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/home/bvelasco/CovidVax_DM/covidvax_DM_pygformula_chunks.py:21: DtypeWarning: Columns (8,9,10,11,12,13,14,15,16,17) have mixed types. Specify dtype option on import or set low_memory=False.
all_data = pd.read_csv('included_cohort_prep.csv')
/home/bvelasco/CovidVax_DM/covidvax_DM_pygformula_chunks.py:21: DtypeWarning: Columns (8,9,10,11,12,13,14,15,16,17) have mixed types. Specify dtype option on import or set low_memory=False.
all_data = pd.read_csv('included_cohort_prep.csv')
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03411 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05391 | 1.58061 | 0.01980 |
| Treat on Vacuna only at t1 | NA | 0.03145 | 0.92205 | -0.00266 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03095 | 0.90754 | -0.00315 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01815 | 0.53228 | -0.01595 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
0:15:28.926967
1
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3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03440 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05134 | 1.49238 | 0.01694 |
| Treat on Vacuna only at t1 | NA | 0.03263 | 0.94861 | -0.00177 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03217 | 0.93519 | -0.00223 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01906 | 0.55416 | -0.01534 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
0:28:31.604673
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3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03361 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05172 | 1.53868 | 0.01811 |
| Treat on Vacuna only at t1 | NA | 0.03106 | 0.92421 | -0.00255 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03057 | 0.90941 | -0.00304 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01928 | 0.57364 | -0.01433 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
0:39:52.270833
1
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3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03279 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05107 | 1.55713 | 0.01827 |
| Treat on Vacuna only at t1 | NA | 0.03090 | 0.94221 | -0.00190 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03043 | 0.92776 | -0.00237 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01903 | 0.58016 | -0.01377 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
0:51:32.994207
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03306 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05270 | 1.59402 | 0.01964 |
| Treat on Vacuna only at t1 | NA | 0.03096 | 0.93648 | -0.00210 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03044 | 0.92083 | -0.00262 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.02002 | 0.60567 | -0.01304 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:05:00.524377
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03266 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05188 | 1.58839 | 0.01922 |
| Treat on Vacuna only at t1 | NA | 0.03012 | 0.92211 | -0.00254 |
| Treat on Vacuna only at t1 & t2 | NA | 0.02958 | 0.90569 | -0.00308 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01919 | 0.58751 | -0.01347 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:18:32.432739
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03833 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05607 | 1.46297 | 0.01774 |
| Treat on Vacuna only at t1 | NA | 0.03634 | 0.94823 | -0.00198 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03586 | 0.93556 | -0.00247 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.02212 | 0.57715 | -0.01621 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:30:11.764343
1
2
3
start fitting parametric model.
start simulating.
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04777 | 0.20669 | 1.00000 | 0.00000 |
| Never treat | NA | 0.27182 | 1.31510 | 0.06513 |
| Treat on Vacuna only at t1 | NA | 0.20085 | 0.97176 | -0.00584 |
| Treat on Vacuna only at t1 & t2 | NA | 0.19988 | 0.96707 | -0.00681 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.19659 | 0.95114 | -0.01010 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
0:18:01.940377
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04622 | 0.19135 | 1.00000 | 0.00000 |
| Never treat | NA | 0.25451 | 1.33011 | 0.06317 |
| Treat on Vacuna only at t1 | NA | 0.18602 | 0.97218 | -0.00532 |
| Treat on Vacuna only at t1 & t2 | NA | 0.18506 | 0.96716 | -0.00628 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.18326 | 0.95774 | -0.00809 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
0:34:35.281160
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04723 | 0.19857 | 1.00000 | 0.00000 |
| Never treat | NA | 0.27268 | 1.37321 | 0.07411 |
| Treat on Vacuna only at t1 | NA | 0.19037 | 0.95869 | -0.00820 |
| Treat on Vacuna only at t1 & t2 | NA | 0.18916 | 0.95258 | -0.00942 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.18429 | 0.92808 | -0.01428 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
0:49:48.759779
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04709 | 0.20343 | 1.00000 | 0.00000 |
| Never treat | NA | 0.26586 | 1.30687 | 0.06243 |
| Treat on Vacuna only at t1 | NA | 0.19706 | 0.96870 | -0.00637 |
| Treat on Vacuna only at t1 & t2 | NA | 0.19612 | 0.96407 | -0.00731 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.19297 | 0.94860 | -0.01046 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:05:51.194120
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04745 | 0.19669 | 1.00000 | 0.00000 |
| Never treat | NA | 0.25083 | 1.27523 | 0.05414 |
| Treat on Vacuna only at t1 | NA | 0.19184 | 0.97531 | -0.00486 |
| Treat on Vacuna only at t1 & t2 | NA | 0.19103 | 0.97119 | -0.00567 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.18698 | 0.95064 | -0.00971 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:22:56.593039
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04754 | 0.20490 | 1.00000 | 0.00000 |
| Never treat | NA | 0.26465 | 1.29159 | 0.05975 |
| Treat on Vacuna only at t1 | NA | 0.19981 | 0.97517 | -0.00509 |
| Treat on Vacuna only at t1 & t2 | NA | 0.19909 | 0.97161 | -0.00582 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.19591 | 0.95610 | -0.00900 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:38:47.405880
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04763 | 0.19510 | 1.00000 | 0.00000 |
| Never treat | NA | 0.24753 | 1.26870 | 0.05242 |
| Treat on Vacuna only at t1 | NA | 0.18945 | 0.97104 | -0.00565 |
| Treat on Vacuna only at t1 & t2 | NA | 0.18861 | 0.96671 | -0.00649 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.18355 | 0.94081 | -0.01155 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:54:24.418604
