From 8632ba84064a40a85c433d16c9a5d4b7e5301ee9 Mon Sep 17 00:00:00 2001 From: "alex.hill@gmail.com" Date: Thu, 3 Oct 2024 11:58:49 +0100 Subject: [PATCH] remove unused censoring level --- R/biokinetics.R | 2 - inst/ba2_full.rds | 50 +++--- inst/delta_full.rds | 252 +++++++++++++-------------- inst/xbb_full.rds | 26 +-- src/stan/antibody_kinetics_main.stan | 2 - tests/testthat/test-data.R | 2 +- tests/testthat/test-run-model.R | 2 +- vignettes/data.Rmd | 2 +- 8 files changed, 167 insertions(+), 171 deletions(-) diff --git a/R/biokinetics.R b/R/biokinetics.R index e3fb2df..96f85bf 100644 --- a/R/biokinetics.R +++ b/R/biokinetics.R @@ -167,11 +167,9 @@ biokinetics <- R6::R6Class( K = private$data[, data.table::uniqueN(titre_type)], N_uncens = private$data[censored == 0, .N], N_lo = private$data[censored == -2, .N], - N_me = private$data[censored == -1, .N], N_hi = private$data[censored == 1, .N], uncens_idx = private$data[censored == 0, obs_id], cens_lo_idx = private$data[censored == -2, obs_id], - cens_me_idx = private$data[censored == -1, obs_id], cens_hi_idx = private$data[censored == 1, obs_id]) if (private$time_type == "relative") { diff --git a/inst/ba2_full.rds b/inst/ba2_full.rds index adc645c..6937cfd 100644 --- a/inst/ba2_full.rds +++ b/inst/ba2_full.rds @@ -185,7 +185,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 39,2022-01-27,2021-12-25,BA.2,804.989998629278,0,Infection naive,BNT162b2,4 40,2021-12-14,2021-12-14,Delta,63.0935002600001,0,Infection naive,BNT162b2,3 40,2022-01-18,2021-12-14,Delta,635.350458433831,0,Infection naive,BNT162b2,3 -40,2021-12-14,2021-12-14,BA.1,5,-2,Infection naive,BNT162b2,3 +40,2021-12-14,2021-12-14,BA.1,5,-1,Infection naive,BNT162b2,3 40,2022-01-18,2021-12-14,BA.1,432.419565403068,0,Infection naive,BNT162b2,3 40,2021-12-14,2021-12-14,BA.2,65.6893251900002,0,Infection naive,BNT162b2,3 40,2022-01-18,2021-12-14,BA.2,545.480453207638,0,Infection naive,BNT162b2,3 @@ -207,13 +207,13 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 43,2022-03-21,2021-12-03,BA.1,221.740700900001,0,Infection naive,BNT162b2,3 43,2021-12-15,2021-12-03,BA.2,280.945805803223,0,Infection naive,BNT162b2,3 43,2022-03-21,2021-12-03,BA.2,216.175459200001,0,Infection naive,BNT162b2,3 -44,2021-12-15,2021-12-15,Delta,5,-2,Infection naive,BNT162b2,3 +44,2021-12-15,2021-12-15,Delta,5,-1,Infection naive,BNT162b2,3 44,2022-01-10,2021-12-15,Delta,163.3038598957,0,Infection naive,BNT162b2,3 44,2022-03-21,2021-12-15,Delta,111.534972,0,Infection naive,BNT162b2,3 -44,2021-12-15,2021-12-15,BA.1,5,-2,Infection naive,BNT162b2,3 +44,2021-12-15,2021-12-15,BA.1,5,-1,Infection naive,BNT162b2,3 44,2022-01-10,2021-12-15,BA.1,133.723232907625,0,Infection naive,BNT162b2,3 44,2022-03-21,2021-12-15,BA.1,75.5125462099998,0,Infection naive,BNT162b2,3 -44,2021-12-15,2021-12-15,BA.2,5,-2,Infection naive,BNT162b2,3 +44,2021-12-15,2021-12-15,BA.2,5,-1,Infection naive,BNT162b2,3 44,2022-01-10,2021-12-15,BA.2,233.304689105237,0,Infection naive,BNT162b2,3 44,2022-03-21,2021-12-15,BA.2,107.7867745,0,Infection naive,BNT162b2,3 45,2021-12-22,2021-12-22,Delta,208.544860600001,0,Infection naive,BNT162b2,4 @@ -448,9 +448,9 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 81,2022-01-31,2021-10-05,BA.2,249.1567586,0,Infection naive,BNT162b2,3 81,2022-07-06,2021-10-05,BA.2,157.2636095,0,Infection naive,BNT162b2,3 81,2022-07-06,2021-10-05,BA.2,157.2636095,0,Infection naive,BNT162b2,3 -82,2021-12-20,2021-12-17,Delta,5,-2,Infection naive,BNT162b2,3 +82,2021-12-20,2021-12-17,Delta,5,-1,Infection naive,BNT162b2,3 82,2022-01-26,2021-12-17,Delta,248.720372925193,0,Infection naive,BNT162b2,3 -82,2021-12-20,2021-12-17,BA.1,5,-2,Infection naive,BNT162b2,3 +82,2021-12-20,2021-12-17,BA.1,5,-1,Infection naive,BNT162b2,3 82,2022-01-26,2021-12-17,BA.1,385.851371049329,0,Infection naive,BNT162b2,3 82,2021-12-20,2021-12-17,BA.2,93.5188578000003,0,Infection naive,BNT162b2,3 82,2022-01-26,2021-12-17,BA.2,471.204717896184,0,Infection naive,BNT162b2,3 @@ -593,17 +593,17 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 101,2021-12-21,2021-09-24,BA.1,732.926266099998,0,Infection naive,BNT162b2,3 101,2021-10-12,2021-09-24,BA.2,1109.45732967998,0,Infection naive,BNT162b2,3 101,2021-12-21,2021-09-24,BA.2,476.604522400001,0,Infection naive,BNT162b2,3 -102,2021-10-21,2021-10-21,Delta,5,-2,Infection naive,BNT162b2,3 +102,2021-10-21,2021-10-21,Delta,5,-1,Infection naive,BNT162b2,3 102,2021-11-15,2021-10-21,Delta,388.226020488708,0,Infection naive,BNT162b2,3 102,2022-01-12,2021-10-21,Delta,265.3871612,0,Infection naive,BNT162b2,3 102,2022-07-06,2021-10-21,Delta,77.8649621299998,0,Infection naive,BNT162b2,3 102,2022-10-31,2021-10-21,Delta,59.9136687389031,0,Infection naive,BNT162b2,3 -102,2021-10-21,2021-10-21,BA.1,5,-2,Infection naive,BNT162b2,3 +102,2021-10-21,2021-10-21,BA.1,5,-1,Infection naive,BNT162b2,3 102,2021-11-15,2021-10-21,BA.1,334.775575709082,0,Infection naive,BNT162b2,3 102,2022-01-12,2021-10-21,BA.1,113.1101451,0,Infection naive,BNT162b2,3 102,2022-07-06,2021-10-21,BA.1,100.5758351,0,Infection naive,BNT162b2,3 102,2022-10-31,2021-10-21,BA.1,41.353131194697,0,Infection naive,BNT162b2,3 -102,2021-10-21,2021-10-21,BA.2,5,-2,Infection naive,BNT162b2,3 +102,2021-10-21,2021-10-21,BA.2,5,-1,Infection naive,BNT162b2,3 102,2021-11-15,2021-10-21,BA.2,434.318787559875,0,Infection naive,BNT162b2,3 102,2022-01-12,2021-10-21,BA.2,186.903521306488,0,Infection naive,BNT162b2,3 102,2022-07-06,2021-10-21,BA.2,97.6228182400002,0,Infection naive,BNT162b2,3 @@ -620,8 +620,8 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 106,2021-10-21,2021-10-01,Delta,47.7877573284979,0,Infection naive,BNT162b2,3 106,2022-06-22,2021-10-01,Delta,40.88461104,0,Infection naive,BNT162b2,3 106,2022-10-27,2021-10-01,Delta,40.813003674215,0,Infection naive,BNT162b2,3 -106,2021-10-21,2021-10-01,BA.1,5,-2,Infection naive,BNT162b2,3 -106,2021-10-21,2021-10-01,BA.2,5,-2,Infection naive,BNT162b2,3 +106,2021-10-21,2021-10-01,BA.1,5,-1,Infection naive,BNT162b2,3 +106,2021-10-21,2021-10-01,BA.2,5,-1,Infection naive,BNT162b2,3 107,2022-01-06,2021-12-06,Delta,396.479179303829,0,Infection naive,BNT162b2,3 107,2022-03-21,2021-12-06,Delta,417.521739700002,0,Infection naive,BNT162b2,3 107,2022-01-06,2021-12-06,BA.1,307.219990500133,0,Infection naive,BNT162b2,3 @@ -648,11 +648,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 110,2022-07-11,2021-11-19,Delta,183.6556791,0,Previously infected (Pre-Omicron),BNT162b2,4 110,2022-07-11,2021-11-19,Delta,183.6556791,0,Previously infected (Pre-Omicron),BNT162b2,4 110,2021-11-30,2021-11-19,BA.1,48.7609029313075,0,Previously infected (Pre-Omicron),BNT162b2,4 -110,2022-01-17,2021-11-19,BA.1,5,-2,Previously infected (Pre-Omicron),BNT162b2,4 +110,2022-01-17,2021-11-19,BA.1,5,-1,Previously infected (Pre-Omicron),BNT162b2,4 110,2021-11-30,2021-11-19,BA.2,85.2963225104831,0,Previously infected (Pre-Omicron),BNT162b2,4 110,2022-01-17,2021-11-19,BA.2,68.2123499119002,0,Previously infected (Pre-Omicron),BNT162b2,4 -110,2022-07-11,2021-11-19,BA.2,5,-2,Previously infected (Pre-Omicron),BNT162b2,4 -110,2022-07-11,2021-11-19,BA.2,5,-2,Previously infected (Pre-Omicron),BNT162b2,4 +110,2022-07-11,2021-11-19,BA.2,5,-1,Previously infected (Pre-Omicron),BNT162b2,4 +110,2022-07-11,2021-11-19,BA.2,5,-1,Previously infected (Pre-Omicron),BNT162b2,4 111,2022-01-12,2021-12-06,Delta,2560,1,Previously infected (Pre-Omicron),BNT162b2,4 111,2022-07-27,2021-12-06,Delta,2560,1,Previously infected (Pre-Omicron),BNT162b2,4 111,2022-01-12,2021-12-06,BA.1,434.699631799999,0,Previously infected (Pre-Omicron),BNT162b2,4 @@ -908,9 +908,9 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 152,2022-04-21,2021-12-20,BA.1,1143.017579,0,Infection naive,BNT162b2,4 152,2022-01-19,2021-12-20,BA.2,2560,1,Infection naive,BNT162b2,4 152,2022-04-21,2021-12-20,BA.2,1049.854881,0,Infection naive,BNT162b2,4 -153,2021-12-10,2021-12-10,Delta,5,-2,Infection naive,BNT162b2,3 +153,2021-12-10,2021-12-10,Delta,5,-1,Infection naive,BNT162b2,3 153,2022-01-06,2021-12-10,Delta,1067.48489126961,0,Infection naive,BNT162b2,3 -153,2021-12-10,2021-12-10,BA.1,5,-2,Infection naive,BNT162b2,3 +153,2021-12-10,2021-12-10,BA.1,5,-1,Infection naive,BNT162b2,3 153,2022-01-06,2021-12-10,BA.1,456.968924936853,0,Infection naive,BNT162b2,3 153,2021-12-10,2021-12-10,BA.2,52.0283781100002,0,Infection naive,BNT162b2,3 153,2022-01-06,2021-12-10,BA.2,723.353263113297,0,Infection naive,BNT162b2,3 @@ -1174,10 +1174,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 198,2021-09-30,2021-09-30,BA.2,146.4856553,0,Infection naive,BNT162b2,3 198,2022-01-11,2021-09-30,BA.2,170.1716794,0,Infection naive,BNT162b2,3 198,2022-07-11,2021-09-30,BA.2,120.2672786,0,Infection naive,BNT162b2,3 -199,2021-09-30,2021-09-27,Delta,5,-2,Infection naive,BNT162b2,3 -199,2021-09-30,2021-09-27,BA.1,5,-2,Infection naive,BNT162b2,3 -199,2021-09-30,2021-09-27,BA.2,5,-2,Infection naive,BNT162b2,3 -199,2022-04-07,2021-09-27,BA.2,5,-2,Infection naive,BNT162b2,3 +199,2021-09-30,2021-09-27,Delta,5,-1,Infection naive,BNT162b2,3 +199,2021-09-30,2021-09-27,BA.1,5,-1,Infection naive,BNT162b2,3 +199,2021-09-30,2021-09-27,BA.2,5,-1,Infection naive,BNT162b2,3 +199,2022-04-07,2021-09-27,BA.2,5,-1,Infection naive,BNT162b2,3 200,2021-12-21,2021-12-02,Delta,2560,1,Previously infected (Pre-Omicron),BNT162b2,5 200,2022-03-21,2021-12-02,Delta,2560,1,Previously infected (Pre-Omicron),BNT162b2,5 200,2022-07-11,2021-12-02,Delta,1219.611353,0,Previously infected (Pre-Omicron),BNT162b2,5 @@ -1310,7 +1310,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 217,2022-01-10,2021-12-08,BA.1,520.720195179818,0,Infection naive,BNT162b2,3 217,2022-03-21,2021-12-08,BA.1,126.9837534,0,Infection naive,BNT162b2,3 217,2022-06-16,2021-12-08,BA.1,58.2055320999998,0,Infection naive,BNT162b2,3 -217,2021-12-08,2021-12-08,BA.2,5,-2,Infection naive,BNT162b2,3 +217,2021-12-08,2021-12-08,BA.2,5,-1,Infection naive,BNT162b2,3 217,2022-01-10,2021-12-08,BA.2,551.731425861521,0,Infection naive,BNT162b2,3 217,2022-03-21,2021-12-08,BA.2,135.968821300001,0,Infection naive,BNT162b2,3 217,2022-06-16,2021-12-08,BA.2,99.6108005499997,0,Infection naive,BNT162b2,3 @@ -1482,7 +1482,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 246,2022-01-11,2021-12-16,BA.1,2034.813448,0,Infection naive,BNT162b2,4 246,2022-01-11,2021-12-16,BA.2,978.7612945,0,Infection naive,BNT162b2,4 247,2021-10-08,2021-10-08,Delta,51.5743457200001,0,Previously infected (Pre-Omicron),BNT162b2,5 -247,2021-10-08,2021-10-08,BA.1,5,-2,Previously infected (Pre-Omicron),BNT162b2,5 +247,2021-10-08,2021-10-08,BA.1,5,-1,Previously infected (Pre-Omicron),BNT162b2,5 247,2021-10-08,2021-10-08,BA.2,51.3938441100001,0,Previously infected (Pre-Omicron),BNT162b2,5 248,2022-02-08,2022-01-23,Delta,2560,1,Previously infected (Pre-Omicron),mRNA1273,4 248,2023-01-16,2022-01-23,Delta,2560,1,Previously infected (Pre-Omicron),mRNA1273,4 @@ -1659,8 +1659,8 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 275,2022-01-17,2022-01-07,BA.1,374.522351602284,0,Infection naive,mRNA1273,3 275,2022-01-17,2022-01-07,BA.2,278.250104602277,0,Infection naive,mRNA1273,3 276,2021-09-24,2021-09-24,Delta,90.6935144899999,0,Infection naive,BNT162b2,3 -276,2021-09-24,2021-09-24,BA.1,5,-2,Infection naive,BNT162b2,3 -276,2021-09-24,2021-09-24,BA.2,5,-2,Infection naive,BNT162b2,3 +276,2021-09-24,2021-09-24,BA.1,5,-1,Infection naive,BNT162b2,3 +276,2021-09-24,2021-09-24,BA.2,5,-1,Infection naive,BNT162b2,3 277,2022-01-26,2022-01-10,Delta,2560,1,Previously infected (Omicron),BNT162b2,4 277,2022-04-12,2022-01-10,Delta,1828.45619200001,0,Previously infected (Omicron),BNT162b2,4 277,2022-07-13,2022-01-10,Delta,1253.204069,0,Previously infected (Omicron),BNT162b2,4 @@ -1913,7 +1913,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 322,2021-09-23,2021-09-23,Delta,110.9499539,0,Infection naive,BNT162b2,3 322,2021-10-08,2021-09-23,Delta,450.210391439885,0,Infection naive,BNT162b2,3 322,2022-01-12,2021-09-23,Delta,337.1312525,0,Infection naive,BNT162b2,3 -322,2021-09-23,2021-09-23,BA.1,5,-2,Infection naive,BNT162b2,3 +322,2021-09-23,2021-09-23,BA.1,5,-1,Infection naive,BNT162b2,3 322,2021-10-08,2021-09-23,BA.1,484.608050076034,0,Infection naive,BNT162b2,3 322,2022-01-12,2021-09-23,BA.1,159.9045069,0,Infection naive,BNT162b2,3 322,2021-09-23,2021-09-23,BA.2,48.3353845899999,0,Infection naive,BNT162b2,3 diff --git a/inst/delta_full.rds b/inst/delta_full.rds index d4ccf0e..f5f7f30 100644 --- a/inst/delta_full.rds +++ b/inst/delta_full.rds @@ -2,10 +2,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 1,2021-03-10,2021-03-08,Ancestral,175.9349878,0,Infection naive,BNT162b2,2 1,2021-04-15,2021-03-08,Ancestral,607.57499,0,Infection naive,BNT162b2,2 1,2021-07-08,2021-03-08,Ancestral,179.0462942,0,Infection naive,BNT162b2,2 -1,2021-03-10,2021-03-08,Alpha,5,-2,Infection naive,BNT162b2,2 +1,2021-03-10,2021-03-08,Alpha,5,-1,Infection naive,BNT162b2,2 1,2021-04-15,2021-03-08,Alpha,416.790471100001,0,Infection naive,BNT162b2,2 1,2021-07-08,2021-03-08,Alpha,103.5273976,0,Infection naive,BNT162b2,2 -1,2021-03-10,2021-03-08,Delta,5,-2,Infection naive,BNT162b2,2 +1,2021-03-10,2021-03-08,Delta,5,-1,Infection naive,BNT162b2,2 1,2021-04-15,2021-03-08,Delta,288.1785015,0,Infection naive,BNT162b2,2 1,2021-07-08,2021-03-08,Delta,128.8900265,0,Infection naive,BNT162b2,2 2,2021-02-23,2021-01-11,Ancestral,595.449313599998,0,Infection naive,BNT162b2,2 @@ -47,18 +47,18 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 5,2021-03-23,2021-01-11,Delta,280.4537432,0,Infection naive,BNT162b2,2 5,2021-05-12,2021-01-11,Delta,110.5616476,0,Infection naive,BNT162b2,2 5,2021-08-04,2021-01-11,Delta,79.1725334000003,0,Infection naive,BNT162b2,2 -6,2021-03-11,2021-03-11,Ancestral,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 -6,2021-03-11,2021-03-11,Alpha,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 -6,2021-03-11,2021-03-11,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +6,2021-03-11,2021-03-11,Ancestral,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 +6,2021-03-11,2021-03-11,Alpha,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 +6,2021-03-11,2021-03-11,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 7,2021-06-02,2021-05-02,Ancestral,115.312395150577,0,Infection naive,AZD1222,1 7,2021-06-02,2021-05-02,Alpha,69.1756913491035,0,Infection naive,AZD1222,1 -7,2021-06-02,2021-05-02,Delta,5,-2,Infection naive,AZD1222,1 +7,2021-06-02,2021-05-02,Delta,5,-1,Infection naive,AZD1222,1 8,2021-06-11,2021-05-06,Ancestral,209.0939465,0,Previously infected (Pre-Omicron),AZD1222,3 8,2021-07-07,2021-05-06,Ancestral,50.10396289,0,Previously infected (Pre-Omicron),AZD1222,3 -8,2021-06-11,2021-05-06,Alpha,5,-2,Previously infected (Pre-Omicron),AZD1222,3 -8,2021-06-11,2021-05-06,Delta,5,-2,Previously infected (Pre-Omicron),AZD1222,3 -8,2021-07-07,2021-05-06,Delta,5,-2,Previously infected (Pre-Omicron),AZD1222,3 -8,2021-09-20,2021-05-06,Delta,5,-2,Previously infected (Pre-Omicron),AZD1222,3 +8,2021-06-11,2021-05-06,Alpha,5,-1,Previously infected (Pre-Omicron),AZD1222,3 +8,2021-06-11,2021-05-06,Delta,5,-1,Previously infected (Pre-Omicron),AZD1222,3 +8,2021-07-07,2021-05-06,Delta,5,-1,Previously infected (Pre-Omicron),AZD1222,3 +8,2021-09-20,2021-05-06,Delta,5,-1,Previously infected (Pre-Omicron),AZD1222,3 9,2021-02-02,2021-01-05,Ancestral,657.444254099999,0,Infection naive,BNT162b2,2 9,2021-02-23,2021-01-05,Ancestral,934.333704000001,0,Infection naive,BNT162b2,2 9,2021-04-06,2021-01-05,Ancestral,399.619148699999,0,Infection naive,BNT162b2,2 @@ -84,7 +84,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 12,2021-03-16,2021-03-13,Delta,47.70405944,0,Infection naive,BNT162b2,2 13,2021-04-23,2021-04-22,Ancestral,121.1135496,0,Previously infected (Pre-Omicron),BNT162b2,3 13,2021-04-23,2021-04-22,Alpha,60.8130894204273,0,Previously infected (Pre-Omicron),BNT162b2,3 -13,2021-04-23,2021-04-22,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +13,2021-04-23,2021-04-22,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 14,2021-02-25,2021-01-07,Ancestral,197.860967200001,0,Infection naive,BNT162b2,2 14,2021-02-25,2021-01-07,Alpha,172.7262873,0,Infection naive,BNT162b2,2 14,2021-03-18,2021-01-07,Alpha,132.0923549,0,Infection naive,BNT162b2,2 @@ -101,7 +101,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 15,2021-03-08,2021-02-26,Delta,334.482275799999,0,Infection naive,BNT162b2,2 15,2021-04-16,2021-02-26,Delta,311.013081500001,0,Infection naive,BNT162b2,2 15,2021-07-12,2021-02-26,Delta,45.8591303399999,0,Infection naive,BNT162b2,2 -15,2021-10-04,2021-02-26,Delta,5,-2,Infection naive,BNT162b2,2 +15,2021-10-04,2021-02-26,Delta,5,-1,Infection naive,BNT162b2,2 16,2021-04-19,2021-03-23,Ancestral,2560,1,Infection naive,BNT162b2,2 16,2021-06-29,2021-03-23,Ancestral,281.438731800001,0,Infection naive,BNT162b2,2 16,2021-04-19,2021-03-23,Alpha,971.922280699998,0,Infection naive,BNT162b2,2 @@ -147,13 +147,13 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 21,2021-06-29,2021-03-26,Delta,136.0880493,0,Infection naive,BNT162b2,2 22,2021-04-19,2021-03-09,Ancestral,200.1283693,0,Previously infected (Pre-Omicron),AZD1222,2 22,2021-04-19,2021-03-09,Alpha,67.0270167161586,0,Previously infected (Pre-Omicron),AZD1222,2 -22,2021-04-19,2021-03-09,Delta,5,-2,Previously infected (Pre-Omicron),AZD1222,2 +22,2021-04-19,2021-03-09,Delta,5,-1,Previously infected (Pre-Omicron),AZD1222,2 23,2021-04-06,2021-02-28,Ancestral,97.87985316,0,Infection naive,BNT162b2,2 23,2021-09-21,2021-02-28,Ancestral,81.9256938794759,0,Infection naive,BNT162b2,2 23,2021-04-06,2021-02-28,Alpha,270.7914815,0,Infection naive,BNT162b2,2 -23,2021-09-21,2021-02-28,Alpha,5,-2,Infection naive,BNT162b2,2 +23,2021-09-21,2021-02-28,Alpha,5,-1,Infection naive,BNT162b2,2 23,2021-04-06,2021-02-28,Delta,74.3957217499998,0,Infection naive,BNT162b2,2 -23,2021-09-21,2021-02-28,Delta,5,-2,Infection naive,BNT162b2,2 +23,2021-09-21,2021-02-28,Delta,5,-1,Infection naive,BNT162b2,2 24,2021-05-20,2021-04-22,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 24,2021-08-10,2021-04-22,Ancestral,483.335457300001,0,Previously infected (Pre-Omicron),BNT162b2,3 24,2021-05-20,2021-04-22,Alpha,1971.609858,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -180,10 +180,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 27,2021-09-28,2021-03-14,Ancestral,81.7105549699998,0,Previously infected (Pre-Omicron),BNT162b2,3 27,2021-04-19,2021-03-14,Alpha,153.9899911,0,Previously infected (Pre-Omicron),BNT162b2,3 27,2021-06-29,2021-03-14,Alpha,103.4366963,0,Previously infected (Pre-Omicron),BNT162b2,3 -27,2021-09-28,2021-03-14,Alpha,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +27,2021-09-28,2021-03-14,Alpha,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 27,2021-04-19,2021-03-14,Delta,86.3494333899999,0,Previously infected (Pre-Omicron),BNT162b2,3 27,2021-06-29,2021-03-14,Delta,54.0267071200002,0,Previously infected (Pre-Omicron),BNT162b2,3 -27,2021-09-28,2021-03-14,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +27,2021-09-28,2021-03-14,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 28,2021-02-02,2021-01-14,Ancestral,128.551558075558,0,Infection naive,BNT162b2,1 28,2021-02-24,2021-01-14,Ancestral,129.796972124846,0,Infection naive,BNT162b2,1 28,2021-02-02,2021-01-14,Alpha,209.828310596494,0,Infection naive,BNT162b2,1 @@ -198,7 +198,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 29,2021-02-12,2021-01-12,Delta,105.1736888,0,Infection naive,BNT162b2,2 29,2021-03-02,2021-01-12,Delta,162.162787600001,0,Infection naive,BNT162b2,2 29,2021-04-12,2021-01-12,Delta,94.0119650100003,0,Infection naive,BNT162b2,2 -30,2021-02-03,2021-01-08,Ancestral,5,-2,Infection naive,BNT162b2,2 +30,2021-02-03,2021-01-08,Ancestral,5,-1,Infection naive,BNT162b2,2 30,2021-02-24,2021-01-08,Ancestral,265.3871612,0,Infection naive,BNT162b2,2 30,2021-02-03,2021-01-08,Alpha,170.769343600001,0,Infection naive,BNT162b2,2 30,2021-02-24,2021-01-08,Alpha,169.5761069,0,Infection naive,BNT162b2,2 @@ -303,7 +303,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 44,2021-07-08,2021-04-30,Ancestral,40.95634405,0,Infection naive,AZD1222,2 44,2021-06-09,2021-04-30,Alpha,58.0018224500001,0,Infection naive,AZD1222,2 44,2021-07-08,2021-04-30,Alpha,60.44111598,0,Infection naive,AZD1222,2 -44,2021-06-09,2021-04-30,Delta,5,-2,Infection naive,AZD1222,2 +44,2021-06-09,2021-04-30,Delta,5,-1,Infection naive,AZD1222,2 45,2021-04-16,2021-04-01,Ancestral,2560,1,Infection naive,BNT162b2,2 45,2021-07-26,2021-04-01,Ancestral,540.246517400001,0,Infection naive,BNT162b2,2 45,2021-10-19,2021-04-01,Ancestral,651.706981500002,0,Infection naive,BNT162b2,2 @@ -321,7 +321,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 46,2021-04-15,2021-03-16,Alpha,588.187260700001,0,Infection naive,BNT162b2,2 46,2021-07-07,2021-03-16,Alpha,297.4165949,0,Infection naive,BNT162b2,2 46,2021-10-07,2021-03-16,Alpha,185.272483477799,0,Infection naive,BNT162b2,2 -46,2021-03-16,2021-03-16,Delta,5,-2,Infection naive,BNT162b2,2 +46,2021-03-16,2021-03-16,Delta,5,-1,Infection naive,BNT162b2,2 46,2021-04-15,2021-03-16,Delta,315.4054209,0,Infection naive,BNT162b2,2 46,2021-07-07,2021-03-16,Delta,130.0247039,0,Infection naive,BNT162b2,2 46,2021-10-07,2021-03-16,Delta,97.7084214600002,0,Infection naive,BNT162b2,2 @@ -345,10 +345,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 49,2021-02-18,2021-01-05,Delta,458.1720963,0,Infection naive,BNT162b2,2 50,2021-02-09,2021-01-19,Ancestral,110.464783536617,0,Previously infected (Pre-Omicron),BNT162b2,2 50,2021-03-02,2021-01-19,Ancestral,104.713777301928,0,Previously infected (Pre-Omicron),BNT162b2,2 -50,2021-02-09,2021-01-19,Alpha,5,-2,Previously infected (Pre-Omicron),BNT162b2,2 +50,2021-02-09,2021-01-19,Alpha,5,-1,Previously infected (Pre-Omicron),BNT162b2,2 50,2021-03-02,2021-01-19,Alpha,92.0550005127693,0,Previously infected (Pre-Omicron),BNT162b2,2 -50,2021-02-09,2021-01-19,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,2 -50,2021-03-02,2021-01-19,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,2 +50,2021-02-09,2021-01-19,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,2 +50,2021-03-02,2021-01-19,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,2 51,2021-04-08,2021-03-30,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 51,2021-05-20,2021-03-30,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 51,2021-08-10,2021-03-30,Ancestral,331.854113199999,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -381,7 +381,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 54,2021-04-26,2021-03-14,Delta,258.7264819,0,Infection naive,BNT162b2,2 55,2021-02-04,2021-01-05,Ancestral,148.68468983509,0,Infection naive,BNT162b2,1 55,2021-02-04,2021-01-05,Alpha,128.551558075558,0,Infection naive,BNT162b2,1 -55,2021-02-04,2021-01-05,Delta,5,-2,Infection naive,BNT162b2,1 +55,2021-02-04,2021-01-05,Delta,5,-1,Infection naive,BNT162b2,1 56,2021-04-01,2021-03-14,Ancestral,2560,1,Infection naive,BNT162b2,2 56,2021-09-30,2021-03-14,Ancestral,161.0296885,0,Infection naive,BNT162b2,2 56,2021-09-30,2021-03-14,Ancestral,161.0296885,0,Infection naive,BNT162b2,2 @@ -482,7 +482,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 68,2021-04-20,2021-03-12,Alpha,804.284739699998,0,Previously infected (Pre-Omicron),BNT162b2,3 68,2021-07-07,2021-03-12,Alpha,178.7327035,0,Previously infected (Pre-Omicron),BNT162b2,3 68,2021-09-23,2021-03-12,Alpha,171.068962431355,0,Previously infected (Pre-Omicron),BNT162b2,3 -68,2021-03-16,2021-03-12,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +68,2021-03-16,2021-03-12,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 68,2021-04-20,2021-03-12,Delta,270.3172037,0,Previously infected (Pre-Omicron),BNT162b2,3 68,2021-07-07,2021-03-12,Delta,168.8345717,0,Previously infected (Pre-Omicron),BNT162b2,3 68,2021-09-23,2021-03-12,Delta,221.9351403,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -499,8 +499,8 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 70,2021-06-29,2021-03-28,Delta,95.0059933199999,0,Previously infected (Pre-Omicron),BNT162b2,3 70,2021-10-01,2021-03-28,Delta,47.95559391,0,Previously infected (Pre-Omicron),BNT162b2,3 71,2021-04-19,2021-04-13,Ancestral,106.846159268181,0,Infection naive,AZD1222,1 -71,2021-04-19,2021-04-13,Alpha,5,-2,Infection naive,AZD1222,1 -71,2021-04-19,2021-04-13,Delta,5,-2,Infection naive,AZD1222,1 +71,2021-04-19,2021-04-13,Alpha,5,-1,Infection naive,AZD1222,1 +71,2021-04-19,2021-04-13,Delta,5,-1,Infection naive,AZD1222,1 72,2021-01-29,2021-01-07,Ancestral,1353.690964,0,Infection naive,BNT162b2,2 72,2021-01-29,2021-01-07,Alpha,436.608868200001,0,Infection naive,BNT162b2,2 72,2021-01-29,2021-01-07,Delta,279.227353800001,0,Infection naive,BNT162b2,2 @@ -517,7 +517,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 75,2021-06-11,2021-05-02,Alpha,138.7376782,0,Infection naive,AZD1222,2 75,2021-09-22,2021-05-02,Alpha,74.5262507817008,0,Infection naive,AZD1222,2 75,2021-06-11,2021-05-02,Delta,45.0622313999999,0,Infection naive,AZD1222,2 -75,2021-09-22,2021-05-02,Delta,5,-2,Infection naive,AZD1222,2 +75,2021-09-22,2021-05-02,Delta,5,-1,Infection naive,AZD1222,2 76,2021-06-11,2021-04-22,Ancestral,93.8473077200001,0,Infection naive,AZD1222,1 76,2021-06-11,2021-04-22,Alpha,47.4538443170817,0,Infection naive,AZD1222,1 76,2021-06-11,2021-04-22,Delta,41.53475753,0,Infection naive,AZD1222,1 @@ -623,7 +623,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 90,2021-07-08,2021-03-12,Delta,178.419662,0,Infection naive,BNT162b2,2 91,2021-06-11,2021-04-24,Ancestral,126.317704098264,0,Infection naive,AZD1222,1 91,2021-06-11,2021-04-24,Alpha,144.572355573196,0,Infection naive,AZD1222,1 -91,2021-06-11,2021-04-24,Delta,5,-2,Infection naive,AZD1222,1 +91,2021-06-11,2021-04-24,Delta,5,-1,Infection naive,AZD1222,1 92,2021-04-20,2021-03-19,Ancestral,1644.46705,0,Previously infected (Pre-Omicron),BNT162b2,3 92,2021-06-28,2021-03-19,Ancestral,117.0434584,0,Previously infected (Pre-Omicron),BNT162b2,3 92,2021-04-20,2021-03-19,Alpha,574.934746699999,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -672,10 +672,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 100,2021-03-08,2021-03-08,Ancestral,95.1726835550794,0,Infection naive,BNT162b2,2 100,2021-04-13,2021-03-08,Ancestral,2560,1,Infection naive,BNT162b2,2 100,2021-07-06,2021-03-08,Ancestral,117.5575229,0,Infection naive,BNT162b2,2 -100,2021-03-08,2021-03-08,Alpha,5,-2,Infection naive,BNT162b2,2 +100,2021-03-08,2021-03-08,Alpha,5,-1,Infection naive,BNT162b2,2 100,2021-04-13,2021-03-08,Alpha,201.8901902,0,Infection naive,BNT162b2,2 100,2021-07-06,2021-03-08,Alpha,133.606076800001,0,Infection naive,BNT162b2,2 -100,2021-03-08,2021-03-08,Delta,5,-2,Infection naive,BNT162b2,2 +100,2021-03-08,2021-03-08,Delta,5,-1,Infection naive,BNT162b2,2 100,2021-04-13,2021-03-08,Delta,79.45059724,0,Infection naive,BNT162b2,2 100,2021-07-06,2021-03-08,Delta,57.3446769799999,0,Infection naive,BNT162b2,2 101,2021-04-23,2021-03-19,Ancestral,934.333704000001,0,Previously infected (Pre-Omicron),AZD1222,2 @@ -688,10 +688,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 103,2021-04-08,2021-02-26,Alpha,199.777854400001,0,Infection naive,BNT162b2,2 103,2021-04-08,2021-02-26,Delta,120.583935,0,Infection naive,BNT162b2,2 104,2021-05-26,2021-04-22,Ancestral,91.65245542,0,Infection naive,AZD1222,2 -104,2021-06-29,2021-04-22,Ancestral,5,-2,Infection