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prediction results for question 1
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jreps committed Mar 29, 2020
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13 changes: 13 additions & 0 deletions Covid19PredictingHospitalizationInFluPatients/PLPViewer.Rproj
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Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX
40 changes: 40 additions & 0 deletions Covid19PredictingHospitalizationInFluPatients/data/Analysis_1/plpLog.txt
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2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_1
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction CohortID: 5894
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction OutcomeID: 5892
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction Cohort size: 150000
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction Covariates: 31917
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction Population size: 150000
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction Cases: 6712
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction splitSeed: 6118764
2020-03-28 23:07:48 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead.
2020-03-28 23:07:48 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-03-28 23:07:49 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 37500 test cases and 112500 train cases (37500, 37500, 37500)
2020-03-28 23:07:49 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-03-28 23:08:34 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-03-28 23:13:04 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-03-28 23:13:04 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-03-28 23:13:04 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 4.75 mins
2020-03-28 23:13:04 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-03-28 23:13:04 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-03-28 23:13:15 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 4.52 secs
2020-03-28 23:13:27 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 1.41 secs
2020-03-28 23:13:27 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-03-28 23:13:28 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 87.34
2020-03-28 23:13:28 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 26.61
2020-03-28 23:13:28 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.04
2020-03-28 23:13:38 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.08 intercept: -0.00
2020-03-28 23:13:41 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.27
2020-03-28 23:13:41 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-03-28 23:13:41 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 85.22
2020-03-28 23:13:41 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 22.36
2020-03-28 23:13:41 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.04
2020-03-28 23:13:48 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.95 intercept: 0.00
2020-03-28 23:13:49 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.22
2020-03-28 23:13:49 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 23:13:49
2020-03-28 23:13:49 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-03-28 23:14:59 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 23:14:59
2020-03-28 23:14:59 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-03-28 23:15:02 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_1\plpResult
2020-03-28 23:15:02 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_1/plplog.txt
2020-03-28 23:15:02 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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40 changes: 40 additions & 0 deletions Covid19PredictingHospitalizationInFluPatients/data/Analysis_2/plpLog.txt
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2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_2
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction CohortID: 5894
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction OutcomeID: 5893
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction Cohort size: 150000
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction Covariates: 31917
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction Population size: 150000
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction Cases: 10468
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction splitSeed: -5092062
2020-03-28 23:16:22 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead.
2020-03-28 23:16:22 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-03-28 23:16:23 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 37500 test cases and 112500 train cases (37500, 37500, 37500)
2020-03-28 23:16:23 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-03-28 23:17:08 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-03-28 23:21:15 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-03-28 23:21:15 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-03-28 23:21:15 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 4.37 mins
2020-03-28 23:21:15 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-03-28 23:21:15 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-03-28 23:21:26 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 5.13 secs
2020-03-28 23:21:38 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 1.55 secs
2020-03-28 23:21:38 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-03-28 23:21:39 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 88.92
2020-03-28 23:21:39 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 40.81
2020-03-28 23:21:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.05
2020-03-28 23:21:49 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.06 intercept: -0.00
2020-03-28 23:21:51 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.41
2020-03-28 23:21:51 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-03-28 23:21:52 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 87.21
2020-03-28 23:21:52 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 35.42
2020-03-28 23:21:52 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.05
2020-03-28 23:21:59 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.96 intercept: 0.00
2020-03-28 23:22:00 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.35
2020-03-28 23:22:00 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 23:22:00
2020-03-28 23:22:00 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-03-28 23:23:03 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 23:23:03
2020-03-28 23:23:03 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_2\plpResult
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_2/plplog.txt
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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40 changes: 40 additions & 0 deletions Covid19PredictingHospitalizationInFluPatients/data/Analysis_3/plpLog.txt
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2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_3
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction CohortID: 5894
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction OutcomeID: 5892
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction Cohort size: 150000
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction Covariates: 18
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction Population size: 150000
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction Cases: 6712
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction splitSeed: 1710568
2020-03-28 23:16:00 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead.