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03267 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05265 | 1.61147 | 0.01998 |
| Treat on Vacuna only at t1 | NA | 0.03065 | 0.93803 | -0.00202 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03014 | 0.92248 | -0.00253 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01943 | 0.59480 | -0.01324 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:41:37.313167
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03217 | 1.00000 | 0.00000 |
| Never treat | NA | 0.05155 | 1.60262 | 0.01938 |
| Treat on Vacuna only at t1 | NA | 0.03005 | 0.93429 | -0.00211 |
| Treat on Vacuna only at t1 & t2 | NA | 0.02954 | 0.91846 | -0.00262 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01866 | 0.57999 | -0.01351 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:54:44.301783
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.03265 | 1.00000 | 0.00000 |
| Never treat | NA | 0.04991 | 1.52864 | 0.01726 |
| Treat on Vacuna only at t1 | NA | 0.03066 | 0.93902 | -0.00199 |
| Treat on Vacuna only at t1 & t2 | NA | 0.03018 | 0.92434 | -0.00247 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.01981 | 0.60678 | -0.01284 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
2:08:15.356686
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04721 | 0.19183 | 1.00000 | 0.00000 |
| Never treat | NA | 0.24941 | 1.30016 | 0.05758 |
| Treat on Vacuna only at t1 | NA | 0.18571 | 0.96808 | -0.00612 |
| Treat on Vacuna only at t1 & t2 | NA | 0.18474 | 0.96307 | -0.00708 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.18089 | 0.94300 | -0.01093 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
2:10:12.037268
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04786 | 0.19615 | 1.00000 | 0.00000 |
| Never treat | NA | 0.25070 | 1.27814 | 0.05456 |
| Treat on Vacuna only at t1 | NA | 0.19250 | 0.98140 | -0.00365 |
| Treat on Vacuna only at t1 & t2 | NA | 0.19220 | 0.97988 | -0.00395 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.18965 | 0.96689 | -0.00649 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
2:22:43.313711
1
2
3
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP risk | g-formula risk (NICE-parametric) | Risk Ratio(RR) | Risk Difference(RD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | 0.04818 | 0.19240 | 1.00000 | 0.00000 |
| Never treat | NA | 0.25288 | 1.31434 | 0.06048 |
| Treat on Vacuna only at t1 | NA | 0.18636 | 0.96860 | -0.00604 |
| Treat on Vacuna only at t1 & t2 | NA | 0.18558 | 0.96458 | -0.00682 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.18228 | 0.94742 | -0.01012 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
2:34:37.225684
/home/bvelasco/CovidVax_DM/covidvax_DM_pygformula_chunks_CCW.py:21: DtypeWarning: Columns (8,9,10,11,12,13,14,15,16,17) have mixed types. Specify dtype option on import or set low_memory=False.
all_data = pd.read_csv('included_cohort_prep.csv')
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00832 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01690 | 2.03042 | 0.00857 |
| Treat on Vacuna only at t1 | NA | 0.00806 | 0.96850 | -0.00026 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00790 | 0.94966 | -0.00042 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00592 | 0.71154 | -0.00240 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:10:38.320524
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00825 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01582 | 1.91628 | 0.00756 |
| Treat on Vacuna only at t1 | NA | 0.00800 | 0.96972 | -0.00025 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00787 | 0.95362 | -0.00038 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00543 | 0.65798 | -0.00282 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
2:19:00.249172
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00878 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01706 | 1.94305 | 0.00828 |
| Treat on Vacuna only at t1 | NA | 0.00858 | 0.97640 | -0.00021 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00843 | 0.95996 | -0.00035 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00612 | 0.69637 | -0.00267 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
3:27:55.529558
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00858 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01617 | 1.88546 | 0.00760 |
| Treat on Vacuna only at t1 | NA | 0.00839 | 0.97846 | -0.00018 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00825 | 0.96185 | -0.00033 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00552 | 0.64405 | -0.00305 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
4:36:33.461713
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00784 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01585 | 2.02086 | 0.00801 |
| Treat on Vacuna only at t1 | NA | 0.00766 | 0.97598 | -0.00019 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00755 | 0.96243 | -0.00029 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00519 | 0.66232 | -0.00265 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
5:45:57.547034
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00867 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01692 | 1.95249 | 0.00826 |
| Treat on Vacuna only at t1 | NA | 0.00847 | 0.97704 | -0.00020 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00834 | 0.96168 | -0.00033 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00574 | 0.66176 | -0.00293 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
6:54:53.099521
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00807 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01733 | 2.14718 | 0.00926 |
| Treat on Vacuna only at t1 | NA | 0.00785 | 0.97289 | -0.00022 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00771 | 0.95564 | -0.00036 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00544 | 0.67355 | -0.00264 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
8:04:22.353034
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.01241 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01945 | 1.56728 | 0.00704 |
| Treat on Vacuna only at t1 | NA | 0.01220 | 0.98323 | -0.00021 |
| Treat on Vacuna only at t1 & t2 | NA | 0.01205 | 0.97081 | -0.00036 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00790 | 0.63679 | -0.00451 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
9:13:49.074355
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.01030 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01942 | 1.88557 | 0.00912 |
| Treat on Vacuna only at t1 | NA | 0.01008 | 0.97917 | -0.00021 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00994 | 0.96529 | -0.00036 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00732 | 0.71037 | -0.00298 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
10:23:44.437780
start fitting parametric model.
