,Gen Lognormal,674.3847379218339,544.5774514022264,426.84802116982684,276.9610036893575
var_q975,icu_stay,Gen Lognormal,662.1128089467198,540.3716284587507,430.18427412277026,294.9984335581107
var_q025,icu_stay,Gen Lognormal,696.1988942186892,570.6692796814876,428.58689679030357,283.25898583524514
var_observed,icu_stay,NA,216.94706272193096,159.11525242155997,139.82752157518934,90.00975884324825
mean,onset_hosp,Gen Lognormal,7.335978148873134,7.951345629875516,7.774285612510823,5.54334349798486
q975,onset_hosp,Gen Lognormal,7.409108388200213,8.033498160569602,7.823202142479176,5.578070091062677
q025,onset_hosp,Gen Lognormal,7.26387018220525,7.870891313607352,7.720915680432316,5.490745440006846
observed,onset_hosp,NA,6.862764484872454,7.359475731258991,7.087862490202967,4.776954732510288
var_mean,onset_hosp,Gen Lognormal,81.79710843969296,94.90139895698057,83.137128437679,75.64793421517626
var_q975,onset_hosp,Gen Lognormal,82.90694268319902,96.1261225141566,83.8277250160431,79.32609563912119
var_q025,onset_hosp,Gen Lognormal,80.71012253214981,93.79115520290955,82.29809811473478,68.14063757911589
var_observed,onset_hosp,NA,54.7844482231681,34.21790373194891,19.95803673092972,15.572414377152521
mean,onset_icu,Gen Lognormal,12.676163958323768,10.831487791805761,9.168637828572221,7.839244582793024
q975,onset_icu,Gen Lognormal,12.648599844522362,10.988274046391195,9.269449048068465,8.207074558907069
q025,onset_icu,Gen Lognormal,12.69533496197036,10.698779780256137,9.069087760602766,7.548884537013278
observed,onset_icu,NA,11.043735653014377,10.208265582655827,8.255364511691884,7.326547921967769
var_mean,onset_icu,Gen Lognormal,876.3979367201861,260.15292528035565,120.47827332363393,101.90037384645557
var_q975,onset_icu,Gen Lognormal,627.9273298917121,254.8018878876131,122.2295038337157,108.03735217479938
var_q025,onset_icu,Gen Lognormal,1788.8146178036388,270.8183997148091,118.9169193951247,101.6310670512406
var_observed,onset_icu,NA,205.80572350091882,134.17196040106722,24.45992376147574,48.54777508492564
mean,onset_death,Gamma,17.320680432822332,18.74785988704019,17.465118300457423,14.945536370256836
q975,onset_death,Gamma,17.22968677356316,18.65464768925945,17.411789126237245,14.747200201423315
q025,onset_death,Gamma,17.39177013652593,18.84073020314616,17.533756048249295,15.038874269507273
observed,onset_death,NA,16.820547737933122,18.261264348124037,16.964399533618344,14.364452423698385
var_mean,onset_death,Gamma,146.6962509466473,169.7370529455047,143.94438963489378,110.55784860479842
var_q975,onset_death,Gamma,141.677429569909,163.39648469153715,139.77541336627215,103.30315923379156
var_q025,onset_death,Gamma,152.19228089439648,176.46788476743643,148.22712876670667,119.26610109601442
var_observed,onset_death,NA,171.0122835377102,224.13443657798072,173.3679800207056,152.7515260323158
mean,hosp_stay,Gen Lognormal,10.843918885260958,8.832255634439251,8.774564299513393,7.852424741547418
q975,hosp_stay,Gen Lognormal,10.9805865483633,8.932864646779185,8.859571996909477,8.013741566812755
q025,hosp_stay,Gen Lognormal,10.721015887728516,8.738019103593837,8.694178612165071,7.703711315449967
observed,hosp_stay,NA,10.745172300930472,8.561534628799203,8.404271789999648,7.344090470279961
var_mean,hosp_stay,Gen Lognormal,275.47644613019537,151.9695954164345,139.84514089787805,99.59893227662299
var_q975,hosp_stay,Gen Lognormal,277.16182970280494,152.91358704030748,141.26494279038144,103.35475549424916
var_q025,hosp_stay,Gen Lognormal,275.4336157973775,151.5909330075601,138.8287446308629,96.47362432384074
var_observed,hosp_stay,NA,221.4041517366535,117.52526598716032,86.40947010362073,56.14710265884848
mean,icu_stay,Gen Lognormal,16.19088008970775,15.398620434032583,14.433647872331916,12.405724475384627
q975,icu_stay,Gen Lognormal,16.525630460136103,15.662454556810916,14.621375361766939,13.069329383181465
q025,icu_stay,Gen Lognormal,15.908088284362725,15.147607919140778,14.270656680321967,11.945510073993413
observed,icu_stay,NA,14.788504155124654,13.749482972563078,13.25779175401817,11.622134387351778
var_mean,icu_stay,Gen Lognormal,647.8395343824777,546.7359054005029,426.96345331873624,273.3145122958198