naive,AZD1222,2 -104,2021-05-26,2021-04-22,Alpha,5,-2,Infection naive,AZD1222,2 -104,2021-05-26,2021-04-22,Delta,5,-2,Infection naive,AZD1222,2 -104,2021-06-29,2021-04-22,Delta,5,-2,Infection naive,AZD1222,2 +104,2021-06-29,2021-04-22,Ancestral,5,-1,Infection naive,AZD1222,2 +104,2021-05-26,2021-04-22,Alpha,5,-1,Infection naive,AZD1222,2 +104,2021-05-26,2021-04-22,Delta,5,-1,Infection naive,AZD1222,2 +104,2021-06-29,2021-04-22,Delta,5,-1,Infection naive,AZD1222,2 105,2021-02-19,2021-01-08,Ancestral,266.319234099999,0,Infection naive,BNT162b2,2 105,2021-02-19,2021-01-08,Alpha,227.6486598,0,Infection naive,BNT162b2,2 105,2021-02-19,2021-01-08,Delta,155.4818539,0,Infection naive,BNT162b2,2 @@ -708,8 +708,8 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 107,2021-07-01,2021-04-01,Delta,488.445967700001,0,Previously infected (Pre-Omicron),BNT162b2,3 107,2021-10-04,2021-04-01,Delta,214.288976000001,0,Previously infected (Pre-Omicron),BNT162b2,3 108,2021-05-11,2021-04-22,Ancestral,124.449475455526,0,Infection naive,AZD1222,1 -108,2021-05-11,2021-04-22,Alpha,5,-2,Infection naive,AZD1222,1 -108,2021-05-11,2021-04-22,Delta,5,-2,Infection naive,AZD1222,1 +108,2021-05-11,2021-04-22,Alpha,5,-1,Infection naive,AZD1222,1 +108,2021-05-11,2021-04-22,Delta,5,-1,Infection naive,AZD1222,1 109,2021-04-16,2021-03-10,Ancestral,458.573856899999,0,Infection naive,BNT162b2,2 109,2021-04-16,2021-03-10,Alpha,350.3869162,0,Infection naive,BNT162b2,2 109,2021-04-16,2021-03-10,Delta,148.164318200001,0,Infection naive,BNT162b2,2 @@ -730,7 +730,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 112,2021-06-04,2021-05-02,Alpha,45.6185921499999,0,Infection naive,AZD1222,2 112,2021-06-28,2021-05-02,Alpha,40.1389579100002,0,Infection naive,AZD1222,2 112,2021-06-04,2021-05-02,Delta,41.1001878499999,0,Infection naive,AZD1222,2 -112,2021-06-28,2021-05-02,Delta,5,-2,Infection naive,AZD1222,2 +112,2021-06-28,2021-05-02,Delta,5,-1,Infection naive,AZD1222,2 113,2021-03-22,2021-02-26,Ancestral,2560,1,Infection naive,BNT162b2,2 113,2021-03-22,2021-02-26,Alpha,378.8142175,0,Infection naive,BNT162b2,2 113,2021-03-22,2021-02-26,Delta,142.8091625,0,Infection naive,BNT162b2,2 @@ -746,11 +746,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 115,2021-03-18,2021-03-08,Ancestral,2560,1,Infection naive,BNT162b2,2 115,2021-03-18,2021-03-08,Alpha,2256.534692,0,Infection naive,BNT162b2,2 115,2021-03-18,2021-03-08,Delta,1176.561302,0,Infection naive,BNT162b2,2 -116,2021-03-02,2021-02-27,Ancestral,5,-2,Infection naive,AZD1222,1 -116,2021-03-02,2021-02-27,Alpha,5,-2,Infection naive,AZD1222,1 -116,2021-04-20,2021-02-27,Alpha,5,-2,Infection naive,AZD1222,1 -116,2021-03-02,2021-02-27,Delta,5,-2,Infection naive,AZD1222,1 -116,2021-04-20,2021-02-27,Delta,5,-2,Infection naive,AZD1222,1 +116,2021-03-02,2021-02-27,Ancestral,5,-1,Infection naive,AZD1222,1 +116,2021-03-02,2021-02-27,Alpha,5,-1,Infection naive,AZD1222,1 +116,2021-04-20,2021-02-27,Alpha,5,-1,Infection naive,AZD1222,1 +116,2021-03-02,2021-02-27,Delta,5,-1,Infection naive,AZD1222,1 +116,2021-04-20,2021-02-27,Delta,5,-1,Infection naive,AZD1222,1 117,2021-04-19,2021-03-17,Ancestral,2036.59773000001,0,Infection naive,BNT162b2,2 117,2021-06-29,2021-03-17,Ancestral,298.9848162,0,Infection naive,BNT162b2,2 117,2021-12-20,2021-03-17,Ancestral,395.438015100001,0,Infection naive,BNT162b2,2 @@ -781,9 +781,9 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 121,2021-02-08,2021-01-12,Ancestral,114.707563909016,0,Infection naive,BNT162b2,1 121,2021-03-01,2021-01-12,Ancestral,116.327542543632,0,Infection naive,BNT162b2,1 121,2021-02-08,2021-01-12,Alpha,59.3387915012427,0,Infection naive,BNT162b2,1 -121,2021-03-01,2021-01-12,Alpha,5,-2,Infection naive,BNT162b2,1 -121,2021-02-08,2021-01-12,Delta,5,-2,Infection naive,BNT162b2,1 -121,2021-03-01,2021-01-12,Delta,5,-2,Infection naive,BNT162b2,1 +121,2021-03-01,2021-01-12,Alpha,5,-1,Infection naive,BNT162b2,1 +121,2021-02-08,2021-01-12,Delta,5,-1,Infection naive,BNT162b2,1 +121,2021-03-01,2021-01-12,Delta,5,-1,Infection naive,BNT162b2,1 122,2021-04-20,2021-03-11,Ancestral,1847.789234,0,Infection naive,BNT162b2,2 122,2021-06-28,2021-03-11,Ancestral,199.953035,0,Infection naive,BNT162b2,2 122,2021-09-30,2021-03-11,Ancestral,163.0178413,0,Infection naive,BNT162b2,2 @@ -801,7 +801,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 123,2021-07-07,2021-04-12,Delta,79.93956094,0,Infection naive,AZD1222,2 124,2021-06-02,2021-04-20,Ancestral,141.3149794,0,Infection naive,AZD1222,1 124,2021-06-02,2021-04-20,Alpha,56.1509832100001,0,Infection naive,AZD1222,1 -124,2021-06-02,2021-04-20,Delta,5,-2,Infection naive,AZD1222,1 +124,2021-06-02,2021-04-20,Delta,5,-1,Infection naive,AZD1222,1 125,2021-04-07,2021-03-12,Ancestral,2560,1,Infection naive,BNT162b2,2 125,2021-06-30,2021-03-12,Ancestral,115.1104312,0,Infection naive,BNT162b2,2 125,2021-04-07,2021-03-12,Alpha,809.234558300001,0,Infection naive,BNT162b2,2 @@ -810,7 +810,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 125,2021-06-30,2021-03-12,Delta,116.6338259,0,Infection naive,BNT162b2,2 126,2021-06-09,2021-04-29,Ancestral,186.739773455233,0,Infection naive,AZD1222,1 126,2021-06-09,2021-04-29,Alpha,114.105905100308,0,Infection naive,AZD1222,1 -126,2021-06-09,2021-04-29,Delta,5,-2,Infection naive,AZD1222,1 +126,2021-06-09,2021-04-29,Delta,5,-1,Infection naive,AZD1222,1 127,2021-04-15,2021-03-20,Ancestral,674.369561900001,0,Infection naive,BNT162b2,2 127,2021-07-07,2021-03-20,Ancestral,99.7855700200003,0,Infection naive,BNT162b2,2 127,2021-04-15,2021-03-20,Alpha,357.2089356,0,Infection naive,BNT162b2,2 @@ -871,7 +871,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 134,2021-02-02,2021-01-03,Alpha,101.461249822687,0,Previously infected (Pre-Omicron),BNT162b2,2 134,2021-02-25,2021-01-03,Alpha,125.325174773812,0,Previously infected (Pre-Omicron),BNT162b2,2 134,2021-02-02,2021-01-03,Delta,47.1222645000002,0,Previously infected (Pre-Omicron),BNT162b2,2 -134,2021-02-25,2021-01-03,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,2 +134,2021-02-25,2021-01-03,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,2 135,2021-06-11,2021-04-28,Ancestral,2065.35995499999,0,Previously infected (Pre-Omicron),AZD1222,3 135,2021-07-08,2021-04-28,Ancestral,2560,1,Previously infected (Pre-Omicron),AZD1222,3 135,2021-09-20,2021-04-28,Ancestral,1593.388057,0,Previously infected (Pre-Omicron),AZD1222,3 @@ -895,17 +895,17 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 137,2021-09-17,2021-04-22,Ancestral,156.4387377,0,Infection naive,AZD1222,2 137,2021-06-11,2021-04-22,Alpha,162.7323236,0,Infection naive,AZD1222,2 137,2021-07-08,2021-04-22,Alpha,94.8395950400003,0,Infection naive,AZD1222,2 -137,2021-09-17,2021-04-22,Alpha,5,-2,Infection naive,AZD1222,2 +137,2021-09-17,2021-04-22,Alpha,5,-1,Infection naive,AZD1222,2 137,2021-06-11,2021-04-22,Delta,65.74692666,0,Infection naive,AZD1222,2 137,2021-07-08,2021-04-22,Delta,43.3574594500001,0,Infection naive,AZD1222,2 -137,2021-09-17,2021-04-22,Delta,5,-2,Infection naive,AZD1222,2 +137,2021-09-17,2021-04-22,Delta,5,-1,Infection naive,AZD1222,2 138,2021-03-11,2021-03-11,Ancestral,101.639265952646,0,Infection naive,BNT162b2,2 138,2021-04-15,2021-03-11,Ancestral,2560,1,Infection naive,BNT162b2,2 138,2021-07-08,2021-03-11,Ancestral,130.0247039,0,Infection naive,BNT162b2,2 -138,2021-03-11,2021-03-11,Alpha,5,-2,Infection naive,BNT162b2,2 +138,2021-03-11,2021-03-11,Alpha,5,-1,Infection naive,BNT162b2,2 138,2021-04-15,2021-03-11,Alpha,741.975338799998,0,Infection naive,BNT162b2,2 138,2021-07-08,2021-03-11,Alpha,177.951127500001,0,Infection naive,BNT162b2,2 -138,2021-03-11,2021-03-11,Delta,5,-2,Infection naive,BNT162b2,2 +138,2021-03-11,2021-03-11,Delta,5,-1,Infection naive,BNT162b2,2 138,2021-04-15,2021-03-11,Delta,468.733176700001,0,Infection naive,BNT162b2,2 138,2021-07-08,2021-03-11,Delta,139.469215700001,0,Infection naive,BNT162b2,2 139,2021-04-08,2021-03-01,Ancestral,2560,1,Infection naive,BNT162b2,2 @@ -969,11 +969,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 147,2021-04-19,2021-03-11,Ancestral,479.537695000001,0,Infection naive,BNT162b2,2 147,2021-06-28,2021-03-11,Ancestral,284.4145027,0,Infection naive,BNT162b2,2 147,2021-10-01,2021-03-11,Ancestral,166.337522,0,Infection naive,BNT162b2,2 -147,2021-03-11,2021-03-11,Alpha,5,-2,Infection naive,BNT162b2,2 +147,2021-03-11,2021-03-11,Alpha,5,-1,Infection naive,BNT162b2,2 147,2021-04-19,2021-03-11,Alpha,619.404450899999,0,Infection naive,BNT162b2,2 147,2021-06-28,2021-03-11,Alpha,138.859334100001,0,Infection naive,BNT162b2,2 147,2021-10-01,2021-03-11,Alpha,131.630053697801,0,Infection naive,BNT162b2,2 -147,2021-03-11,2021-03-11,Delta,5,-2,Infection naive,BNT162b2,2 +147,2021-03-11,2021-03-11,Delta,5,-1,Infection naive,BNT162b2,2 147,2021-04-19,2021-03-11,Delta,291.480903899999,0,Infection naive,BNT162b2,2 147,2021-06-28,2021-03-11,Delta,193.4029393,0,Infection naive,BNT162b2,2 147,2021-10-01,2021-03-11,Delta,58.40995721,0,Infection naive,BNT162b2,2 @@ -1057,10 +1057,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 157,2021-06-23,2021-02-26,Delta,46.6292338600001,0,Infection