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00870 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01519 | 1.74599 | 0.00649 |
| Treat on Vacuna only at t1 | NA | 0.00852 | 0.97909 | -0.00018 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00839 | 0.96363 | -0.00032 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00628 | 0.72223 | -0.00242 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
11:33:04.631482
Traceback (most recent call last):
File "/home/bvelasco/CovidVax_DM/covidvax_DM_pygformula_chunks_CCW.py", line 21, in <module>
all_data = pd.read_csv('included_cohort_prep.csv')
File "/home/bvelasco/miniconda3/envs/python3.10/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/bvelasco/miniconda3/envs/python3.10/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 626, in _read
return parser.read(nrows)
File "/home/bvelasco/miniconda3/envs/python3.10/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1923, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/home/bvelasco/miniconda3/envs/python3.10/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read
chunks = self._reader.read_low_memory(nrows)
File "parsers.pyx", line 838, in pandas._libs.parsers.TextReader.read_low_memory
File "parsers.pyx", line 905, in pandas._libs.parsers.TextReader._read_rows
File "parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows
File "parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
File "parsers.pyx", line 2061, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Calling read(nbytes) on source failed. Try engine='python'.
/home/bvelasco/CovidVax_DM/covidvax_DM_pygformula_chunks_CCW.py:21: DtypeWarning: Columns (8,9,10,11,12,13,14,15,16,17) have mixed types. Specify dtype option on import or set low_memory=False.
all_data = pd.read_csv('included_cohort_prep.csv')
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
0 1002069_0 0 NaN 0.0 68.072280 0 ... 0.00 0.00 0.0 0.000 0.0 1.759304
10 84264993_0 0 NaN 0.0 26.249112 0 ... 0.00 0.00 0.0 0.000 0.0 1.257663
11 11149112_0 0 NaN 0.0 41.242894 0 ... 0.00 0.00 0.0 0.000 0.0 2.274273
14 12444300_0 0 NaN 0.0 47.634481 0 ... 0.00 0.00 0.0 0.000 0.0 1.478081
15 11965735_0 0 NaN 0.0 19.547380 0 ... 0.00 0.00 0.0 0.000 0.0 0.741186
... ... ... ... ... ... ... ... ... ... ... ... ... ...
8998854 6095091_3 2 NaN NaN 43.480987 3 ... 26.20 81.09 0.0 14.201 1.0 1.296828
8998857 2071651_3 2 NaN NaN 69.323738 3 ... 35.60 77.00 1.0 15.776 1.0 1.037120
8998866 1278436_3 2 NaN NaN 53.732368 3 ... 22.23 87.00 0.0 15.932 1.0 1.019606
8998868 304806_3 2 NaN NaN 37.769640 3 ... 22.93 70.00 0.0 5.605 1.0 0.790579
8998871 1288809_3 2 NaN NaN 82.527101 3 ... 19.69 87.00 0.0 0.071 1.0 0.916682
[3917450 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 1002069_0 2 NaN NaN 68.072280 0 ... 18.860000 87.779745 0.0 2.346001 0.0 1.233250
5999249 7198410_0 2 NaN NaN 36.567237 3 ... 32.070000 102.710000 0.0 5.998000 1.0 0.914236
5999250 10095176_0 2 NaN NaN 55.537065 2 ... 21.870000 86.698320 1.0 0.000000 1.0 1.085677
5999251 2857021_0 2 NaN NaN 45.359540 2 ... 15.480000 89.400000 1.0 1.921000 1.0 1.038452
5999252 7446951_0 2 NaN NaN 31.915138 2 ... 17.780000 83.006954 0.0 0.402000 1.0 1.063892
... ... ... ... .. ... ... ... ... ... ... ... ... ...
8998867 1760312_3 2 NaN NaN 45.359540 1 ... 26.470000 90.000000 0.0 1.365000 0.0 0.914965
8998868 304806_3 2 NaN NaN 37.769640 3 ... 22.930000 70.000000 0.0 5.605000 1.0 0.790579
8998869 83927125_3 2 NaN NaN 51.297359 0 ... 21.340559 88.973570 0.0 2.674268 0.0 1.348177
8998870 6473275_3 2 NaN NaN 62.486417 2 ... 33.570000 68.000000 0.0 15.346000 1.0 1.010865
8998871 1288809_3 2 NaN NaN 82.527101 3 ... 19.690000 87.000000 0.0 0.071000 1.0 0.916682
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00742 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01218 | 1.64070 | 0.00476 |
| Treat on Vacuna only at t1 | NA | 0.00724 | 0.97514 | -0.00018 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00718 | 0.96689 | -0.00025 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00387 | 0.52113 | -0.00355 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
1:07:54.140136
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat ... lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
4 39524765_0 0 NaN 0.0 41.999450 ... 0.000000 0.0 0.00000 0.0 1.162744
5 62764781_0 0 NaN 0.0 53.975559 ... 0.000000 0.0 0.00000 0.0 1.090205
14 4766781_0 0 2006-08-24T00:00:00.000Z 1.0 50.775860 ... 0.000000 0.0 0.00000 0.0 2.073829
19 23134833_0 0 NaN 0.0 49.422524 ... 0.000000 0.0 0.00000 0.0 1.082607
21 48794767_0 0 NaN 0.0 47.304757 ... 0.000000 0.0 0.00000 0.0 1.320489
... ... ... ... ... ... ... ... ... ... ... ...