2020-03-28 23:16:00 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-03-28 23:16:01 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 37500 test cases and 112500 train cases (37500, 37500, 37500)
2020-03-28 23:16:01 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-03-28 23:16:02 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-03-28 23:16:08 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-03-28 23:16:08 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-03-28 23:16:08 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 6.82 secs
2020-03-28 23:16:08 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-03-28 23:16:08 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-03-28 23:16:09 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.493 secs
2020-03-28 23:16:09 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.17 secs
2020-03-28 23:16:09 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-03-28 23:16:10 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 55.61
2020-03-28 23:16:10 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 5.63
2020-03-28 23:16:10 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.04
2020-03-28 23:16:13 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.02 intercept: -0.00
2020-03-28 23:16:15 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.06
2020-03-28 23:16:15 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-03-28 23:16:15 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 56.71
2020-03-28 23:16:15 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 6.19
2020-03-28 23:16:15 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.04
2020-03-28 23:16:17 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.37 intercept: -0.02
2020-03-28 23:16:18 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.06
2020-03-28 23:16:18 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 23:16:18
2020-03-28 23:16:18 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-03-28 23:16:19 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 23:16:19
2020-03-28 23:16:19 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-03-28 23:16:20 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_3\plpResult
2020-03-28 23:16:20 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_3/plplog.txt
2020-03-28 23:16:20 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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40 changes: 40 additions & 0 deletions Covid19PredictingHospitalizationInFluPatients/data/Analysis_4/plpLog.txt
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2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_4
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction CohortID: 5894
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction OutcomeID: 5893
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction Cohort size: 150000
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction Covariates: 18
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction Population size: 150000
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction Cases: 10468
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction splitSeed: -7970845
2020-03-28 23:23:05 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead.
2020-03-28 23:23:05 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-03-28 23:23:06 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 37500 test cases and 112500 train cases (37500, 37500, 37500)
2020-03-28 23:23:06 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-03-28 23:23:07 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-03-28 23:23:10 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-03-28 23:23:10 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-03-28 23:23:10 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 4.02 secs
2020-03-28 23:23:10 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-03-28 23:23:10 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-03-28 23:23:11 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.476 secs
2020-03-28 23:23:12 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.17 secs
2020-03-28 23:23:12 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-03-28 23:23:12 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 56.29
2020-03-28 23:23:12 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 9.01
2020-03-28 23:23:12 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.06
2020-03-28 23:23:15 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.06 intercept: -0.00
2020-03-28 23:23:18 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.09
2020-03-28 23:23:18 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-03-28 23:23:18 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 55.16
2020-03-28 23:23:18 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 8.78
2020-03-28 23:23:18 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.06
2020-03-28 23:23:19 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.95 intercept: 0.00
2020-03-28 23:23:20 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.09
2020-03-28 23:23:20 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 23:23:20
2020-03-28 23:23:20 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-03-28 23:23:21 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 23:23:21
2020-03-28 23:23:21 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-03-28 23:23:22 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_4\plpResult
2020-03-28 23:23:22 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_4/plplog.txt
2020-03-28 23:23:22 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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5 changes: 5 additions & 0 deletions Covid19PredictingHospitalizationInFluPatients/data/settings.csv
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"outcomeId","cohortId","modelSettingsId","analysisId","devDatabase","populationSettingId","modelSettingId","covariateSettingId","modelSettingName","addExposureDaysToStart","riskWindowStart","addExposureDaysToEnd","riskWindowEnd","plpDataFolder","studyPopFile","plpResultFolder","cohortName","outcomeName"
5892,5894,1,1,"optumDod",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/PlpData_L1_T5894","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/StudyPop_L1_T5894_O5892.rds","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_1","[COVID ID13 v1] GP/OP/ER visits of patients presenting with Covid flu or flu-like symptoms AND no symptoms or pneumonia in prior 60d","[COVID19 ID25 V1] Hospitalizations with pneumonia"
5892,5894,2,3,"optumDod",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/PlpData_L2_T5894","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/StudyPop_L1_T5894_O5892.rds","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_3","[COVID ID13 v1] GP/OP/ER visits of patients presenting with Covid flu or flu-like symptoms AND no symptoms or pneumonia in prior 60d","[COVID19 ID25 V1] Hospitalizations with pneumonia"
5893,5894,1,2,"optumDod",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/PlpData_L1_T5894","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/StudyPop_L1_T5894_O5893.rds","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_2","[COVID ID13 v1] GP/OP/ER visits of patients presenting with Covid flu or flu-like symptoms AND no symptoms or pneumonia in prior 60d","[COVID19 ID26 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI"
5893,5894,2,4,"optumDod",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/PlpData_L2_T5894","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/StudyPop_L1_T5894_O5893.rds","T:/covid19Studies/covid19Results/HospitalizationInSymptomaticPatientsResults/optumDod/Analysis_4","[COVID ID13 v1] GP/OP/ER visits of patients presenting with Covid flu or flu-like symptoms AND no symptoms or pneumonia in prior 60d","[COVID19 ID26 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI"
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