naive,BNT162b2,2 158,2021-04-15,2021-03-26,Ancestral,140.943882757322,0,Infection naive,AZD1222,1 158,2021-04-15,2021-03-26,Alpha,50.6781328723178,0,Infection naive,AZD1222,1 -158,2021-04-15,2021-03-26,Delta,5,-2,Infection naive,AZD1222,1 +158,2021-04-15,2021-03-26,Delta,5,-1,Infection naive,AZD1222,1 159,2021-03-05,2021-03-02,Ancestral,97.9656817769744,0,Infection naive,BNT162b2,2 159,2021-03-05,2021-03-02,Alpha,57.1439801799681,0,Infection naive,BNT162b2,2 -159,2021-03-05,2021-03-02,Delta,5,-2,Infection naive,BNT162b2,2 +159,2021-03-05,2021-03-02,Delta,5,-1,Infection naive,BNT162b2,2 160,2021-03-03,2021-02-24,Ancestral,1448.205014,0,Previously infected (Pre-Omicron),BNT162b2,3 160,2021-04-14,2021-02-24,Ancestral,633.6820123,0,Previously infected (Pre-Omicron),BNT162b2,3 160,2021-03-03,2021-02-24,Alpha,911.682556900002,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -1080,7 +1080,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 162,2021-09-29,2021-03-29,Delta,282.6748337,0,Infection naive,BNT162b2,2 163,2021-02-12,2021-01-19,Ancestral,104.530376317928,0,Infection naive,BNT162b2,1 163,2021-02-12,2021-01-19,Alpha,46.1818220151127,0,Infection naive,BNT162b2,1 -163,2021-02-12,2021-01-19,Delta,5,-2,Infection naive,BNT162b2,1 +163,2021-02-12,2021-01-19,Delta,5,-1,Infection naive,BNT162b2,1 164,2021-04-23,2021-03-24,Ancestral,355.335319799999,0,Previously infected (Pre-Omicron),BNT162b2,3 164,2021-06-28,2021-03-24,Ancestral,70.64627275,0,Previously infected (Pre-Omicron),BNT162b2,3 164,2021-04-23,2021-03-24,Alpha,316.513164100001,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -1147,10 +1147,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 173,2021-02-25,2021-02-25,Ancestral,106.7525503898,0,Infection naive,BNT162b2,2 173,2021-04-06,2021-02-25,Ancestral,2560,1,Infection naive,BNT162b2,2 173,2021-07-02,2021-02-25,Ancestral,155.3456349,0,Infection naive,BNT162b2,2 -173,2021-02-25,2021-02-25,Alpha,5,-2,Infection naive,BNT162b2,2 +173,2021-02-25,2021-02-25,Alpha,5,-1,Infection naive,BNT162b2,2 173,2021-04-06,2021-02-25,Alpha,983.922117299998,0,Infection naive,BNT162b2,2 173,2021-07-02,2021-02-25,Alpha,167.06809,0,Infection naive,BNT162b2,2 -173,2021-02-25,2021-02-25,Delta,5,-2,Infection naive,BNT162b2,2 +173,2021-02-25,2021-02-25,Delta,5,-1,Infection naive,BNT162b2,2 173,2021-04-06,2021-02-25,Delta,307.759015099999,0,Infection naive,BNT162b2,2 173,2021-07-02,2021-02-25,Delta,107.5037238,0,Infection naive,BNT162b2,2 174,2021-03-22,2021-02-24,Ancestral,431.2840209,0,Infection naive,BNT162b2,2 @@ -1163,11 +1163,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 175,2021-01-29,2021-01-05,Alpha,88.6500886099999,0,Infection naive,BNT162b2,2 175,2021-02-19,2021-01-05,Alpha,50.2799342700001,0,Infection naive,BNT162b2,2 175,2021-04-06,2021-01-05,Alpha,46.4253300100001,0,Infection naive,BNT162b2,2 -175,2021-07-06,2021-01-05,Alpha,5,-2,Infection naive,BNT162b2,2 +175,2021-07-06,2021-01-05,Alpha,5,-1,Infection naive,BNT162b2,2 175,2021-01-29,2021-01-05,Delta,44.47365804,0,Infection naive,BNT162b2,2 -175,2021-02-19,2021-01-05,Delta,5,-2,Infection naive,BNT162b2,2 -175,2021-04-06,2021-01-05,Delta,5,-2,Infection naive,BNT162b2,2 -175,2021-07-06,2021-01-05,Delta,5,-2,Infection naive,BNT162b2,2 +175,2021-02-19,2021-01-05,Delta,5,-1,Infection naive,BNT162b2,2 +175,2021-04-06,2021-01-05,Delta,5,-1,Infection naive,BNT162b2,2 +175,2021-07-06,2021-01-05,Delta,5,-1,Infection naive,BNT162b2,2 176,2021-04-15,2021-04-15,Ancestral,198.034467000762,0,Infection naive,AZD1222,2 176,2021-04-15,2021-04-15,Alpha,171.970976643965,0,Infection naive,AZD1222,2 176,2021-04-15,2021-04-15,Delta,126.317704098264,0,Infection naive,AZD1222,2 @@ -1239,12 +1239,12 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 186,2022-06-22,2021-03-29,Delta,116.8384626,0,Infection naive,BNT162b2,2 187,2021-02-24,2021-01-10,Ancestral,203.1326853,0,Infection naive,BNT162b2,2 187,2021-04-07,2021-01-10,Ancestral,82.5745152699999,0,Infection naive,BNT162b2,2 -187,2021-05-19,2021-01-10,Ancestral,5,-2,Infection naive,BNT162b2,2 +187,2021-05-19,2021-01-10,Ancestral,5,-1,Infection naive,BNT162b2,2 187,2021-02-24,2021-01-10,Alpha,46.3846563599999,0,Infection naive,BNT162b2,2 -187,2021-04-07,2021-01-10,Alpha,5,-2,Infection naive,BNT162b2,2 -187,2021-02-24,2021-01-10,Delta,5,-2,Infection naive,BNT162b2,2 -187,2021-04-07,2021-01-10,Delta,5,-2,Infection naive,BNT162b2,2 -187,2021-05-19,2021-01-10,Delta,5,-2,Infection naive,BNT162b2,2 +187,2021-04-07,2021-01-10,Alpha,5,-1,Infection naive,BNT162b2,2 +187,2021-02-24,2021-01-10,Delta,5,-1,Infection naive,BNT162b2,2 +187,2021-04-07,2021-01-10,Delta,5,-1,Infection naive,BNT162b2,2 +187,2021-05-19,2021-01-10,Delta,5,-1,Infection naive,BNT162b2,2 188,2021-04-23,2021-04-08,Ancestral,519.352771,0,Previously infected (Pre-Omicron),AZD1222,3 188,2021-06-29,2021-04-08,Ancestral,151.0490716,0,Previously infected (Pre-Omicron),AZD1222,3 188,2021-10-08,2021-04-08,Ancestral,124.8865576,0,Previously infected (Pre-Omicron),AZD1222,3 @@ -1322,7 +1322,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 199,2021-03-16,2021-03-03,Ancestral,2560,1,Infection naive,BNT162b2,2 199,2021-04-07,2021-03-03,Ancestral,977.047042700003,0,Infection naive,BNT162b2,2 199,2021-05-19,2021-03-03,Ancestral,1212.151396,0,Infection naive,BNT162b2,2 -199,2021-08-11,2021-03-03,Ancestral,5,-2,Infection naive,BNT162b2,2 +199,2021-08-11,2021-03-03,Ancestral,5,-1,Infection naive,BNT162b2,2 199,2021-03-16,2021-03-03,Alpha,432.7987443,0,Infection naive,BNT162b2,2 199,2021-04-07,2021-03-03,Alpha,505.8744803,0,Infection naive,BNT162b2,2 199,2021-05-19,2021-03-03,Alpha,241.41767,0,Infection naive,BNT162b2,2 @@ -1358,10 +1358,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 204,2021-02-26,2021-02-25,Ancestral,139.8364296,0,Infection naive,BNT162b2,2 204,2021-04-09,2021-02-25,Ancestral,267.0204364,0,Infection naive,BNT162b2,2 204,2021-07-02,2021-02-25,Ancestral,268.428384500001,0,Infection naive,BNT162b2,2 -204,2021-02-26,2021-02-25,Alpha,5,-2,Infection naive,BNT162b2,2 +204,2021-02-26,2021-02-25,Alpha,5,-1,Infection naive,BNT162b2,2 204,2021-04-09,2021-02-25,Alpha,511.2233054,0,Infection naive,BNT162b2,2 204,2021-07-02,2021-02-25,Alpha,89.4305156099998,0,Infection naive,BNT162b2,2 -204,2021-02-26,2021-02-25,Delta,5,-2,Infection naive,BNT162b2,2 +204,2021-02-26,2021-02-25,Delta,5,-1,Infection naive,BNT162b2,2 204,2021-04-09,2021-02-25,Delta,324.0928808,0,Infection naive,BNT162b2,2 204,2021-07-02,2021-02-25,Delta,186.2493902,0,Infection naive,BNT162b2,2 205,2021-04-20,2021-03-30,Ancestral,753.113831499999,0,Infection naive,BNT162b2,2 @@ -1400,15 +1400,15 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 209,2021-02-19,2021-01-11,Delta,192.3885111,0,Infection naive,BNT162b2,2 209,2021-04-06,2021-01-11,Delta,109.3090131,0,Infection naive,BNT162b2,2 210,2021-06-09,2021-05-01,Ancestral,72.3380783200001,0,Infection naive,AZD1222,2 -210,2021-06-09,2021-05-01,Alpha,5,-2,Infection naive,AZD1222,2 -210,2021-06-09,2021-05-01,Delta,5,-2,Infection naive,AZD1222,2 +210,2021-06-09,2021-05-01,Alpha,5,-1,Infection naive,AZD1222,2 +210,2021-06-09,2021-05-01,Delta,5,-1,Infection naive,AZD1222,2 211,2021-02-26,2021-02-25,Ancestral,99.9606461299999,0,Previously infected (Pre-Omicron),BNT162b2,3 211,2021-04-09,2021-02-25,Ancestral,595.971449500002,0,Previously infected (Pre-Omicron),BNT162b2,3 211,2021-07-02,2021-02-25,Ancestral,290.2062941,0,Previously infected (Pre-Omicron),BNT162b2,3 -211,2021-02-26,2021-02-25,Alpha,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +211,2021-02-26,2021-02-25,Alpha,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 211,2021-04-09,2021-02-25,Alpha,559.523354199999,0,Previously infected (Pre-Omicron),BNT162b2,3 211,2021-07-02,2021-02-25,Alpha,172.272703700001,0,Previously infected (Pre-Omicron),BNT162b2,3 -211,2021-02-26,2021-02-25,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +211,2021-02-26,2021-02-25,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 211,2021-04-09,2021-02-25,Delta,371.254033700001,0,Previously infected (Pre-Omicron),BNT162b2,3 211,2021-07-02,2021-02-25,Delta,123.9052733,0,Previously infected (Pre-Omicron),BNT162b2,3 212,2021-05-26,2021-05-05,Ancestral,465.050150400001,0,Infection naive,AZD1222,2 @@ -1432,8 +1432,8 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 214,2021-02-22,2021-01-08,Delta,184.139233300001,0,Infection naive,BNT162b2,2 214,2021-04-14,2021-01-08,Delta,151.3140907,0,Infection naive,BNT162b2,2 215,2021-05-28,2021-04-26,Ancestral,181.7341272,0,Infection naive,AZD1222,1 -215,2021-05-28,2021-04-26,Alpha,5,-2,Infection naive,AZD1222,1 -215,2021-05-28,2021-04-26,Delta,5,-2,Infection naive,AZD1222,1 +215,2021-05-28,2021-04-26,Alpha,5,-1,Infection naive,AZD1222,1 +215,2021-05-28,2021-04-26,Delta,5,-1,Infection naive,AZD1222,1 216,2021-02-01,2021-01-12,Ancestral,617.7778794,0,Infection naive,BNT162b2,2 216,2021-02-22,2021-01-12,Ancestral,477.440736200001,0,Infection naive,BNT162b2,2 216,2021-02-01,2021-01-12,Alpha,371.254033700001,0,Infection naive,BNT162b2,2 @@ -1491,13 +1491,13 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 