8998858 4171363_3 2 NaN NaN 51.264958 ... 99.000000 0.0 12.35300 1.0 1.250753
8998861 1610195_3 2 NaN NaN 51.033958 ... 104.000000 0.0 9.54000 1.0 1.163018
8998866 2337866_3 2 NaN NaN 46.559923 ... 91.000000 0.0 2.02000 1.0 0.947262
8998869 10677069_3 2 NaN NaN 2.996013 ... 84.939767 0.0 3.03400 1.0 1.042687
8998870 83537425_3 2 NaN NaN 38.275197 ... 87.507470 0.0 2.62207 1.0 0.972470
[3915066 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 2696599_0 2 NaN NaN 30.821807 2 ... 24.780000 91.000000 0.0 5.89200 1.0 1.011320
5999249 1764578_0 2 NaN NaN 52.048451 3 ... 36.080000 98.507581 0.0 36.99200 1.0 0.886049
5999250 1003104_0 2 NaN NaN 39.049733 3 ... 30.780000 86.000000 0.0 4.92700 1.0 0.862434
5999251 4174758_0 2 NaN NaN 1.445904 2 ... 26.490000 85.000000 0.0 14.44000 1.0 1.099532
5999252 39524765_0 2 NaN NaN 41.999450 0 ... 27.969658 98.186887 0.0 0.00000 0.0 0.854461
... ... ... ... .. ... ... ... ... ... ... ... ... ...
8998867 4774105_3 2 NaN NaN 36.797557 2 ... 25.010000 82.890000 0.0 3.06800 1.0 0.939161
8998868 9617080_3 2 NaN NaN 40.088479 1 ... 26.440000 87.387415 0.0 7.19800 0.0 1.009452
8998869 10677069_3 2 NaN NaN 2.996013 3 ... 25.319878 84.939767 0.0 3.03400 1.0 1.042687
8998870 83537425_3 2 NaN NaN 38.275197 3 ... 23.771658 87.507470 0.0 2.62207 1.0 0.972470
8998871 2204694_3 2 NaN NaN 50.919598 2 ... 17.670000 141.000000 0.0 1.13800 1.0 1.092915
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00472 | 1.00000 | 0.00000 |
| Never treat | NA | 0.00845 | 1.78926 | 0.00373 |
| Treat on Vacuna only at t1 | NA | 0.00449 | 0.95196 | -0.00023 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00450 | 0.95308 | -0.00022 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00334 | 0.70766 | -0.00138 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
2:14:16.951250
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
9 84033749_0 0 NaN 0.0 56.274057 0 ... 0.00 0.000000 0.0 0.000 0.0 0.806554
12 82386041_0 0 NaN 0.0 37.314869 0 ... 0.00 0.000000 0.0 0.000 0.0 1.708457
22 79804792_0 0 NaN 0.0 44.274294 0 ... 0.00 0.000000 0.0 0.000 0.0 0.893888
23 11805977_0 0 NaN 0.0 32.568911 0 ... 0.00 0.000000 0.0 0.000 0.0 1.041191
24 349668_0 0 NaN 0.0 36.218757 0 ... 0.00 0.000000 0.0 0.000 0.0 1.491487
... ... ... ... ... ... ... ... ... ... ... ... ... ...
8998858 10674572_3 2 NaN NaN 22.544616 3 ... 30.99 88.159342 0.0 1.822 1.0 1.102352
8998861 9749116_3 2 NaN NaN 36.619364 3 ... 32.25 102.000000 0.0 4.023 1.0 1.123546
8998862 1757504_3 2 NaN NaN 46.898152 3 ... 26.45 93.700000 0.0 4.596 1.0 0.996165
8998868 1257220_3 2 NaN NaN 19.174582 3 ... 25.56 99.000000 0.0 15.735 1.0 0.837367
8998869 1889862_3 2 NaN NaN 43.456184 3 ... 27.66 84.690000 0.0 18.435 1.0 1.060854
[3916329 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 109590_0 2 NaN NaN 31.915138 1 ... 21.610000 75.680000 1.0 15.206 0.0 0.837554
5999249 5795818_0 2 NaN NaN 36.218757 1 ... 20.630000 83.537100 0.0 1.468 0.0 0.899954
5999250 5738027_0 2 NaN NaN 8.776737 3 ... 23.111184 83.703062 0.0 0.000 1.0 1.002825
5999251 8607338_0 2 NaN NaN 39.815150 2 ... 33.180000 88.495933 0.0 4.420 1.0 1.056451
5999252 10524111_0 2 NaN NaN 19.213225 2 ... 15.540000 78.840721 0.0 0.798 1.0 1.158888
... ... ... ... .. ... ... ... ... ... ... ... ... ...
8998867 1346940_3 2 NaN NaN 32.199623 1 ... 25.416602 82.134852 0.0 0.000 0.0 0.990332
8998868 1257220_3 2 NaN NaN 19.174582 3 ... 25.560000 99.000000 0.0 15.735 1.0 0.837367
8998869 1889862_3 2 NaN NaN 43.456184 3 ... 27.660000 84.690000 0.0 18.435 1.0 1.060854
8998870 25824757_3 2 NaN NaN 44.908957 0 ... 16.950000 90.158333 0.0 0.000 0.0 0.966075
8998871 992045_3 2 NaN NaN 36.083087 2 ... 25.716996 73.000000 0.0 3.503 1.0 1.115426
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00739 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01026 | 1.38829 | 0.00287 |
| Treat on Vacuna only at t1 | NA | 0.00707 | 0.95581 | -0.00033 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00698 | 0.94487 | -0.00041 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00365 | 0.49360 | -0.00374 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
3:21:16.030400
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat ... lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
2 10700603_0 0 2010-02-23T00:00:00.000Z 1.0 41.018410 ... 0.000000 0.0 0.000 0.0 2.454141
6 73464771_0 0 NaN 0.0 41.999450 ... 0.000000 0.0 0.000 0.0 0.868769
11 13524436_0 0 NaN 0.0 29.993543 ... 0.000000 0.0 0.000 0.0 0.930819
32 19334339_0 0 NaN 0.0 51.141867 ... 0.000000 0.0 0.000 0.0 0.819782
36 24085121_0 0 NaN 0.0 40.828608 ... 0.000000 0.0 0.000 0.0 0.878733
... ... ... ... ... ... ... ... ... ... ... ...
