diff --git a/test_example/expected_titers_for_test.csv b/test_example/expected_titers_for_test.csv index 5a0d76d..ea05991 100644 --- a/test_example/expected_titers_for_test.csv +++ b/test_example/expected_titers_for_test.csv @@ -1,195 +1,194 @@ -group,serum,virus,n_replicates,titer_bound,titer -pilot,A23038d0_r32_75K,A/Bangkok/P3599/2023,2,interpolated,1863 -pilot,A23038d0_r32_75K,A/Bangkok/P3755/2023,3,interpolated,851.5 -pilot,A23038d0_r32_75K,A/Bhutan/0006/2023,3,interpolated,611.9 -pilot,A23038d0_r32_75K,A/Bhutan/FLU-BTG-00988/2022,3,interpolated,552 -pilot,A23038d0_r32_75K,A/Brisbane/429/2023,2,interpolated,1534 -pilot,A23038d0_r32_75K,A/Busan/1301/2023,2,interpolated,773.6 -pilot,A23038d0_r32_75K,A/California/81/2023,2,interpolated,1454 -pilot,A23038d0_r32_75K,A/Cambodia/e0826360/2020_egg,3,interpolated,8843 -pilot,A23038d0_r32_75K,A/Catalonia/2041146NS/2023,2,interpolated,747 -pilot,A23038d0_r32_75K,A/Catalonia/NSVH102124476/2023,3,interpolated,655.3 -pilot,A23038d0_r32_75K,A/Chipata/15-NIC-001/2023,3,interpolated,1137 -pilot,A23038d0_r32_75K,A/EHIME/50/2023,3,interpolated,1167 -pilot,A23038d0_r32_75K,A/Georgia/40/2023,3,interpolated,1123 -pilot,A23038d0_r32_75K,A/Hong_Kong/2671/2019,3,interpolated,8785 -pilot,A23038d0_r32_75K,A/Hong_Kong/45/2019,3,interpolated,1040 -pilot,A23038d0_r32_75K,A/Hong_Kong/4801/2014,2,interpolated,5075 -pilot,A23038d0_r32_75K,A/Hong_Kong/4801/2014_(15/192),3,lower,1.28e+04 -pilot,A23038d0_r32_75K,A/Jeju/1047/2023,2,interpolated,1049 -pilot,A23038d0_r32_75K,A/Kansas/14/2017,2,interpolated,4041 -pilot,A23038d0_r32_75K,A/Krabi/THIS050/2023,2,interpolated,3116 -pilot,A23038d0_r32_75K,A/Malaysia/IMR-SARI1989/2023,2,interpolated,1422 -pilot,A23038d0_r32_75K,A/Massachusets/18/2022,2,interpolated,1241 -pilot,A23038d0_r32_75K,A/Netherlands/01685/2023,2,interpolated,1424 -pilot,A23038d0_r32_75K,A/Netherlands/01760/2023,3,interpolated,1764 -pilot,A23038d0_r32_75K,A/Ontario/RV00796/2023,3,interpolated,1238 -pilot,A23038d0_r32_75K,A/SOUTH_AFRICA/R07876/202023,3,interpolated,797.5 -pilot,A23038d0_r32_75K,A/Saint-Petersburg/RII-MH144113/2023,3,interpolated,1685 -pilot,A23038d0_r32_75K,A/Saskatchewan/SKFLU317847/2023,2,interpolated,2104 -pilot,A23038d0_r32_75K,A/Schleswig-Holstein/4/2023,3,interpolated,1451 -pilot,A23038d0_r32_75K,A/Singapore/INFIMH-16-0019/2016,3,interpolated,3345 -pilot,A23038d0_r32_75K,A/Singapore/INFIMH-16-0019/2016_X-307A,3,lower,1.28e+04 -pilot,A23038d0_r32_75K,A/SouthAfrica/PET28931/2023,3,interpolated,1104 -pilot,A23038d0_r32_75K,A/SouthSudan/631/2023,3,interpolated,721.3 -pilot,A23038d0_r32_75K,A/South_Africa/K056872/2023,2,interpolated,1115 -pilot,A23038d0_r32_75K,A/South_Africa/R05384/2023,3,interpolated,448.6 -pilot,A23038d0_r32_75K,A/South_Africa/R05510/2023,2,interpolated,3338 -pilot,A23038d0_r32_75K,A/South_Africa/R06240/2023,2,interpolated,1397 -pilot,A23038d0_r32_75K,A/South_Africa/R06359/2023,2,interpolated,558.4 -pilot,A23038d0_r32_75K,A/South_Africa/R06477/2023,2,interpolated,1876 -pilot,A23038d0_r32_75K,A/South_Africa/R06506/2023,3,interpolated,1036 -pilot,A23038d0_r32_75K,A/South_Africa/R07188/2023,2,interpolated,1987 -pilot,A23038d0_r32_75K,A/Switzerland/9715293/2013,2,interpolated,4503 -pilot,A23038d0_r32_75K,A/Switzerland/9715293/2013_NIB-88,2,interpolated,6760 -pilot,A23038d0_r32_75K,A/Sydney/332/2023,3,interpolated,1350 -pilot,A23038d0_r32_75K,A/Sydney/710/2023,3,interpolated,805.1 -pilot,A23038d0_r32_75K,A/Sydney/715/2023,2,interpolated,1176 -pilot,A23038d0_r32_75K,A/Sydney/749/2023,3,interpolated,1952 -pilot,A23038d0_r32_75K,A/TECPAN/017FLU/2023,3,interpolated,756 -pilot,A23038d0_r32_75K,A/Texas/50/2012,3,lower,1.28e+04 -pilot,A23038d0_r32_75K,A/Townsville/68/2023,3,interpolated,780 -pilot,A23038d0_r32_75K,A/Victoria/1033/2023,2,interpolated,1089 -pilot,A23038d0_r32_75K,A/Wisconsin/27/2023,2,interpolated,2235 -serum,M099d0,A/Bangladesh/2221/2021,6,interpolated,280.5 -serum,M099d0,A/Bangladesh/3210810034/2021,4,interpolated,227.6 -serum,M099d0,A/Bangladesh/8002/2021,6,interpolated,294.7 -serum,M099d0,A/Bangladesh/8036/2021,6,interpolated,313.6 -serum,M099d0,A/Belgium/H0017/2022,6,interpolated,670.2 -serum,M099d0,A/Belgium/H0038/2022,6,interpolated,905.3 -serum,M099d0,A/Brisbane/02/2018,8,interpolated,752.6 -serum,M099d0,A/Brisbane/48/2022,6,interpolated,271.7 -serum,M099d0,A/California/07/2009,8,interpolated,845 -serum,M099d0,A/Chester/5355/2022,6,interpolated,420.2 -serum,M099d0,A/Cote_DIvoire/1448/2021,6,interpolated,756 -serum,M099d0,A/England/220200318/2022,6,interpolated,802.8 -serum,M099d0,A/Ghana/138/2020,6,interpolated,758.8 -serum,M099d0,A/Ghana/2080/2020,6,interpolated,710.5 -serum,M099d0,A/Hawaii/70/2019,8,interpolated,782.1 -serum,M099d0,A/India-PUN-NIV328484/2021,6,interpolated,310.8 -serum,M099d0,A/India-Pune-Nivcov2221170/2022,4,interpolated,205.1 -serum,M099d0,A/India/Pun-NIV312851/2021,6,interpolated,293.1 -serum,M099d0,A/Michigan/19/2021,6,interpolated,392.9 -serum,M099d0,A/Michigan/45/2015,8,interpolated,854.6 -serum,M099d0,A/Newcastle/2/2022,6,interpolated,303.7 -serum,M099d0,A/Niger/10217/2021,6,interpolated,757.7 -serum,M099d0,A/Nimes/871/2021,6,interpolated,924.1 -serum,M099d0,A/Paris/30353/2021,6,interpolated,769.6 -serum,M099d0,A/Paris/31196/2021,6,interpolated,879 -serum,M099d0,A/Perth/1/2022,6,interpolated,341.2 -serum,M099d0,A/SouthAfrica/R14850/2021,6,interpolated,432.7 -serum,M099d0,A/SouthAfrica/R16462/2021,6,interpolated,866.5 -serum,M099d0,A/Sydney/43/2022,6,interpolated,279.3 -serum,M099d0,A/Togo/0274/2021,6,interpolated,770.9 -serum,M099d0,A/Togo/0304/2021,6,interpolated,958.9 -serum,M099d0,A/Togo/845/2020,6,interpolated,852.5 -serum,M099d0,A/Utah/27/2022,6,interpolated,251.2 -serum,M099d0,A/Washington/23/2020,6,interpolated,398.2 -serum,M099d0,A/Wisconsin/588/2019,5,interpolated,297 -serum,M099d30,A/Bangladesh/2221/2021,6,interpolated,1491 -serum,M099d30,A/Bangladesh/3210810034/2021,4,interpolated,1378 -serum,M099d30,A/Bangladesh/8002/2021,6,interpolated,1526 -serum,M099d30,A/Bangladesh/8036/2021,6,interpolated,1721 -serum,M099d30,A/Belgium/H0017/2022,6,interpolated,2830 -serum,M099d30,A/Belgium/H0038/2022,6,interpolated,2932 -serum,M099d30,A/Brisbane/02/2018,8,interpolated,4975 -serum,M099d30,A/Brisbane/48/2022,6,interpolated,1257 -serum,M099d30,A/California/07/2009,8,interpolated,4498 -serum,M099d30,A/Chester/5355/2022,6,interpolated,1416 -serum,M099d30,A/Cote_DIvoire/1448/2021,6,interpolated,3649 -serum,M099d30,A/England/220200318/2022,6,interpolated,2973 -serum,M099d30,A/Ghana/138/2020,6,interpolated,2261 -serum,M099d30,A/Ghana/2080/2020,6,interpolated,3078 -serum,M099d30,A/Hawaii/70/2019,8,interpolated,2861 -serum,M099d30,A/India-PUN-NIV328484/2021,6,interpolated,2532 -serum,M099d30,A/India-Pune-Nivcov2221170/2022,4,interpolated,1005 -serum,M099d30,A/India/Pun-NIV312851/2021,6,interpolated,1621 -serum,M099d30,A/Michigan/19/2021,6,interpolated,1795 -serum,M099d30,A/Michigan/45/2015,8,interpolated,5004 -serum,M099d30,A/Newcastle/2/2022,6,interpolated,1462 -serum,M099d30,A/Niger/10217/2021,6,interpolated,1984 -serum,M099d30,A/Nimes/871/2021,6,interpolated,3136 -serum,M099d30,A/Norway/25089/2022,5,interpolated,826.4 -serum,M099d30,A/Paris/30353/2021,6,interpolated,1799 -serum,M099d30,A/Paris/31196/2021,6,interpolated,3247 -serum,M099d30,A/Perth/1/2022,6,interpolated,1797 -serum,M099d30,A/SouthAfrica/R14850/2021,6,interpolated,1124 -serum,M099d30,A/SouthAfrica/R16462/2021,6,interpolated,2627 -serum,M099d30,A/Sydney/43/2022,6,interpolated,1107 -serum,M099d30,A/Togo/0274/2021,6,interpolated,2629 -serum,M099d30,A/Togo/0304/2021,6,interpolated,1988 -serum,M099d30,A/Togo/845/2020,6,interpolated,2076 -serum,M099d30,A/Utah/27/2022,6,interpolated,1388 -serum,M099d30,A/Wisconsin/588/2019,6,interpolated,2318 -serum,Y044d30,A/Bangladesh/2221/2021,3,interpolated,2083 -serum,Y044d30,A/Bangladesh/3210810034/2021,2,interpolated,516.4 -serum,Y044d30,A/Bangladesh/8002/2021,3,interpolated,1606 -serum,Y044d30,A/Bangladesh/8036/2021,3,interpolated,1620 -serum,Y044d30,A/Belgium/H0017/2022,3,interpolated,1.396e+04 -serum,Y044d30,A/Belgium/H0038/2022,3,interpolated,1.441e+04 -serum,Y044d30,A/Brisbane/02/2018,4,interpolated,1.326e+04 -serum,Y044d30,A/Brisbane/48/2022,3,interpolated,1525 -serum,Y044d30,A/California/07/2009,4,interpolated,8685 -serum,Y044d30,A/Chester/5355/2022,3,interpolated,1402 -serum,Y044d30,A/Cote_DIvoire/1448/2021,3,interpolated,1.962e+04 -serum,Y044d30,A/England/220200318/2022,3,interpolated,1.96e+04 -serum,Y044d30,A/Ghana/138/2020,3,interpolated,2.031e+04 -serum,Y044d30,A/Ghana/2080/2020,3,interpolated,1.858e+04 -serum,Y044d30,A/Hawaii/70/2019,4,interpolated,1.534e+04 -serum,Y044d30,A/India-PUN-NIV328484/2021,3,interpolated,1588 -serum,Y044d30,A/India-Pune-Nivcov2221170/2022,2,interpolated,1617 -serum,Y044d30,A/India/Pun-NIV312851/2021,3,interpolated,1391 -serum,Y044d30,A/Michigan/19/2021,3,interpolated,1472 -serum,Y044d30,A/Michigan/45/2015,4,interpolated,1.274e+04 -serum,Y044d30,A/Newcastle/2/2022,3,interpolated,1398 -serum,Y044d30,A/Niger/10217/2021,3,interpolated,1.169e+04 -serum,Y044d30,A/Nimes/871/2021,3,interpolated,1.706e+04 -serum,Y044d30,A/Norway/25089/2022,3,interpolated,929.4 -serum,Y044d30,A/Paris/30353/2021,3,interpolated,1.003e+04 -serum,Y044d30,A/Paris/31196/2021,3,interpolated,1.299e+04 -serum,Y044d30,A/Perth/1/2022,3,interpolated,1423 -serum,Y044d30,A/SouthAfrica/R14850/2021,3,interpolated,548.7 -serum,Y044d30,A/SouthAfrica/R16462/2021,3,interpolated,1.717e+04 -serum,Y044d30,A/Sydney/43/2022,3,interpolated,1620 -serum,Y044d30,A/Togo/0274/2021,3,interpolated,2.312e+04 -serum,Y044d30,A/Togo/0304/2021,3,interpolated,8907 -serum,Y044d30,A/Togo/845/2020,3,interpolated,1.969e+04 -serum,Y044d30,A/Utah/27/2022,3,interpolated,1595 -serum,Y044d30,A/Washington/23/2020,3,interpolated,3396 -serum,Y044d30,A/Wisconsin/588/2019,3,interpolated,1501 -serum,Y154d182,A/Bangladesh/2221/2021,3,interpolated,199.3 -serum,Y154d182,A/Bangladesh/3210810034/2021,2,interpolated,244.8 -serum,Y154d182,A/Bangladesh/8002/2021,3,interpolated,273.8 -serum,Y154d182,A/Bangladesh/8036/2021,3,interpolated,259.2 -serum,Y154d182,A/Belgium/H0017/2022,3,interpolated,1978 -serum,Y154d182,A/Belgium/H0038/2022,3,interpolated,3448 -serum,Y154d182,A/Brisbane/02/2018,4,interpolated,4279 -serum,Y154d182,A/Brisbane/48/2022,3,interpolated,251.4 -serum,Y154d182,A/California/07/2009,4,interpolated,4355 -serum,Y154d182,A/Chester/5355/2022,3,interpolated,236.8 -serum,Y154d182,A/Cote_DIvoire/1448/2021,3,interpolated,3436 -serum,Y154d182,A/England/220200318/2022,3,interpolated,2487 -serum,Y154d182,A/Ghana/138/2020,3,interpolated,2912 -serum,Y154d182,A/Ghana/2080/2020,3,interpolated,2655 -serum,Y154d182,A/Hawaii/70/2019,4,interpolated,3705 -serum,Y154d182,A/India-PUN-NIV328484/2021,3,interpolated,272.8 -serum,Y154d182,A/India-Pune-Nivcov2221170/2022,2,interpolated,165.5 -serum,Y154d182,A/India/Pun-NIV312851/2021,3,interpolated,285.9 -serum,Y154d182,A/Michigan/19/2021,3,interpolated,248.5 -serum,Y154d182,A/Michigan/45/2015,4,interpolated,6216 -serum,Y154d182,A/Newcastle/2/2022,3,interpolated,272.6 -serum,Y154d182,A/Niger/10217/2021,3,interpolated,2855 -serum,Y154d182,A/Nimes/871/2021,3,interpolated,3384 -serum,Y154d182,A/Norway/25089/2022,3,interpolated,215.8 -serum,Y154d182,A/Paris/30353/2021,3,interpolated,2317 -serum,Y154d182,A/Paris/31196/2021,3,interpolated,4817 -serum,Y154d182,A/Perth/1/2022,3,interpolated,292.4 -serum,Y154d182,A/SouthAfrica/R14850/2021,3,interpolated,226.7 -serum,Y154d182,A/SouthAfrica/R16462/2021,3,interpolated,3079 -serum,Y154d182,A/Sydney/43/2022,3,interpolated,248.9 -serum,Y154d182,A/Togo/0274/2021,3,interpolated,3440 -serum,Y154d182,A/Togo/0304/2021,3,interpolated,3511 -serum,Y154d182,A/Togo/845/2020,3,interpolated,2327 -serum,Y154d182,A/Utah/27/2022,3,interpolated,275.3 -serum,Y154d182,A/Washington/23/2020,3,interpolated,835.2 -serum,Y154d182,A/Wisconsin/588/2019,3,interpolated,1094 +group,serum,virus,titer,titer_bound,titer_sem,n_replicates,titer_as +pilot,A23038d0_r32_75K,A/Bangkok/P3599/2023,1863,interpolated,25.05,2,midpoint +pilot,A23038d0_r32_75K,A/Bangkok/P3755/2023,851.5,interpolated,540.5,3,midpoint +pilot,A23038d0_r32_75K,A/Bhutan/0006/2023,611.9,interpolated,86.66,3,midpoint +pilot,A23038d0_r32_75K,A/Bhutan/FLU-BTG-00988/2022,552,interpolated,183.8,3,midpoint +pilot,A23038d0_r32_75K,A/Brisbane/429/2023,1534,interpolated,331.1,2,midpoint +pilot,A23038d0_r32_75K,A/Busan/1301/2023,773.6,interpolated,57.66,2,midpoint +pilot,A23038d0_r32_75K,A/California/81/2023,1454,interpolated,901.2,2,midpoint +pilot,A23038d0_r32_75K,A/Cambodia/e0826360/2020_egg,8843,interpolated,1407,3,midpoint +pilot,A23038d0_r32_75K,A/Catalonia/2041146NS/2023,747,interpolated,136.9,2,midpoint +pilot,A23038d0_r32_75K,A/Catalonia/NSVH102124476/2023,655.3,interpolated,119.3,3,midpoint +pilot,A23038d0_r32_75K,A/Chipata/15-NIC-001/2023,1137,interpolated,639.8,3,midpoint +pilot,A23038d0_r32_75K,A/EHIME/50/2023,1167,interpolated,285.7,3,midpoint +pilot,A23038d0_r32_75K,A/Georgia/40/2023,1123,interpolated,345,3,midpoint +pilot,A23038d0_r32_75K,A/Hong_Kong/2671/2019,8621,interpolated,1408,3,midpoint +pilot,A23038d0_r32_75K,A/Hong_Kong/45/2019,1040,interpolated,12.96,3,midpoint +pilot,A23038d0_r32_75K,A/Hong_Kong/4801/2014,5075,interpolated,2410,2,midpoint +pilot,A23038d0_r32_75K,A/Hong_Kong/4801/2014_(15/192),1.28e+04,lower,437.4,3,midpoint +pilot,A23038d0_r32_75K,A/Jeju/1047/2023,1039,interpolated,515,2,midpoint +pilot,A23038d0_r32_75K,A/Kansas/14/2017,4041,interpolated,2384,2,midpoint +pilot,A23038d0_r32_75K,A/Krabi/THIS050/2023,3116,interpolated,2069,2,midpoint 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