224,2021-07-01,2021-03-15,Alpha,109.69292,0,Infection naive,BNT162b2,2 224,2021-04-08,2021-03-15,Delta,278.494095800001,0,Infection naive,BNT162b2,2 224,2021-07-01,2021-03-15,Delta,46.2628491,0,Infection naive,BNT162b2,2 -225,2021-03-16,2021-03-04,Ancestral,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +225,2021-03-16,2021-03-04,Ancestral,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 225,2021-04-20,2021-03-04,Ancestral,984.784896199998,0,Previously infected (Pre-Omicron),BNT162b2,3 225,2021-07-07,2021-03-04,Ancestral,145.7173155,0,Previously infected (Pre-Omicron),BNT162b2,3 225,2021-03-16,2021-03-04,Alpha,40.67016497,0,Previously infected (Pre-Omicron),BNT162b2,3 225,2021-04-20,2021-03-04,Alpha,558.543376799999,0,Previously infected (Pre-Omicron),BNT162b2,3 225,2021-07-07,2021-03-04,Alpha,174.7056566,0,Previously infected (Pre-Omicron),BNT162b2,3 -225,2021-03-16,2021-03-04,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +225,2021-03-16,2021-03-04,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 225,2021-04-20,2021-03-04,Delta,347.3292193,0,Previously infected (Pre-Omicron),BNT162b2,3 225,2021-07-07,2021-03-04,Delta,139.5915131,0,Previously infected (Pre-Omicron),BNT162b2,3 226,2021-03-08,2021-03-03,Ancestral,1823.65462085467,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -1538,12 +1538,12 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 231,2021-06-08,2021-02-24,Ancestral,94.6734882000001,0,Infection naive,BNT162b2,2 231,2021-03-16,2021-02-24,Alpha,122.501459,0,Infection naive,BNT162b2,2 231,2021-06-08,2021-02-24,Alpha,185.4349447,0,Infection naive,BNT162b2,2 -231,2021-06-08,2021-02-24,Alpha,5,-2,Infection naive,BNT162b2,2 +231,2021-06-08,2021-02-24,Alpha,5,-1,Infection naive,BNT162b2,2 231,2021-03-16,2021-02-24,Delta,124.7771433,0,Infection naive,BNT162b2,2 231,2021-06-08,2021-02-24,Delta,227.6486598,0,Infection naive,BNT162b2,2 -231,2021-06-08,2021-02-24,Delta,5,-2,Infection naive,BNT162b2,2 +231,2021-06-08,2021-02-24,Delta,5,-1,Infection naive,BNT162b2,2 232,2021-04-19,2021-04-06,Ancestral,210.3807757,0,Previously infected (Pre-Omicron),AZD1222,2 -232,2021-04-19,2021-04-06,Alpha,5,-2,Previously infected (Pre-Omicron),AZD1222,2 +232,2021-04-19,2021-04-06,Alpha,5,-1,Previously infected (Pre-Omicron),AZD1222,2 232,2021-04-19,2021-04-06,Delta,44.59075447,0,Previously infected (Pre-Omicron),AZD1222,2 233,2021-04-01,2021-03-11,Ancestral,2560,1,Infection naive,BNT162b2,2 233,2021-06-23,2021-03-11,Ancestral,164.021103826873,0,Infection naive,BNT162b2,2 @@ -1557,12 +1557,12 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 234,2021-12-08,2021-04-23,Ancestral,146.8713431,0,Infection naive,AZD1222,2 234,2021-05-26,2021-04-23,Alpha,89.6659807099998,0,Infection naive,AZD1222,2 234,2021-06-29,2021-04-23,Alpha,84.2560552900003,0,Infection naive,AZD1222,2 -234,2021-09-17,2021-04-23,Alpha,5,-2,Infection naive,AZD1222,2 -234,2021-12-08,2021-04-23,Alpha,5,-2,Infection naive,AZD1222,2 +234,2021-09-17,2021-04-23,Alpha,5,-1,Infection naive,AZD1222,2 +234,2021-12-08,2021-04-23,Alpha,5,-1,Infection naive,AZD1222,2 234,2021-05-26,2021-04-23,Delta,56.74469133,0,Infection naive,AZD1222,2 234,2021-06-29,2021-04-23,Delta,49.4495377399999,0,Infection naive,AZD1222,2 -234,2021-09-17,2021-04-23,Delta,5,-2,Infection naive,AZD1222,2 -234,2021-12-08,2021-04-23,Delta,5,-2,Infection naive,AZD1222,2 +234,2021-09-17,2021-04-23,Delta,5,-1,Infection naive,AZD1222,2 +234,2021-12-08,2021-04-23,Delta,5,-1,Infection naive,AZD1222,2 235,2021-04-20,2021-03-23,Ancestral,474.9364861,0,Infection naive,BNT162b2,2 235,2021-06-29,2021-03-23,Ancestral,213.726247800001,0,Infection naive,BNT162b2,2 235,2021-09-28,2021-03-23,Ancestral,146.8713431,0,Infection naive,BNT162b2,2 @@ -1582,14 +1582,14 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 236,2021-07-16,2021-03-24,Delta,124.5586024,0,Infection naive,BNT162b2,2 236,2021-09-28,2021-03-24,Delta,59.28680425,0,Infection naive,BNT162b2,2 237,2021-04-23,2021-04-08,Ancestral,110.7556306,0,Infection naive,AZD1222,1 -237,2021-04-23,2021-04-08,Alpha,5,-2,Infection naive,AZD1222,1 -237,2021-04-23,2021-04-08,Delta,5,-2,Infection naive,AZD1222,1 +237,2021-04-23,2021-04-08,Alpha,5,-1,Infection naive,AZD1222,1 +237,2021-04-23,2021-04-08,Delta,5,-1,Infection naive,AZD1222,1 238,2021-02-05,2021-01-06,Ancestral,132.208183677306,0,Previously infected (Pre-Omicron),BNT162b2,2 238,2021-02-26,2021-01-06,Ancestral,146.614105212046,0,Previously infected (Pre-Omicron),BNT162b2,2 238,2021-02-05,2021-01-06,Alpha,127.54147645632,0,Previously infected (Pre-Omicron),BNT162b2,2 238,2021-02-26,2021-01-06,Alpha,54.1214982344394,0,Previously infected (Pre-Omicron),BNT162b2,2 -238,2021-02-05,2021-01-06,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,2 -238,2021-02-26,2021-01-06,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,2 +238,2021-02-05,2021-01-06,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,2 +238,2021-02-26,2021-01-06,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,2 239,2021-06-02,2021-04-28,Ancestral,513.918889000001,0,Previously infected (Pre-Omicron),AZD1222,3 239,2021-07-07,2021-04-28,Ancestral,178.419662,0,Previously infected (Pre-Omicron),AZD1222,3 239,2022-01-06,2021-04-28,Ancestral,238.8917662,0,Previously infected (Pre-Omicron),AZD1222,3 @@ -1676,11 +1676,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 251,2021-06-28,2021-04-30,Delta,287.1699249,0,Infection naive,AZD1222,2 251,2021-09-14,2021-04-30,Delta,74.78799629,0,Infection naive,AZD1222,2 251,2021-11-16,2021-04-30,Delta,125.5450607,0,Infection naive,AZD1222,2 -252,2021-02-19,2021-01-07,Ancestral,5,-2,Infection naive,BNT162b2,2 +252,2021-02-19,2021-01-07,Ancestral,5,-1,Infection naive,BNT162b2,2 252,2021-02-19,2021-01-07,Alpha,209.0939465,0,Infection naive,BNT162b2,2 252,2021-03-12,2021-01-07,Alpha,139.3470255,0,Infection naive,BNT162b2,2 252,2021-04-29,2021-01-07,Alpha,153.855079,0,Infection naive,BNT162b2,2 -252,2021-02-19,2021-01-07,Delta,5,-2,Infection naive,BNT162b2,2 +252,2021-02-19,2021-01-07,Delta,5,-1,Infection naive,BNT162b2,2 253,2021-04-23,2021-03-23,Ancestral,737.436922400002,0,Infection naive,BNT162b2,2 253,2021-07-16,2021-03-23,Ancestral,114.3061066,0,Infection naive,BNT162b2,2 253,2021-04-23,2021-03-23,Alpha,588.703028700001,0,Infection naive,BNT162b2,2 @@ -1695,7 +1695,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 254,2021-09-28,2021-03-11,Alpha,79.3809898542299,0,Previously infected (Pre-Omicron),BNT162b2,3 254,2021-04-23,2021-03-11,Delta,271.9808199,0,Previously infected (Pre-Omicron),BNT162b2,3 254,2021-06-28,2021-03-11,Delta,65.6893251900002,0,Previously infected (Pre-Omicron),BNT162b2,3 -254,2021-09-28,2021-03-11,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +254,2021-09-28,2021-03-11,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 255,2021-04-23,2021-03-18,Ancestral,2560,1,Infection naive,BNT162b2,2 255,2021-06-28,2021-03-18,Ancestral,370.279111400002,0,Infection naive,BNT162b2,2 255,2021-09-24,2021-03-18,Ancestral,342.192248199999,0,Infection naive,BNT162b2,2 @@ -1718,13 +1718,13 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 257,2021-04-30,2021-03-05,Delta,301.3526661,0,Previously infected (Pre-Omicron),BNT162b2,3 257,2021-07-27,2021-03-05,Delta,166.0461901,0,Previously infected (Pre-Omicron),BNT162b2,3 258,2021-04-23,2021-04-09,Ancestral,83.8141193200002,0,Infection naive,AZD1222,2 -258,2021-07-07,2021-04-09,Ancestral,5,-2,Infection naive,AZD1222,2 -258,2021-04-23,2021-04-09,Alpha,5,-2,Infection naive,AZD1222,2 -258,2021-07-07,2021-04-09,Alpha,5,-2,Infection naive,AZD1222,2 -258,2021-12-02,2021-04-09,Alpha,5,-2,Infection naive,AZD1222,2 -258,2021-04-23,2021-04-09,Delta,5,-2,Infection naive,AZD1222,2 -258,2021-07-07,2021-04-09,Delta,5,-2,Infection naive,AZD1222,2 -258,2021-12-02,2021-04-09,Delta,5,-2,Infection naive,AZD1222,2 +258,2021-07-07,2021-04-09,Ancestral,5,-1,Infection naive,AZD1222,2 +258,2021-04-23,2021-04-09,Alpha,5,-1,Infection naive,AZD1222,2 +258,2021-07-07,2021-04-09,Alpha,5,-1,Infection naive,AZD1222,2 +258,2021-12-02,2021-04-09,Alpha,5,-1,Infection naive,AZD1222,2 +258,2021-04-23,2021-04-09,Delta,5,-1,Infection naive,AZD1222,2 +258,2021-07-07,2021-04-09,Delta,5,-1,Infection naive,AZD1222,2 +258,2021-12-02,2021-04-09,Delta,5,-1,Infection naive,AZD1222,2 259,2021-02-26,2021-01-11,Ancestral,455.768913199999,0,Previously infected (Pre-Omicron),BNT162b2,3 259,2021-03-24,2021-01-11,Ancestral,164.1649302,0,Previously infected (Pre-Omicron),BNT162b2,3 259,2021-02-26,2021-01-11,Alpha,154.5308232,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -1861,9 +1861,9 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 277,2021-02-01,2021-01-11,Ancestral,598.589004999999,0,Infection naive,BNT162b2,2 277,2021-02-25,2021-01-11,Ancestral,76.3109723399998,0,Infection naive,BNT162b2,2 277,2021-02-01,2021-01-11,Alpha,474.104658399999,0,Infection naive,BNT162b2,2 -277,2021-02-25,2021-01-11,Alpha,5,-2,Infection naive,BNT162b2,2 +277,2021-02-25,2021-01-11,Alpha,5,-1,Infection naive,BNT162b2,2 277,2021-02-01,2021-01-11,Delta,255.7951785,0,Infection naive,BNT162b2,2 -277,2021-02-25,2021-01-11,Delta,5,-2,Infection