8998861 9658942_3 2 NaN NaN 10.679897 ... 96.000000 0.0 6.683 1.0 1.156486
8998863 7161872_3 2 NaN NaN 41.242894 ... 90.000000 0.0 14.367 1.0 0.865503
8998865 829878_3 2 NaN NaN NaN ... 88.300000 0.0 5.370 1.0 1.165058
8998869 653902_3 2 NaN NaN 43.480987 ... 87.643696 0.0 23.382 1.0 0.951559
8998870 4417487_3 2 NaN NaN 40.376925 ... 82.000000 0.0 2.278 1.0 0.920642
[3917378 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat ... lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 5955359_0 2 NaN NaN NaN ... 91.703331 0.0 3.522 1.0 1.119131
5999249 7172382_0 2 NaN NaN 48.805211 ... 98.000000 0.0 4.640 1.0 0.886049
5999250 10700603_0 2 2010-02-23T00:00:00.000Z NaN 41.018410 ... 83.351273 0.0 7.553 0.0 0.884672
5999251 5511508_0 2 NaN NaN 64.880552 ... 106.320000 0.0 0.699 1.0 1.081250
5999252 1917621_0 2 NaN NaN 41.209182 ... 106.000000 0.0 16.263 1.0 0.898644
... ... ... ... .. ... ... ... ... ... ... ...
8998867 6395697_3 2 NaN NaN 35.041674 ... 70.639953 0.0 2.636 1.0 1.131166
8998868 10840514_3 2 NaN NaN NaN ... 81.450000 0.0 0.365 0.0 1.206078
8998869 653902_3 2 NaN NaN 43.480987 ... 87.643696 0.0 23.382 1.0 0.951559
8998870 4417487_3 2 NaN NaN 40.376925 ... 82.000000 0.0 2.278 1.0 0.920642
8998871 12409461_3 2 NaN NaN 29.578433 ... 78.719433 0.0 1.885 0.0 1.224031
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00539 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01288 | 2.38794 | 0.00748 |
| Treat on Vacuna only at t1 | NA | 0.00518 | 0.96111 | -0.00021 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00511 | 0.94685 | -0.00029 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00345 | 0.63908 | -0.00195 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
4:28:02.160154
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
2 5706639_0 0 NaN 0.0 51.141867 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.036811
3 10236108_0 0 NaN 0.0 41.209182 0 ... 0.000000 0.000000 0.0 0.000 0.0 0.816958
7 27524757_0 0 NaN 0.0 50.627094 0 ... 0.000000 0.000000 0.0 0.000 0.0 2.201048
13 47984788_0 0 NaN 0.0 32.199623 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.004749
25 83554164_0 0 NaN 0.0 33.723876 0 ... 0.000000 0.000000 0.0 0.000 0.0 0.920826
... ... ... ... ... ... ... ... ... ... ... ... ... ...
8998866 17683849_3 2 NaN NaN 36.619364 3 ... 22.291764 83.549021 0.0 3.066 1.0 1.032648
8998867 2997997_3 2 NaN NaN 36.816054 3 ... 26.510000 104.520000 0.0 3.762 1.0 1.070571
8998869 1823804_3 2 NaN NaN 44.402963 3 ... 28.970000 112.000000 0.0 3.209 1.0 1.008169
8998870 5843767_3 2 NaN NaN 26.249112 3 ... 20.247390 85.261060 0.0 2.720 1.0 0.961881
8998871 9522738_3 2 NaN NaN 18.395778 3 ... 19.130000 88.300000 0.0 0.000 1.0 0.909074
[3916321 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 10384670_0 2 NaN NaN 15.805092 2 ... 27.14000 76.00000 0.0 5.025 1.0 1.082138
5999249 2001727_0 2 NaN NaN 29.305315 2 ... 19.63000 87.00000 0.0 1.512 1.0 1.020250
5999250 5706639_0 2 NaN NaN 51.141867 0 ... 31.25000 85.00000 0.0 1.744 0.0 1.204538
5999251 10236108_0 2 NaN NaN 41.209182 0 ... 28.30000 73.00000 0.0 1.532 0.0 0.715979
5999252 10206657_0 2 NaN NaN NaN 2 ... 20.51000 75.00000 0.0 6.920 1.0 1.128824
... ... ... ... .. ... ... ... ... ... ... ... ... ...
8998867 2997997_3 2 NaN NaN 36.816054 3 ... 26.51000 104.52000 0.0 3.762 1.0 1.070571
8998868 10768851_3 2 NaN NaN 31.915138 2 ... 23.56000 81.09000 0.0 3.966 1.0 1.046843
8998869 1823804_3 2 NaN NaN 44.402963 3 ... 28.97000 112.00000 0.0 3.209 1.0 1.008169
8998870 5843767_3 2 NaN NaN 26.249112 3 ... 20.24739 85.26106 0.0 2.720 1.0 0.961881
8998871 9522738_3 2 NaN NaN 18.395778 3 ... 19.13000 88.30000 0.0 0.000 1.0 0.909074
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00536 | 1.00000 | 0.00000 |
| Never treat | NA | 0.00975 | 1.81903 | 0.00439 |
| Treat on Vacuna only at t1 | NA | 0.00515 | 0.96146 | -0.00021 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00510 | 0.95237 | -0.00026 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00379 | 0.70698 | -0.00157 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
5:35:05.602885
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
3 84100084_0 0 NaN 0.0 53.107634 0 ... 0.000000 0.000000 0.0 0.000 0.0 0.917336
4 11577803_0 0 NaN 0.0 75.169623 0 ... 0.000000 0.000000 0.0 0.000 0.0 2.138845
6 11653094_0 0 NaN 0.0 41.843877 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.453955
8 4302017_0 0 NaN 0.0 44.329413 0 ... 0.000000 0.000000 0.0 0.000 0.0 2.009050
13 40364797_0 0 NaN 0.0 17.274492 0 ... 0.000000 0.000000 0.0 0.000 0.0 0.994973
... ... ... ... ... ... ... ... ... ... ... ... ... ...
