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added pneumonia results
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rossdwilliams committed Apr 10, 2020
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2020-04-08 20:57:43 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-08 21:01:52 [Main thread] INFO PatientLevelPrediction No plpData - probably empty cohort issue
2020-04-08 21:01:52 [Main thread] WARN PatientLevelPrediction addExposureDaysToStart is depreciated - please use startAnchor instead
2020-04-08 21:01:52 [Main thread] WARN PatientLevelPrediction addExposureDaysToEnd is depreciated - please use endAnchor instead
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_6
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction CohortID: 5896
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction OutcomeID: 5892
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction Cohort size: 300000
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction Covariates: 35445
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction Population size: 299307
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction Cases: 1941
2020-04-09 04:33:39 [Main thread] INFO PatientLevelPrediction splitSeed: 6265188
2020-04-09 04:33:39 [Main thread] WARN PatientLevelPrediction personSplitter 'personSplitter' is deprecated. Use 'randomSplitter' instead. See help("Deprecated")
2020-04-09 04:33:41 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-04-09 04:33:41 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 74826 test cases and 224481 train cases (74828, 74827, 74826)
2020-04-09 04:33:44 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-04-09 04:35:59 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-04-09 04:47:38 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-04-09 04:47:38 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-04-09 04:47:38 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 12.5 mins
2020-04-09 04:47:38 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-04-09 04:47:38 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-04-09 04:48:09 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 10.8 secs
2020-04-09 04:49:55 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 3.65 secs
2020-04-09 04:49:56 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-04-09 04:50:00 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 81.95
2020-04-09 04:50:00 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 8.50
2020-04-09 04:50:00 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01
2020-04-09 04:50:25 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.14 intercept: -0.00
2020-04-09 04:50:32 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.09
2020-04-09 04:50:32 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-04-09 04:50:32 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 79.42
2020-04-09 04:50:32 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 77.14
2020-04-09 04:50:32 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 81.71
2020-04-09 04:50:34 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 5.31
2020-04-09 04:50:34 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01
2020-04-09 04:50:54 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.04 intercept: -0.00
2020-04-09 04:50:57 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.05
2020-04-09 04:50:57 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-04-09 04:50:57
2020-04-09 04:50:57 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-04-09 04:53:59 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-04-09 04:53:59
2020-04-09 04:53:59 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-04-09 04:54:11 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\./HospitalizationInSentHomePatientsResults/Analysis_6\plpResult
2020-04-09 04:54:13 [Main thread] INFO PatientLevelPrediction Log saved to ./HospitalizationInSentHomePatientsResults/Analysis_6/plplog.txt
2020-04-09 04:54:14 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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2020-04-08 21:33:26 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-08 21:35:39 [Main thread] INFO PatientLevelPrediction No plpData - probably empty cohort issue
2020-04-08 21:35:39 [Main thread] WARN PatientLevelPrediction addExposureDaysToStart is depreciated - please use startAnchor instead
2020-04-08 21:35:39 [Main thread] WARN PatientLevelPrediction addExposureDaysToEnd is depreciated - please use endAnchor instead
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_11
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction CohortID: 5895
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction OutcomeID: 5892
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction Cohort size: 101312
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction Covariates: 18
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction Population size: 101129
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction Cases: 2942
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction splitSeed: -5257171
2020-04-09 04:09:03 [Main thread] WARN PatientLevelPrediction personSplitter 'personSplitter' is deprecated. Use 'randomSplitter' instead. See help("Deprecated")
2020-04-09 04:09:03 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-04-09 04:09:05 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 25281 test cases and 75848 train cases (25283, 25283, 25282)
2020-04-09 04:09:08 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-04-09 04:09:10 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-04-09 04:09:16 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-04-09 04:09:16 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-04-09 04:09:16 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 6.92 secs
2020-04-09 04:09:16 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-04-09 04:09:16 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-04-09 04:09:19 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 2.07 secs
2020-04-09 04:09:21 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.224 secs
2020-04-09 04:09:21 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-04-09 04:09:24 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 62.54
2020-04-09 04:09:24 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 4.31
2020-04-09 04:09:24 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.03
2020-04-09 04:09:29 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.02 intercept: -0.00
2020-04-09 04:09:32 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.04
2020-04-09 04:09:32 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-04-09 04:09:33 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 60.73
2020-04-09 04:09:33 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 58.78
2020-04-09 04:09:33 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 62.69
2020-04-09 04:09:33 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 3.97
2020-04-09 04:09:33 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.03
2020-04-09 04:09:37 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.88 intercept: 0.00
2020-04-09 04:09:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.04
2020-04-09 04:09:39 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-04-09 04:09:39
2020-04-09 04:09:39 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-04-09 04:09:43 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-04-09 04:09:43
2020-04-09 04:09:43 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-04-09 04:09:50 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\./HospitalizationInSentHomePatientsResults/Analysis_11\plpResult
2020-04-09 04:09:53 [Main thread] INFO PatientLevelPrediction Log saved to ./HospitalizationInSentHomePatientsResults/Analysis_11/plplog.txt
