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Results fix (TRACE-LAC#35)
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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

* fix: severe outcomes

* fix: epidemiological distributions

* fix: update date confirmed cases

* fix: summary tables

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Co-authored-by: ntorresd <[email protected]>
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@davidsantiagoquevedo @ntorresd
davidsantiagoquevedo and ntorresd authored Jun 18, 2023
1 parent 4dc41b6 commit 6ab6144
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Showing 43 changed files with 60,077 additions and 60,088 deletions.
48 changes: 24 additions & 24 deletions epidemiological_distributions/outputs/best_fit_summary.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -7,30 +7,30 @@ var_mean,hosp_stay,Gen Lognormal,275.47644613019537,151.9695954164345,139.845140
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,icu_stay,Gen Lognormal,16.200400012899348,15.399345302628157,14.411432134229237,12.400961040507005
q975,icu_stay,Gen Lognormal,16.51906516756985,15.670447538315019,14.609719146222671,13.113478042383761
q025,icu_stay,Gen Lognormal,15.9100555774099,15.163292943845248,14.249167976763248,11.900436288248814
observed,icu_stay,NA,14.788504155124654,13.749482972563078,13.24073815182441,11.622134387351778
var_mean,icu_stay,Gen Lognormal,648.8620687585369,546.7528908036531,424.586670002063,272.6792942156461
var_q975,icu_stay,Gen Lognormal,638.9311664050618,538.1961902047634,426.0980247881326,294.94629689953376
var_q025,icu_stay,Gen Lognormal,668.8858712993774,563.3740810959243,428.9349670078923,272.3072003403722
var_observed,icu_stay,NA,218.67738548897015,159.11525242155918,138.78845842748106,89.75583879521689
mean,onset_hosp,Gen Lognormal,7.41224784965696,7.950976383889824,7.773541504372108,5.54298635378981
q975,onset_hosp,Gen Lognormal,7.48328377901196,8.037649151187411,7.823986150825191,5.5735685975365366
q025,onset_hosp,Gen Lognormal,7.34559038632075,7.868575836473689,7.724601896924851,5.489710310598759
observed,onset_hosp,NA,6.936183967491688,7.359475731258991,7.087862490202967,4.778341329677861
var_mean,onset_hosp,Gen Lognormal,83.48002169122572,94.87956445942504,83.11916773327056,75.56455770499711
var_q975,onset_hosp,Gen Lognormal,84.62748465792355,96.35009196180954,83.88766086905991,78.13206535592195
var_q025,onset_hosp,Gen Lognormal,82.56637668959249,93.55874237511418,82.43856683737673,67.94206226498034
var_observed,onset_hosp,NA,53.65217299667854,34.21790373194776,19.958036730928384,15.572878794912135
mean,onset_icu,Gen Lognormal,12.31238639614275,10.83051214754636,9.16807938692345,7.836598756075708
q975,onset_icu,Gen Lognormal,12.382052350028218,11.007632045168084,9.272096378144866,8.171549860929675
q025,onset_icu,Gen Lognormal,12.220991165809115,10.678178622115464,9.066057134640706,7.547193441735841
observed,onset_icu,NA,11.106341362981263,10.208265582655827,8.255364511691884,7.326547921967769
var_mean,onset_icu,Gen Lognormal,491.75558388903147,260.289013662859,120.4563394189333,102.48591311234163
var_q975,onset_icu,Gen Lognormal,436.2539328087177,257.3319619515187,122.44962069840044,107.22360110064639
var_q025,onset_icu,Gen Lognormal,583.1247028475274,267.7137909009735,118.84329337775372,102.18315643057456
var_observed,onset_icu,NA,189.7077266933018,134.1719604010649,24.459923761475206,48.547775084925654
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
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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,-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
Gamma,0.0,-547.5283709218493,1163.4985791060608,4007.5410287222767,-603.1672240652842
Lognormal,547.5283709218493,0.0,1711.02695002791,4555.069399644126,-55.63885314343497
Weibull,-1163.4985791060608,-1711.02695002791,0.0,2844.042449616216,-1766.665803171345
Exponential,-4007.5410287222767,-4555.069399644126,-2844.042449616216,0.0,-4610.708252787561
Gen Lognormal,603.1672240652842,55.63885314343497,1766.665803171345,4610.708252787561,0.0
10 changes: 5 additions & 5 deletions epidemiological_distributions/outputs/bf_onset_hosp.csv
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@@ -1,6 +1,6 @@
,Gamma,Lognormal,Weibull,Exponential,Gen Lognormal
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
Gamma,0.0,-2771.406982435321,6302.684666462825,33106.205439037876,-3320.6686787450453
Lognormal,2771.406982435321,0.0,9074.091648898146,35877.6124214732,-549.2616963097244
Weibull,-6302.684666462825,-9074.091648898146,0.0,26803.52077257505,-9623.35334520787
Exponential,-33106.205439037876,-35877.6124214732,-26803.52077257505,0.0,-36426.87411778292
Gen Lognormal,3320.6686787450453,549.2616963097244,9623.35334520787,36426.87411778292,0.0
10 changes: 5 additions & 5 deletions epidemiological_distributions/outputs/bf_onset_icu.csv
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@@ -1,6 +1,6 @@
,Gamma,Lognormal,Weibull,Exponential,Gen Lognormal
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
Gamma,0.0,-1758.8175977233623,1222.5893378000765,9009.597201366036,-2143.0580654871883
Lognormal,1758.8175977233623,0.0,2981.4069355234387,10768.414799089398,-384.240467763826
Weibull,-1222.5893378000765,-2981.4069355234387,0.0,7787.007863565959,-3365.6474032872648
Exponential,-9009.597201366036,-10768.414799089398,-7787.007863565959,0.0,-11152.655266853224
Gen Lognormal,2143.0580654871883,384.240467763826,3365.6474032872648,11152.655266853224,0.0
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