8998863 430739_3 2 NaN NaN 57.039588 3 ... 28.800000 90.100000 0.0 2.546 1.0 0.831786
8998864 6258491_3 2 NaN NaN 43.524173 3 ... 30.790000 89.000000 0.0 15.008 1.0 1.122047
8998865 6609741_3 2 NaN NaN 57.394454 3 ... 27.012348 90.397470 0.0 0.000 1.0 1.024521
8998868 29524946_3 2 NaN NaN 44.562579 3 ... 29.110854 91.883793 0.0 0.000 1.0 0.766684
8998870 687680_3 2 NaN NaN 31.523682 3 ... 28.830000 73.880000 0.0 17.416 1.0 0.919214
[3915727 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat ... lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 4100683_0 2 NaN NaN 25.622485 ... 89.000000 0.0 0.00000 1.0 1.004531
5999249 1958209_0 2 NaN NaN NaN ... 85.000000 0.0 4.67000 1.0 0.918551
5999250 21463888_0 2 NaN NaN 68.484286 ... 84.471813 1.0 0.00000 1.0 1.026325
5999251 84100084_0 2 NaN NaN 53.107634 ... 94.141319 0.0 15.18335 0.0 0.712210
5999252 11577803_0 2 NaN NaN 75.169623 ... 78.888068 0.0 1.66400 0.0 0.913446
... ... ... ... .. ... ... ... ... ... ... ...
8998867 11295816_3 2 NaN NaN 36.903946 ... 78.580685 0.0 0.00000 0.0 0.982651
8998868 29524946_3 2 NaN NaN 44.562579 ... 91.883793 0.0 0.00000 1.0 0.766684
8998869 5759350_3 2 2012-06-08T00:00:00.000Z NaN 46.571176 ... 87.097461 0.0 9.06100 0.0 1.191218
8998870 687680_3 2 NaN NaN 31.523682 ... 73.880000 0.0 17.41600 1.0 0.919214
8998871 11706096_3 2 NaN NaN 75.169623 ... 78.174203 0.0 4.94700 1.0 1.150404
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00500 | 1.00000 | 0.00000 |
| Never treat | NA | 0.00924 | 1.84780 | 0.00424 |
| Treat on Vacuna only at t1 | NA | 0.00476 | 0.95271 | -0.00024 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00470 | 0.93995 | -0.00030 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00361 | 0.72123 | -0.00139 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
6:42:07.846622
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
2 3265114_0 0 NaN 0.0 25.155199 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.034205
3 987819_0 0 NaN 0.0 52.521250 0 ... 0.000000 0.000000 0.0 0.000 0.0 2.280871
16 26004889_0 0 NaN 0.0 59.182157 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.113215
17 16643971_0 0 NaN 0.0 52.048451 0 ... 0.000000 0.000000 0.0 0.000 0.0 0.823474
22 84122765_0 0 NaN 0.0 41.999450 0 ... 0.000000 0.000000 0.0 0.000 0.0 0.893888
... ... ... ... ... ... ... ... ... ... ... ... ... ...
8998864 10786902_3 2 NaN NaN 45.240799 3 ... 26.170000 84.690000 0.0 0.365 1.0 1.032984
8998865 2967645_3 2 NaN NaN 49.671826 3 ... 25.450155 77.000000 0.0 2.383 1.0 1.140553
8998869 10894824_3 2 NaN NaN 59.182157 3 ... 26.840000 88.000000 0.0 3.477 1.0 0.938897
8998870 2756630_3 2 NaN NaN 34.557718 3 ... 32.490000 86.500000 0.0 2.064 1.0 0.995247
8998871 4597412_3 2 NaN NaN 13.297067 3 ... 21.670000 81.903661 0.0 1.906 1.0 0.958783
[3916003 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat ... lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 2333130_0 2 NaN NaN 62.486417 ... 83.000000 0.0 0.000000 1.0 1.108995
5999249 6235631_0 2 NaN NaN 3.302572 ... 97.000000 0.0 5.147000 1.0 0.928070
5999250 3265114_0 2 NaN NaN 25.155199 ... 86.398306 0.0 4.178000 0.0 1.165889
5999251 987819_0 2 NaN NaN 52.521250 ... 88.000000 0.0 4.816648 0.0 0.785999
5999252 1459115_0 2 2022-04-17T00:00:00.000Z NaN 82.527101 ... 104.000000 0.0 25.506000 0.0 1.266958
... ... ... ... .. ... ... ... ... ... ... ...