var_q975,icu_stay,Gen Lognormal,640.3055077216246,538.831177543546,427.1893336236636,292.6756553822736
var_q025,icu_stay,Gen Lognormal,670.947198527285,561.0407206014961,431.34641053007306,275.77412436585513
var_observed,icu_stay,NA,218.67738548897015,159.11525242155918,139.82752157519232,89.75583879521689
mean,onset_hosp,Gen Lognormal,7.411779082767016,7.952887832391387,7.7743522940805025,5.543798319116842
q975,onset_hosp,Gen Lognormal,7.484347895885229,8.038935369798462,7.826164776358174,5.574362750656015
q025,onset_hosp,Gen Lognormal,7.337937643190819,7.869024410736836,7.722769080039932,5.491168279243051
observed,onset_hosp,NA,6.935903948279843,7.359475731258991,7.087862490202967,4.778341329677861
var_mean,onset_hosp,Gen Lognormal,83.48375756002378,94.95236454613762,83.13800071202138,75.7374860741251
var_q975,onset_hosp,Gen Lognormal,84.6570915184698,96.35882809616508,83.92212066345024,78.44461884035586
var_q025,onset_hosp,Gen Lognormal,82.24377473669449,93.69998365656022,82.40376846816233,68.23529747281016
var_observed,onset_hosp,NA,53.65295255750496,34.21790373194776,19.958036730928384,15.572878794912135
mean,onset_icu,Gen Lognormal,12.31591870221144,10.83430871174521,9.167823058935356,7.839490690827398
q975,onset_icu,Gen Lognormal,12.373764730330446,10.995186382959142,9.270936650392663,8.185419843144366
q025,onset_icu,Gen Lognormal,12.219745938757166,10.700983800540044,9.067744598903785,7.5448720435189545
observed,onset_icu,NA,11.10614640172964,10.208265582655827,8.255364511691884,7.326547921967769
var_mean,onset_icu,Gen Lognormal,492.8589924825977,260.5577550268623,120.4816874991162,102.60856772883787
var_q975,onset_icu,Gen Lognormal,433.80444129984033,255.83558224933134,122.3140003760835,108.01420998470249
var_q025,onset_icu,Gen Lognormal,586.572415730308,271.54447896517416,118.93231842711076,102.03922055387073
var_observed,onset_icu,NA,189.7268907598658,134.1719604010649,24.459923761475206,48.547775084925654
mean,onset_death,Gamma,17.419022473878897,18.748631952565578,17.4660894755505,14.873382944184756
q975,onset_death,Gamma,17.329731949155544,18.658286471375273,17.415173738690076,14.650375185670137
q025,onset_death,Gamma,17.49524308927829,18.844753577102985,17.514799184588345,15.028467530801382
observed,onset_death,NA,16.91604285923969,18.261264348124037,16.964399533618344,14.296208530805687
var_mean,onset_death,Gamma,148.8468093689864,169.86928802640028,143.9765075419037,109.71176544920885
var_q975,onset_death,Gamma,143.75042863913293,163.40771425705736,139.875966622705,102.19442134431321
var_q025,onset_death,Gamma,154.92658064976155,176.46939627354757,148.01704689758057,118.84682818048407
var_observed,onset_death,NA,175.34233360473942,224.1344365779834,173.36798002070873,151.93710476265392
10 changes: 5 additions & 5 deletions epidemiological_distributions/outputs/bf_hosp_stay.csv
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,Gamma,Lognormal,Weibull,Exponential,Gen Lognormal
Gamma,0.0,-13629.990768045187,3691.2021879722015,6320.802786902408,-13748.769997221767
Lognormal,13629.990768045187,0.0,17321.19295601739,19950.793554947595,-118.77922917657997
Weibull,-3691.2021879722015,-17321.19295601739,0.0,2629.6005989302066,-17439.97218519397
Exponential,-6320.802786902408,-19950.793554947595,-2629.6005989302066,0.0,-20069.572784124175
Gen Lognormal,13748.769997221767,118.77922917657997,17439.97218519397,20069.572784124175,0.0
Gamma,0.0,-13683.60253994679,3687.16266952944,6315.760341889807,-13804.412318136077
Lognormal,13683.60253994679,0.0,17370.76520947623,19999.362881836598,-120.80977818928659
Weibull,-3687.16266952944,-17370.76520947623,0.0,2628.597672360367,-17491.574987665517
Exponential,-6315.760341889807,-19999.362881836598,-2628.597672360367,0.0,-20120.172660025884
Gen Lognormal,13804.412318136077,120.80977818928659,17491.574987665517,20120.172660025884,0.0
10 changes: 5 additions & 5 deletions epidemiological_distributions/outputs/bf_icu_stay.csv
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@@ -1,6 +1,6 @@
,Gamma,Lognormal,Weibull,Exponential,Gen Lognormal
Gamma,0.0,-532.2263048475143,1157.4541012183763,3979.287673478335,-593.3659195934306