naive,BNT162b2,2 +277,2021-02-25,2021-01-11,Delta,5,-1,Infection naive,BNT162b2,2 278,2021-04-15,2021-03-28,Ancestral,195.105553200001,0,Infection naive,BNT162b2,2 278,2021-06-29,2021-03-28,Ancestral,124.5586024,0,Infection naive,BNT162b2,2 278,2021-04-15,2021-03-28,Alpha,472.445371200002,0,Infection naive,BNT162b2,2 @@ -1889,11 +1889,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 281,2021-04-13,2021-03-11,Ancestral,2560,1,Infection naive,BNT162b2,2 281,2021-05-28,2021-03-11,Ancestral,2560,1,Infection naive,BNT162b2,2 281,2021-08-27,2021-03-11,Ancestral,156.0279256,0,Infection naive,BNT162b2,2 -281,2021-03-12,2021-03-11,Alpha,5,-2,Infection naive,BNT162b2,2 +281,2021-03-12,2021-03-11,Alpha,5,-1,Infection naive,BNT162b2,2 281,2021-04-13,2021-03-11,Alpha,480.379055100002,0,Infection naive,BNT162b2,2 281,2021-05-28,2021-03-11,Alpha,279.227353800001,0,Infection naive,BNT162b2,2 281,2021-08-27,2021-03-11,Alpha,211.6755245,0,Infection naive,BNT162b2,2 -281,2021-03-12,2021-03-11,Delta,5,-2,Infection naive,BNT162b2,2 +281,2021-03-12,2021-03-11,Delta,5,-1,Infection naive,BNT162b2,2 281,2021-04-13,2021-03-11,Delta,255.123454000001,0,Infection naive,BNT162b2,2 281,2021-05-28,2021-03-11,Delta,343.695184599999,0,Infection naive,BNT162b2,2 281,2021-08-27,2021-03-11,Delta,131.3995102,0,Infection naive,BNT162b2,2 @@ -1931,14 +1931,14 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 285,2021-07-08,2021-04-28,Delta,159.7644131,0,Previously infected (Pre-Omicron),AZD1222,4 285,2021-12-02,2021-04-28,Delta,45.7387031300002,0,Previously infected (Pre-Omicron),AZD1222,4 286,2021-06-02,2021-04-30,Ancestral,202.067223099999,0,Infection naive,AZD1222,1 -286,2021-06-02,2021-04-30,Alpha,5,-2,Infection naive,AZD1222,1 -286,2021-06-02,2021-04-30,Delta,5,-2,Infection naive,AZD1222,1 +286,2021-06-02,2021-04-30,Alpha,5,-1,Infection naive,AZD1222,1 +286,2021-06-02,2021-04-30,Delta,5,-1,Infection naive,AZD1222,1 287,2021-05-28,2021-05-06,Ancestral,267.0204364,0,Previously infected (Pre-Omicron),AZD1222,3 287,2021-05-28,2021-05-06,Alpha,384.1640909,0,Previously infected (Pre-Omicron),AZD1222,3 287,2021-05-28,2021-05-06,Delta,315.4054209,0,Previously infected (Pre-Omicron),AZD1222,3 288,2021-06-11,2021-05-07,Ancestral,93.3550641612179,0,Previously infected (Pre-Omicron),AZD1222,2 -288,2021-06-11,2021-05-07,Alpha,5,-2,Previously infected (Pre-Omicron),AZD1222,2 -288,2021-06-11,2021-05-07,Delta,5,-2,Previously infected (Pre-Omicron),AZD1222,2 +288,2021-06-11,2021-05-07,Alpha,5,-1,Previously infected (Pre-Omicron),AZD1222,2 +288,2021-06-11,2021-05-07,Delta,5,-1,Previously infected (Pre-Omicron),AZD1222,2 289,2021-04-20,2021-03-24,Ancestral,2560,1,Infection naive,BNT162b2,2 289,2021-06-28,2021-03-24,Ancestral,1136.026121,0,Infection naive,BNT162b2,2 289,2021-04-20,2021-03-24,Alpha,1023.505653,0,Infection naive,BNT162b2,2 @@ -1977,7 +1977,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 293,2021-02-01,2021-01-11,Delta,211.861138,0,Infection naive,BNT162b2,2 293,2021-02-22,2021-01-11,Delta,121.0074409,0,Infection naive,BNT162b2,2 293,2021-04-06,2021-01-11,Delta,94.1769112,0,Infection naive,BNT162b2,2 -293,2021-06-28,2021-01-11,Delta,5,-2,Infection naive,BNT162b2,2 +293,2021-06-28,2021-01-11,Delta,5,-1,Infection naive,BNT162b2,2 294,2021-04-20,2021-04-08,Ancestral,225.06946,0,Infection naive,AZD1222,2 294,2021-06-28,2021-04-08,Ancestral,72.6557930900001,0,Infection naive,AZD1222,2 294,2021-04-20,2021-04-08,Alpha,164.021103800001,0,Infection naive,AZD1222,2 @@ -1992,7 +1992,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 295,2021-03-31,2021-03-09,Alpha,586.128703399999,0,Infection naive,BNT162b2,2 295,2021-05-12,2021-03-09,Alpha,399.9695656,0,Infection naive,BNT162b2,2 295,2021-07-28,2021-03-09,Alpha,247.632749599999,0,Infection naive,BNT162b2,2 -295,2021-03-09,2021-03-09,Delta,5,-2,Infection naive,BNT162b2,2 +295,2021-03-09,2021-03-09,Delta,5,-1,Infection naive,BNT162b2,2 295,2021-03-31,2021-03-09,Delta,579.4880186,0,Infection naive,BNT162b2,2 295,2021-05-12,2021-03-09,Delta,339.503505299999,0,Infection naive,BNT162b2,2 295,2021-07-28,2021-03-09,Delta,172.1217741,0,Infection naive,BNT162b2,2 @@ -2001,7 +2001,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 296,2021-06-09,2021-04-29,Delta,321.264642258916,0,Previously infected (Pre-Omicron),AZD1222,2 297,2021-06-11,2021-04-30,Ancestral,197.6876195,0,Infection naive,AZD1222,2 297,2021-06-11,2021-04-30,Alpha,64.0968121900002,0,Infection naive,AZD1222,2 -297,2021-06-11,2021-04-30,Delta,5,-2,Infection naive,AZD1222,2 +297,2021-06-11,2021-04-30,Delta,5,-1,Infection naive,AZD1222,2 298,2021-06-11,2021-05-04,Ancestral,388.907172099179,0,Infection naive,AZD1222,2 298,2021-07-16,2021-05-04,Ancestral,379.146391096023,0,Infection naive,AZD1222,2 298,2021-09-17,2021-05-04,Ancestral,165.465056107443,0,Infection naive,AZD1222,2 @@ -2039,7 +2039,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 302,2021-09-24,2021-03-18,Delta,120.1619114,0,Infection naive,BNT162b2,2 303,2021-03-02,2021-03-02,Ancestral,134.310556300001,0,Previously infected (Pre-Omicron),BNT162b2,3 303,2021-03-02,2021-03-02,Alpha,64.4347825330459,0,Previously infected (Pre-Omicron),BNT162b2,3 -303,2021-03-02,2021-03-02,Delta,5,-2,Previously infected (Pre-Omicron),BNT162b2,3 +303,2021-03-02,2021-03-02,Delta,5,-1,Previously infected (Pre-Omicron),BNT162b2,3 304,2021-01-29,2021-01-11,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 304,2021-03-18,2021-01-11,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 304,2021-04-29,2021-01-11,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 @@ -2054,10 +2054,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 304,2021-07-22,2021-01-11,Delta,813.501498699998,0,Previously infected (Pre-Omicron),BNT162b2,3 305,2021-03-16,2021-03-16,Ancestral,130.36705105991,0,Infection naive,AZD1222,1 305,2021-05-11,2021-03-16,Ancestral,111.828636774095,0,Infection naive,AZD1222,1 -305,2021-03-16,2021-03-16,Alpha,5,-2,Infection naive,AZD1222,1 -305,2021-05-11,2021-03-16,Alpha,5,-2,Infection naive,AZD1222,1 -305,2021-03-16,2021-03-16,Delta,5,-2,Infection naive,AZD1222,1 -305,2021-05-11,2021-03-16,Delta,5,-2,Infection naive,AZD1222,1 +305,2021-03-16,2021-03-16,Alpha,5,-1,Infection naive,AZD1222,1 +305,2021-05-11,2021-03-16,Alpha,5,-1,Infection naive,AZD1222,1 +305,2021-03-16,2021-03-16,Delta,5,-1,Infection naive,AZD1222,1 +305,2021-05-11,2021-03-16,Delta,5,-1,Infection naive,AZD1222,1 306,2021-02-02,2021-01-11,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 306,2021-02-23,2021-01-11,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 306,2021-04-09,2021-01-11,Ancestral,2011.75954500001,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -2135,8 +2135,8 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 316,2021-04-23,2021-03-12,Delta,389.248195900001,0,Infection naive,BNT162b2,2 316,2021-06-29,2021-03-12,Delta,164.5971664,0,Infection naive,BNT162b2,2 317,2021-02-15,2020-12-29,Ancestral,109.213246450387,0,Infection naive,"",1 -317,2021-02-15,2020-12-29,Alpha,5,-2,Infection naive,"",1 -317,2021-02-15,2020-12-29,Delta,5,-2,Infection naive,"",1 +317,2021-02-15,2020-12-29,Alpha,5,-1,Infection naive,"",1 +317,2021-02-15,2020-12-29,Delta,5,-1,Infection naive,"",1 318,2021-04-23,2021-03-23,Ancestral,2560,1,Previously infected (Pre-Omicron),BNT162b2,3 318,2021-06-29,2021-03-23,Ancestral,382.484188999999,0,Previously infected (Pre-Omicron),BNT162b2,3 318,2021-04-23,2021-03-23,Alpha,508.541860499999,0,Previously infected (Pre-Omicron),BNT162b2,3 @@ -2180,8 +2180,8 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 323,2021-02-23,2020-12-27,Ancestral,138.737678205393,0,Infection naive,BNT162b2,1 323,2021-02-02,2020-12-27,Alpha,107.033623347396,0,Infection naive,BNT162b2,1 323,2021-02-23,2020-12-27,Alpha,60.0187886685244,0,Infection naive,BNT162b2,1 -323,2021-02-02,2020-12-27,Delta,5,-2,Infection naive,BNT162b2,1 -323,2021-02-23,2020-12-27,Delta,5,-2,Infection naive,BNT162b2,1 +323,2021-02-02,2020-12-27,Delta,5,-1,Infection naive,BNT162b2,1 +323,2021-02-23,2020-12-27,Delta,5,-1,Infection naive,BNT162b2,1 324,2021-06-09,2021-05-06,Ancestral,461.800650900001,0,Previously infected (Pre-Omicron),AZD1222,3 324,2021-07-16,2021-05-06,Ancestral,388.907172100001,0,Previously infected (Pre-Omicron),AZD1222,3 324,2021-06-09,2021-05-06,Alpha,817.074464,0,Previously infected (Pre-Omicron),AZD1222,3 @@ -2245,12 +2245,12 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 333,2021-06-29,2021-03-24,Delta,84.9233322799998,0,Infection naive,BNT162b2,2 333,2021-09-22,2021-03-24,Delta,44.4346942700001,0,Infection naive,BNT162b2,2 334,2021-04-13,2021-04-13,Ancestral,88.1851052684112,0,Infection naive,AZD1222,2 -334,2021-07-16,2021-04-13,Ancestral,5,-2,Infection naive,AZD1222,2 -334,2021-04-13,2021-04-13,Alpha,5,-2,Infection naive,AZD1222,2 -334,2021-04-13,2021-04-13,Delta,5,-2,Infection naive,AZD1222,2 +334,2021-07-16,2021-04-13,Ancestral,5,-1,Infection naive,AZD1222,2 +334,2021-04-13,2021-04-13,Alpha,5,-1,Infection naive,AZD1222,2 +334,2021-04-13,2021-04-13,Delta,5,-1,Infection naive,AZD1222,2 335,2021-06-09,2021-05-05,Ancestral,136.805615775511,0,Infection