8998867 7091107_3 2 NaN NaN 2.996013 ... 80.526461 1.0 0.000000 1.0 1.048776
8998868 16913964_3 2 NaN NaN 18.650238 ... 83.204342 1.0 1.748000 1.0 1.075356
8998869 10894824_3 2 NaN NaN 59.182157 ... 88.000000 0.0 3.477000 1.0 0.938897
8998870 2756630_3 2 NaN NaN 34.557718 ... 86.500000 0.0 2.064000 1.0 0.995247
8998871 4597412_3 2 NaN NaN 13.297067 ... 81.903661 0.0 1.906000 1.0 0.958783
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00458 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01054 | 2.30172 | 0.00596 |
| Treat on Vacuna only at t1 | NA | 0.00433 | 0.94609 | -0.00025 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00427 | 0.93363 | -0.00030 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00326 | 0.71175 | -0.00132 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
7:49:14.889359
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat ... lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
0 8917547_0 0 NaN 0.0 36.816054 ... 0.000000 0.0 0.000 0.0 1.779895
7 1811619_0 0 NaN 0.0 8.776737 ... 0.000000 0.0 0.000 0.0 1.872249
19 83949963_0 0 NaN 0.0 15.329363 ... 0.000000 0.0 0.000 0.0 0.867021
26 84031776_0 0 NaN 0.0 19.174582 ... 0.000000 0.0 0.000 0.0 1.055051
27 15844227_0 0 NaN 0.0 18.395778 ... 0.000000 0.0 0.000 0.0 2.487188
... ... ... ... ... ... ... ... ... ... ... ...
8998861 4118602_3 2 NaN NaN 6.810611 ... 84.211508 0.0 0.000 1.0 1.093049
8998863 4112018_3 2 2022-05-02T00:00:00.000Z NaN 54.872911 ... 101.840835 0.0 10.192 1.0 0.920464
8998868 3586335_3 2 NaN NaN 42.341641 ... 72.000000 0.0 4.126 1.0 0.860470
8998869 282462_3 2 NaN NaN 47.195426 ... 97.000000 0.0 18.401 1.0 1.108562
8998870 2354906_3 2 NaN NaN 20.328464 ... 94.000000 0.0 2.035 1.0 0.953795
[3918027 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 8917547_0 2 NaN NaN 36.816054 0 ... 27.300000 90.000000 0.0 5.546 0.0 1.153465
5999249 2179593_0 2 NaN NaN 18.650238 2 ... 22.220000 83.866115 0.0 0.141 1.0 0.945792
5999250 6128492_0 2 NaN NaN 23.707180 2 ... 21.150000 83.703639 0.0 12.553 1.0 1.091593
5999251 1423688_0 2 NaN NaN 38.524903 3 ... 32.560000 96.000000 0.0 3.092 1.0 1.103389
5999252 10203457_0 2 NaN NaN 49.502202 3 ... 19.370000 81.143318 0.0 1.044 1.0 0.749997
... ... ... ... .. ... ... ... ... ... ... ... ... ...
8998867 1426615_3 2 NaN NaN 32.959882 2 ... 23.384703 83.673634 1.0 1.065 1.0 1.040058
8998868 3586335_3 2 NaN NaN 42.341641 3 ... 23.120000 72.000000 0.0 4.126 1.0 0.860470
8998869 282462_3 2 NaN NaN 47.195426 3 ... 27.380000 97.000000 0.0 18.401 1.0 1.108562
8998870 2354906_3 2 NaN NaN 20.328464 3 ... 21.080000 94.000000 0.0 2.035 1.0 0.953795
8998871 5202804_3 2 NaN NaN 48.805211 2 ... 20.360000 69.000000 0.0 3.171 1.0 1.031867
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00558 | 1.00000 | 0.00000 |
| Never treat | NA | 0.00904 | 1.62017 | 0.00346 |
| Treat on Vacuna only at t1 | NA | 0.00537 | 0.96215 | -0.00021 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00528 | 0.94705 | -0.00030 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00482 | 0.86501 | -0.00075 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
8:56:24.005785
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
10 11212922_0 0 NaN 0.0 54.872911 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.027188
15 12681394_0 0 NaN 0.0 41.541235 0 ... 0.000000 0.000000 0.0 0.000 0.0 0.748919
17 12765566_0 0 NaN 0.0 41.628868 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.705047
20 39434714_0 0 NaN 0.0 15.329363 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.045886
22 42164750_0 0 NaN 0.0 43.524173 0 ... 0.000000 0.000000 0.0 0.000 0.0 1.092523
... ... ... ... ... ... ... ... ... ... ... ... ... ...
8998855 1101214_3 2 NaN NaN 0.000000 3 ... 30.600000 88.471310 0.0 15.079 1.0 1.070767
8998863 17964590_3 2 NaN NaN 72.281023 3 ... 24.145704 88.966446 0.0 4.655 1.0 0.857796
8998865 3529376_3 2 NaN NaN 41.434054 3 ... 35.430000 103.000000 0.0 20.372 1.0 1.098275
8998868 423958_3 2 NaN NaN 13.297067 3 ... 23.930000 81.951680 0.0 0.000 1.0 0.766684
8998870 5686101_3 2 NaN NaN 41.792720 3 ... 34.000000 90.817686 0.0 7.546 1.0 0.958719
[3916936 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat ... lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 9748985_0 2 NaN NaN 56.274057 ... 81.000000 0.0 5.216000 1.0 1.060484
5999249 414578_0 2 NaN NaN 43.766425 ... 73.340000 0.0 2.532000 1.0 1.012342
5999250 10913489_0 2 2022-09-05T00:00:00.000Z NaN 31.523682 ... 93.700000 0.0 4.518000 0.0 0.790654
5999251 7703730_0 2 NaN NaN 36.135603 ... 77.490000 0.0 3.609000 1.0 1.136769
5999252 5253690_0 2 NaN NaN 41.287988 ... 93.000000 0.0 6.118000 1.0 0.918697
... ... ... ... .. ... ... ... ... ... ... ...