2020-04-09 04:09:55 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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2020-04-08 22:11:31 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-08 22:15:47 [Main thread] INFO PatientLevelPrediction No plpData - probably empty cohort issue
2020-04-08 22:15:47 [Main thread] WARN PatientLevelPrediction addExposureDaysToStart is depreciated - please use startAnchor instead
2020-04-08 22:15:47 [Main thread] WARN PatientLevelPrediction addExposureDaysToEnd is depreciated - please use endAnchor instead
2020-04-09 04:56:13 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_11
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction CohortID: 5896
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction OutcomeID: 5892
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction Cohort size: 300000
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction Covariates: 18
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction Population size: 299307
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction Cases: 1941
2020-04-09 04:56:14 [Main thread] INFO PatientLevelPrediction splitSeed: 798819
2020-04-09 04:56:14 [Main thread] WARN PatientLevelPrediction personSplitter 'personSplitter' is deprecated. Use 'randomSplitter' instead. See help("Deprecated")
2020-04-09 04:56:16 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-04-09 04:56:19 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 74826 test cases and 224481 train cases (74828, 74827, 74826)
2020-04-09 04:56:21 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-04-09 04:56:24 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-04-09 04:56:32 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-04-09 04:56:32 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-04-09 04:56:32 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 8.9 secs
2020-04-09 04:56:32 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-04-09 04:56:32 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-04-09 04:56:35 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 2.06 secs
2020-04-09 04:56:37 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.377 secs
2020-04-09 04:56:37 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-04-09 04:56:39 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 54.00
2020-04-09 04:56:39 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 0.76
2020-04-09 04:56:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01
2020-04-09 04:56:47 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.25 intercept: -0.00
2020-04-09 04:56:53 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.01
2020-04-09 04:56:53 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-04-09 04:56:54 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 51.98
2020-04-09 04:56:54 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 49.38
2020-04-09 04:56:54 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 54.57
2020-04-09 04:56:54 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 0.70
2020-04-09 04:56:54 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01
2020-04-09 04:56:58 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.76 intercept: 0.00
2020-04-09 04:57:02 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.01
2020-04-09 04:57:02 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-04-09 04:57:02
2020-04-09 04:57:02 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-04-09 04:57:05 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-04-09 04:57:05
2020-04-09 04:57:05 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-04-09 04:57:12 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\./HospitalizationInSentHomePatientsResults/Analysis_11\plpResult
2020-04-09 04:57:16 [Main thread] INFO PatientLevelPrediction Log saved to ./HospitalizationInSentHomePatientsResults/Analysis_11/plplog.txt
2020-04-09 04:57:17 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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2020-04-08 20:16:44 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-08 20:19:03 [Main thread] INFO PatientLevelPrediction No plpData - probably empty cohort issue
2020-04-08 20:19:03 [Main thread] WARN PatientLevelPrediction addExposureDaysToStart is depreciated - please use startAnchor instead
2020-04-08 20:19:03 [Main thread] WARN PatientLevelPrediction addExposureDaysToEnd is depreciated - please use endAnchor instead
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_5
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction CohortID: 5895
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction OutcomeID: 5892
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction Cohort size: 101312
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction Covariates: 32181
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction Population size: 101129
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction Cases: 2942
2020-04-09 03:57:28 [Main thread] INFO PatientLevelPrediction splitSeed: 6861583
2020-04-09 03:57:28 [Main thread] WARN PatientLevelPrediction personSplitter 'personSplitter' is deprecated. Use 'randomSplitter' instead. See help("Deprecated")
2020-04-09 03:57:31 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class
2020-04-09 03:57:36 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 25281 test cases and 75848 train cases (25283, 25283, 25282)
2020-04-09 03:57:39 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model
2020-04-09 03:58:40 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops
2020-04-09 04:03:28 [Main thread] INFO PatientLevelPrediction fitGLMModel Done.
2020-04-09 04:03:28 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK
2020-04-09 04:03:28 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 5.14 mins
2020-04-09 04:03:28 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame
2020-04-09 04:03:28 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set
2020-04-09 04:03:44 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 5.92 secs
2020-04-09 04:04:05 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 2.85 secs
2020-04-09 04:04:05 [Main thread] INFO PatientLevelPrediction Train set evaluation
2020-04-09 04:04:09 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 73.61
2020-04-09 04:04:12 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 10.53
2020-04-09 04:04:12 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.03
2020-04-09 04:04:27 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.15 intercept: -0.00
2020-04-09 04:04:33 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.11
2020-04-09 04:04:33 [Main thread] INFO PatientLevelPrediction Test set evaluation
2020-04-09 04:04:36 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 70.82
2020-04-09 04:04:36 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 68.98
2020-04-09 04:04:36 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 72.66
2020-04-09 04:04:39 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 7.84
2020-04-09 04:04:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.03
2020-04-09 04:04:55 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.93 intercept: 0.00
2020-04-09 04:04:59 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.08
2020-04-09 04:05:00 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-04-09 04:04:59
2020-04-09 04:05:00 [Main thread] INFO PatientLevelPrediction This can take a while...
2020-04-09 04:06:16 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-04-09 04:06:16
2020-04-09 04:06:16 [Main thread] INFO PatientLevelPrediction Saving PlpResult
2020-04-09 04:06:31 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\./HospitalizationInSentHomePatientsResults/Analysis_5\plpResult
2020-04-09 04:06:36 [Main thread] INFO PatientLevelPrediction Log saved to ./HospitalizationInSentHomePatientsResults/Analysis_5/plplog.txt
2020-04-09 04:06:41 [Main thread] INFO PatientLevelPrediction Run finished successfully.
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