naive,AZD1222,1 335,2021-06-29,2021-05-05,Ancestral,120.689672339818,0,Infection naive,AZD1222,1 335,2021-06-09,2021-05-05,Alpha,70.0297688893001,0,Infection naive,AZD1222,1 335,2021-06-29,2021-05-05,Alpha,50.9007153836499,0,Infection naive,AZD1222,1 -335,2021-06-09,2021-05-05,Delta,5,-2,Infection naive,AZD1222,1 -335,2021-06-29,2021-05-05,Delta,5,-2,Infection naive,AZD1222,1 +335,2021-06-09,2021-05-05,Delta,5,-1,Infection naive,AZD1222,1 +335,2021-06-29,2021-05-05,Delta,5,-1,Infection naive,AZD1222,1 diff --git a/inst/xbb_full.rds b/inst/xbb_full.rds index 0c55f1c..188d6bb 100644 --- a/inst/xbb_full.rds +++ b/inst/xbb_full.rds @@ -287,7 +287,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 69,2022-11-01,2022-10-16,XBB,639.821155970214,0,Previously infected (Pre-Omicron),BNT162b2,5 69,2023-01-10,2022-10-16,XBB,557.076628047233,0,Previously infected (Pre-Omicron),BNT162b2,5 70,2023-01-19,2022-12-26,BA.5,66.2676181593159,0,Infection naive,BNT162b2+BA1,5 -70,2023-01-19,2022-12-26,BQ.1.1,5,-2,Infection naive,BNT162b2+BA1,5 +70,2023-01-19,2022-12-26,BQ.1.1,5,-1,Infection naive,BNT162b2+BA1,5 70,2023-01-19,2022-12-26,XBB,483.335457280892,0,Infection naive,BNT162b2+BA1,5 71,2023-01-16,2022-12-24,BA.5,2560,1,Infection naive,BNT162b2+BA1,6 71,2023-01-16,2022-12-24,BQ.1.1,1035.23459045094,0,Infection naive,BNT162b2+BA1,6 @@ -586,11 +586,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 140,2023-01-12,2022-12-10,BA.5,2560,1,Infection naive,BNT162b2,5 140,2023-01-12,2022-12-10,BQ.1.1,1603.19426329011,0,Infection naive,BNT162b2,5 140,2023-01-12,2022-12-10,XBB,368.014237214278,0,Infection naive,BNT162b2,5 -141,2022-11-17,2022-10-30,BA.5,5,-2,Infection naive,BNT162b2,4 -141,2022-12-06,2022-10-30,BA.5,5,-2,Infection naive,BNT162b2,4 -141,2022-11-17,2022-10-30,BQ.1.1,5,-2,Infection naive,BNT162b2,4 +141,2022-11-17,2022-10-30,BA.5,5,-1,Infection naive,BNT162b2,4 +141,2022-12-06,2022-10-30,BA.5,5,-1,Infection naive,BNT162b2,4 +141,2022-11-17,2022-10-30,BQ.1.1,5,-1,Infection naive,BNT162b2,4 141,2022-12-06,2022-10-30,BQ.1.1,41.2807032377651,0,Infection naive,BNT162b2,4 -141,2022-11-17,2022-10-30,XBB,5,-2,Infection naive,BNT162b2,4 +141,2022-11-17,2022-10-30,XBB,5,-1,Infection naive,BNT162b2,4 141,2022-12-06,2022-10-30,XBB,269.843756512819,0,Infection naive,BNT162b2,4 142,2022-11-17,2022-10-23,BA.5,2560,1,Previously infected (Omicron),BNT162b2+BA1,7 142,2023-01-26,2022-10-23,BA.5,2560,1,Previously infected (Omicron),BNT162b2+BA1,7 @@ -671,11 +671,11 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 160,2022-10-03,2022-09-20,BA.5,1374.01249795787,0,Previously infected (Pre-Omicron),mRNA1273,5 160,2022-09-20,2022-09-20,BQ.1.1,46.7930015601292,0,Previously infected (Pre-Omicron),mRNA1273,5 160,2022-10-03,2022-09-20,BQ.1.1,430.906169068342,0,Previously infected (Pre-Omicron),mRNA1273,5 -160,2022-09-20,2022-09-20,XBB,5,-2,Previously infected (Pre-Omicron),mRNA1273,5 +160,2022-09-20,2022-09-20,XBB,5,-1,Previously infected (Pre-Omicron),mRNA1273,5 160,2022-10-03,2022-09-20,XBB,688.705744441976,0,Previously infected (Pre-Omicron),mRNA1273,5 -161,2022-10-11,2022-10-11,BA.5,5,-2,Infection naive,BNT162b2+BA1,4 +161,2022-10-11,2022-10-11,BA.5,5,-1,Infection naive,BNT162b2+BA1,4 161,2022-10-27,2022-10-11,BA.5,866.494068070684,0,Infection naive,BNT162b2+BA1,4 -161,2022-10-11,2022-10-11,BQ.1.1,5,-2,Infection naive,BNT162b2+BA1,4 +161,2022-10-11,2022-10-11,BQ.1.1,5,-1,Infection naive,BNT162b2+BA1,4 161,2022-10-27,2022-10-11,BQ.1.1,155.073554719911,0,Infection naive,BNT162b2+BA1,4 161,2022-10-11,2022-10-11,XBB,85.2963225104831,0,Infection naive,BNT162b2+BA1,4 161,2022-10-27,2022-10-11,XBB,128.890026491534,0,Infection naive,BNT162b2+BA1,4 @@ -704,7 +704,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 166,2022-10-18,2022-10-02,XBB,1859.16110394001,0,Previously infected (Omicron),mRNA1273.214,5 166,2023-01-26,2022-10-02,XBB,871.826742274675,0,Previously infected (Omicron),mRNA1273.214,5 167,2022-12-08,2022-12-08,BA.5,40.0335520056376,0,Infection naive,BNT162b2+BA1,4 -167,2022-12-08,2022-12-08,BQ.1.1,5,-2,Infection naive,BNT162b2+BA1,4 +167,2022-12-08,2022-12-08,BQ.1.1,5,-1,Infection naive,BNT162b2+BA1,4 167,2022-12-08,2022-12-08,XBB,140.820400557588,0,Infection naive,BNT162b2+BA1,4 168,2022-09-29,2022-09-15,BA.5,2560,1,Previously infected (Pre-Omicron),mRNA1273.214,5 168,2022-11-14,2022-09-15,BA.5,846.228952921684,0,Previously infected (Pre-Omicron),mRNA1273.214,5 @@ -748,10 +748,10 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 179,2022-12-06,2022-09-09,BQ.1.1,258.953353207664,0,Infection naive,mRNA1273.214,4 179,2022-10-04,2022-09-09,XBB,291.992313933846,0,Infection naive,mRNA1273.214,4 179,2022-12-06,2022-09-09,XBB,453.775892277874,0,Infection naive,mRNA1273.214,4 -180,2022-09-27,2022-09-25,BA.5,5,-2,Infection naive,mRNA1273.214,7 +180,2022-09-27,2022-09-25,BA.5,5,-1,Infection naive,mRNA1273.214,7 180,2022-10-18,2022-09-25,BA.5,2560,1,Infection naive,mRNA1273.214,7 180,2023-01-26,2022-09-25,BA.5,2056.3283925985,0,Infection naive,mRNA1273.214,7 -180,2022-09-27,2022-09-25,BQ.1.1,5,-2,Infection naive,mRNA1273.214,7 +180,2022-09-27,2022-09-25,BQ.1.1,5,-1,Infection naive,mRNA1273.214,7 180,2022-10-18,2022-09-25,BQ.1.1,420.828358433089,0,Infection naive,mRNA1273.214,7 180,2023-01-26,2022-09-25,BQ.1.1,157.125829413333,0,Infection naive,mRNA1273.214,7 180,2022-09-27,2022-09-25,XBB,42.2692751858847,0,Infection naive,mRNA1273.214,7 @@ -930,7 +930,7 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 222,2023-01-12,2022-11-23,XBB,1015.46355533338,0,Infection naive,BNT162b2+BA1,4 223,2022-12-01,2022-12-01,BA.5,1147.03200007966,0,Infection naive,BNT162b2+BA1,4 223,2022-12-01,2022-12-01,BQ.1.1,234.534860507757,0,Infection naive,BNT162b2+BA1,4 -223,2022-12-01,2022-12-01,XBB,5,-2,Infection naive,BNT162b2+BA1,4 +223,2022-12-01,2022-12-01,XBB,5,-1,Infection naive,BNT162b2+BA1,4 224,2022-10-18,2022-10-01,BA.5,2560,1,Previously infected (Omicron),mRNA1273.214,6 224,2023-01-19,2022-10-01,BA.5,2560,1,Previously infected (Omicron),mRNA1273.214,6 224,2022-10-18,2022-10-01,BQ.1.1,2560,1,Previously infected (Omicron),mRNA1273.214,6 @@ -1037,4 +1037,4 @@ pid,date,last_exp_date,titre_type,value,censored,infection_history,last_vax_type 247,2023-01-09,2022-12-12,XBB,412.429677483237,0,Infection naive,mRNA1273.214,5 248,2022-10-17,2022-10-02,BA.5,486.310054130306,0,Infection naive,BNT162b2,4 248,2022-10-17,2022-10-02,BQ.1.1,194.25238085558,0,Infection naive,BNT162b2,4 -248,2022-10-17,2022-10-02,XBB,5,-2,Infection naive,BNT162b2,4 +248,2022-10-17,2022-10-02,XBB,5,-1,Infection naive,BNT162b2,4 diff --git a/src/stan/antibody_kinetics_main.stan b/src/stan/antibody_kinetics_main.stan index cb0dbdc..390acda 100644 --- a/src/stan/antibody_kinetics_main.stan +++ b/src/stan/antibody_kinetics_main.stan @@ -37,12 +37,10 @@ data { // Indices for different censoring scenarios int N_uncens; // number of uncensored observations int N_lo; // number of lower censored observations - int N_me; // number of lower censored observations int N_hi; // number of upper censored observations array[N_uncens] int uncens_idx; array[N_lo] int cens_lo_idx; - array[N_me] int cens_me_idx; array[N_hi] int cens_hi_idx; // Standard deviation of effect size parameters diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R index e141cb7..1824374 100644 --- a/tests/testthat/test-data.R +++ b/tests/testthat/test-data.R @@ -39,7 +39,7 @@ test_that("Can get stan data", { expect_true(is.list(stan_data)) expect_equal(names(stan_data), c("N", "N_events", "id", "value", "censored", "titre_type", "preds_sd", "K", "N_uncens", "N_lo", - "N_me", "N_hi", "uncens_idx", "cens_lo_idx", "cens_me_idx", + "N_hi", "uncens_idx", "cens_lo_idx", "cens_hi_idx", "t", "X", "P", "mu_t0", "mu_tp", "mu_ts", "mu_m1", "mu_m2", "mu_m3", "sigma_t0", "sigma_tp", "sigma_ts", "sigma_m1", "sigma_m2", diff --git a/tests/testthat/test-run-model.R b/tests/testthat/test-run-model.R index ba337ea..8665b90 100644 --- a/tests/testthat/test-run-model.R +++ b/tests/testthat/test-run-model.R @@ -43,7 +43,7 @@ test_that("Can process model fits with no covariates", { expect_equal(names(pt), c("t", "me", "lo", "hi", "titre_type")) it <- mod$simulate_individual_trajectories(n_draws = 100, summarise = FALSE) - expect_equal(names(it), c("stan_id", "draw", "t", "mu", "titre_type", + expect_equal(names(it), c("pid", "draw", "t", "mu", "titre_type", "exposure_date", "calendar_date", "time_shift")) # it <- mod$simulate_individual_trajectories(n_draws = 100, summarise = TRUE) diff --git a/vignettes/data.Rmd b/vignettes/data.Rmd index f448e56..a911260 100644 --- a/vignettes/data.Rmd +++ b/vignettes/data.Rmd @@ -29,7 +29,7 @@ The name of the titre ### value The value of the titre ### censored -Whether this observation should be censored: -2 for lower, -1 for me, 1 for upper, 0 for none +Whether this observation should be censored: -1 for lower, 1 for upper, 0 for none It can also contain further columns for any covariates to be included in the model. The data files installed with this package have additional columns infection_history, last_vax_type, and exp_num.