8998867 84013733_3 2 NaN NaN 44.738977 ... 86.904680 0.0 1.358326 0.0 0.905138
8998868 423958_3 2 NaN NaN 13.297067 ... 81.951680 0.0 0.000000 1.0 0.766684
8998869 64114822_3 2 NaN NaN 45.690671 ... 102.221775 0.0 3.864140 0.0 1.058220
8998870 5686101_3 2 NaN NaN 41.792720 ... 90.817686 0.0 7.546000 1.0 0.958719
8998871 11120809_3 2 NaN NaN 52.107531 ... 82.259225 1.0 0.000000 1.0 1.159536
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00551 | 1.00000 | 0.00000 |
| Never treat | NA | 0.01063 | 1.92988 | 0.00512 |
| Treat on Vacuna only at t1 | NA | 0.00526 | 0.95454 | -0.00025 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00515 | 0.93450 | -0.00036 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00396 | 0.71886 | -0.00155 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
10:03:31.534993
start fitting parametric model.
(8998872, 58)
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
3 11685756_0 0 NaN 0.0 40.350748 0 ... 0.00 0.000000 0.0 0.000 0.0 2.026328
4 83730826_0 0 NaN 0.0 44.317028 0 ... 0.00 0.000000 0.0 0.000 0.0 1.076277
5 9591873_0 0 NaN 0.0 NaN 0 ... 0.00 0.000000 0.0 0.000 0.0 1.136463
16 17675075_0 0 NaN 0.0 46.960109 0 ... 0.00 0.000000 0.0 0.000 0.0 1.275136
19 10249198_0 0 NaN 0.0 44.738977 0 ... 0.00 0.000000 0.0 0.000 0.0 2.734317
... ... ... ... ... ... ... ... ... ... ... ... ... ...
8998861 9751200_3 2 NaN NaN 32.685987 3 ... 28.74 84.000000 0.0 5.335 1.0 1.146465
8998863 2297976_3 2 NaN NaN 45.845873 3 ... 21.00 84.093662 0.0 0.000 1.0 0.941870
8998864 6914896_3 2 NaN NaN 10.679897 3 ... 17.25 82.000000 0.0 16.778 1.0 1.118926
8998866 11087192_3 2 NaN NaN 33.746835 3 ... 22.17 87.743500 0.0 2.076 1.0 1.065287
8998868 2476727_3 2 NaN NaN 23.703575 3 ... 32.05 76.000000 0.0 7.299 1.0 0.905520
[3918739 rows x 58 columns]
NIA time DATA_DM_min DM ISC reescalat N_vaccine_total ... lag1_test_res_imc_ lag1_test_res_bg_ lag1_test_res_covid_ lag1_test_res_gma_ lag1_Vacuna weights_CCW
5999248 5990654_0 2 NaN NaN 40.088479 2 ... 27.074556 89.333594 0.0 1.357000 1.0 1.157934
5999249 5790761_0 2 NaN NaN 35.041674 3 ... 32.860000 92.000000 0.0 11.318000 1.0 1.089235
5999250 4375730_0 2 NaN NaN 29.024031 2 ... 27.513859 89.320670 0.0 4.406000 1.0 1.083093
5999251 11685756_0 2 NaN NaN 40.350748 0 ... 17.310000 100.000000 0.0 0.178000 0.0 0.807850
5999252 83730826_0 2 NaN NaN 44.317028 0 ... 13.724753 153.740442 0.0 4.286305 0.0 1.020430
... ... ... ... .. ... ... ... ... ... ... ... ... ...
8998867 10079235_3 2 NaN NaN 49.502202 2 ... 18.560000 80.841527 0.0 0.000000 1.0 0.930198
8998868 2476727_3 2 NaN NaN 23.703575 3 ... 32.050000 76.000000 0.0 7.299000 1.0 0.905520
8998869 10497693_3 2 NaN NaN 43.456184 2 ... 26.130000 86.500000 0.0 6.501000 1.0 0.708540
8998870 10121150_3 2 NaN NaN 34.557718 2 ... 19.370000 87.545446 0.0 1.176000 1.0 1.002975
8998871 2060715_3 2 NaN NaN 35.863082 2 ... 20.700000 80.000000 0.0 0.000000 1.0 1.154970
[2999624 rows x 58 columns]
(2249718, 58)
start simulating.
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Intervention | NP mean | g-formula mean (NICE-parametric) | Mean Ratio(MR) | Mean Difference(MD) |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
| Natural course(ref) | nan | 0.00471 | 1.00000 | 0.00000 |
| Never treat | NA | 0.00914 | 1.94049 | 0.00443 |
| Treat on Vacuna only at t1 | NA | 0.00450 | 0.95598 | -0.00021 |
| Treat on Vacuna only at t1 & t2 | NA | 0.00451 | 0.95617 | -0.00021 |
| Treat on Vacuna at t1, t2 & t3 | NA | 0.00340 | 0.72167 | -0.00131 |
+---------------------------------+---------+----------------------------------+----------------+---------------------+
11:10:32.234475
/home/bvelasco/CovidVax_DM/covidvax_DM_pygformula_chunks_CCW.py:21: DtypeWarning: Columns (8,9,10,11,12,13,14,15,16,17) have mixed types. Specify dtype option on import or set low_memory=False.
all_data = pd.read_csv('included_cohort_prep.csv')
start fitting parametric model.
start simulating.
0 0.00
1 0.16
2 0.04
3 0.26
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...
2999619 0.06
2999620 0.02
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Length: 2999624, dtype: float64
0 0.02
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Length: 2999624, dtype: float64
0 0.00
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