Lognormal,532.2263048475143,0.0,1689.6804060658906,4511.513978325849,-61.13961474591633
Weibull,-1157.4541012183763,-1689.6804060658906,0.0,2821.8335722599586,-1750.820020811807
Exponential,-3979.287673478335,-4511.513978325849,-2821.8335722599586,0.0,-4572.6535930717655
Gen Lognormal,593.3659195934306,61.13961474591633,1750.820020811807,4572.6535930717655,0.0
Gamma,0.0,-562.1207735075732,1166.0487400438287,3994.0908468821726,-618.3517885057663
Lognormal,562.1207735075732,0.0,1728.169513551402,4556.211620389746,-56.23101499819313
Weibull,-1166.0487400438287,-1728.169513551402,0.0,2828.042106838344,-1784.400528549595
Exponential,-3994.0908468821726,-4556.211620389746,-2828.042106838344,0.0,-4612.442635387939
Gen Lognormal,618.3517885057663,56.23101499819313,1784.400528549595,4612.442635387939,0.0
10 changes: 5 additions & 5 deletions epidemiological_distributions/outputs/bf_onset_death.csv
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@@ -1,6 +1,6 @@
,Gamma,Lognormal,Weibull,Exponential,Gen Lognormal
Gamma,0.0,667.6564079592354,1372.0711572351865,6918.517303316155,381.16074793366715
Lognormal,-667.6564079592354,0.0,704.4147492759512,6250.86089535692,-286.4956600255682
Weibull,-1372.0711572351865,-704.4147492759512,0.0,5546.446146080969,-990.9104093015194
Exponential,-6918.517303316155,-6250.86089535692,-5546.446146080969,0.0,-6537.356555382488
Gen Lognormal,-381.16074793366715,286.4956600255682,990.9104093015194,6537.356555382488,0.0
Gamma,0.0,658.862720019184,1390.759217872721,6954.734369549726,366.5771801180381
Lognormal,-658.862720019184,0.0,731.8964978535369,6295.871649530542,-292.28553990114597
Weibull,-1390.759217872721,-731.8964978535369,0.0,5563.975151677005,-1024.1820377546828
Exponential,-6954.734369549726,-6295.871649530542,-5563.975151677005,0.0,-6588.157189431688
Gen Lognormal,-366.5771801180381,292.28553990114597,1024.1820377546828,6588.157189431688,0.0
10 changes: 5 additions & 5 deletions epidemiological_distributions/outputs/bf_onset_hosp.csv
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
,Gamma,Lognormal,Weibull,Exponential,Gen Lognormal
Gamma,0.0,-2770.3815629879828,6208.369470785896,32695.223027575295,-3325.920238451683
Lognormal,2770.3815629879828,0.0,8978.751033773879,35465.60459056328,-555.5386754637002
Weibull,-6208.369470785896,-8978.751033773879,0.0,26486.8535567894,-9534.289709237579
Exponential,-32695.223027575295,-35465.60459056328,-26486.8535567894,0.0,-36021.14326602698
Gen Lognormal,3325.920238451683,555.5386754637002,9534.289709237579,36021.14326602698,0.0
Gamma,0.0,-2772.0828999018995,6302.787957385415,33105.66278190556,-3321.511633026239
Lognormal,2772.0828999018995,0.0,9074.870857287315,35877.74568180746,-549.4287331243395
Weibull,-6302.787957385415,-9074.870857287315,0.0,26802.874824520142,-9624.299590411654
Exponential,-33105.66278190556,-35877.74568180746,-26802.874824520142,0.0,-36427.1744149318
Gen Lognormal,3321.511633026239,549.4287331243395,9624.299590411654,36427.1744149318,0.0
10 changes: 5 additions & 5 deletions epidemiological_distributions/outputs/bf_onset_icu.csv
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
,Gamma,Lognormal,Weibull,Exponential,Gen Lognormal
Gamma,0.0,-1718.7509951143293,1117.642060142709,8799.554502968589,-2181.8535272428708
Lognormal,1718.7509951143293,0.0,2836.393055257038,10518.305498082918,-463.1025321285415
Weibull,-1117.642060142709,-2836.393055257038,0.0,7681.91244282588,-3299.4955873855797
Exponential,-8799.554502968589,-10518.305498082918,-7681.91244282588,0.0,-10981.40803021146
Gen Lognormal,2181.8535272428708,463.1025321285415,3299.4955873855797,10981.40803021146,0.0
Gamma,0.0,-1759.0193324124557,1222.3167177802243,9009.450350037223,-2143.343283491442
Lognormal,1759.0193324124557,0.0,2981.33605019268,10768.469682449679,-384.3239510789863
Weibull,-1222.3167177802243,-2981.33605019268,0.0,7787.133632256999,-3365.6600012716663
Exponential,-9009.450350037223,-10768.469682449679,-7787.133632256999,0.0,-11152.793633528665
Gen Lognormal,2143.343283491442,384.3239510789863,3365.6600012716663,11152.793633528665,0.0
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