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PredictingSevereInHospResults/data/Analysis_1002/plpLog.txt
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2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_1 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction CohortID: 5891 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction OutcomeID: 5889 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction Cohort size: 21544 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction Covariates: 16061 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction Population size: 21544 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction Cases: 1316 | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction splitSeed: 6948678 | ||
2020-03-28 22:47:13 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead. | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 5386 test cases and 16158 train cases (5386, 5386, 5386) | ||
2020-03-28 22:47:13 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
2020-03-28 22:47:28 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
2020-03-28 22:48:18 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
2020-03-28 22:48:18 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
2020-03-28 22:48:18 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 55.4 secs | ||
2020-03-28 22:48:18 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame | ||
2020-03-28 22:48:18 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set | ||
2020-03-28 22:48:21 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.993 secs | ||
2020-03-28 22:48:25 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.33 secs | ||
2020-03-28 22:48:25 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
2020-03-28 22:48:25 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 77.19 | ||
2020-03-28 22:48:25 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 75.77 | ||
2020-03-28 22:48:25 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 78.61 | ||
2020-03-28 22:48:25 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 20.84 | ||
2020-03-28 22:48:25 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.05 | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.33 intercept: -0.02 | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.21 | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 73.07 | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 70.39 | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 75.75 | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 16.06 | ||
2020-03-28 22:48:28 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.05 | ||
2020-03-28 22:48:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.15 intercept: -0.01 | ||
2020-03-28 22:48:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.16 | ||
2020-03-28 22:48:30 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 22:48:30 | ||
2020-03-28 22:48:30 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
2020-03-28 22:48:53 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 22:48:53 | ||
2020-03-28 22:48:53 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
2020-03-28 22:48:54 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_1\plpResult | ||
2020-03-28 22:48:54 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_1/plplog.txt | ||
2020-03-28 22:48:54 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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PredictingSevereInHospResults/data/Analysis_2002/plpLog.txt
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2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_2 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction CohortID: 5891 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction OutcomeID: 5890 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Cohort size: 21544 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Covariates: 16061 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Population size: 21544 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Cases: 538 | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction splitSeed: 2825243 | ||
2020-03-28 22:49:19 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead. | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 5385 test cases and 16159 train cases (5387, 5387, 5385) | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
2020-03-28 22:49:35 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
2020-03-28 22:50:59 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
2020-03-28 22:50:59 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
2020-03-28 22:50:59 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 1.47 mins | ||
2020-03-28 22:50:59 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame | ||
2020-03-28 22:50:59 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set | ||
2020-03-28 22:51:02 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 1.26 secs | ||
2020-03-28 22:51:06 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.467 secs | ||
2020-03-28 22:51:06 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
2020-03-28 22:51:06 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 84.18 | ||
2020-03-28 22:51:06 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 82.32 | ||
2020-03-28 22:51:06 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 86.04 | ||
2020-03-28 22:51:06 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 21.07 | ||
2020-03-28 22:51:06 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.38 intercept: -0.01 | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.21 | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 74.36 | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 70.07 | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 78.66 | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 9.47 | ||
2020-03-28 22:51:09 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
2020-03-28 22:51:13 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.92 intercept: 0.00 | ||
2020-03-28 22:51:13 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.10 | ||
2020-03-28 22:51:13 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 22:51:13 | ||
2020-03-28 22:51:13 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
2020-03-28 22:51:35 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 22:51:35 | ||
2020-03-28 22:51:35 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_2\plpResult | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_2/plplog.txt | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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PredictingSevereInHospResults/data/Analysis_3002/plpLog.txt
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2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_3 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction CohortID: 5891 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction OutcomeID: 5889 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction Cohort size: 21544 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction Covariates: 15 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction Population size: 21544 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction Cases: 1316 | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction splitSeed: 7557842 | ||
2020-03-28 22:49:14 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead. | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 5386 test cases and 16158 train cases (5386, 5386, 5386) | ||
2020-03-28 22:49:14 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
2020-03-28 22:49:15 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
2020-03-28 22:49:15 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
2020-03-28 22:49:15 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
2020-03-28 22:49:15 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 0.87 secs | ||
2020-03-28 22:49:15 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame | ||
2020-03-28 22:49:15 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.106 secs | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.086 secs | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 60.76 | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 59.01 | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 62.51 | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 8.72 | ||
2020-03-28 22:49:16 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.06 | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.06 intercept: -0.00 | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.09 | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 58.53 | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 55.48 | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 61.57 | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 7.73 | ||
2020-03-28 22:49:17 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.06 | ||
2020-03-28 22:49:18 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.78 intercept: 0.01 | ||
2020-03-28 22:49:18 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.08 | ||
2020-03-28 22:49:18 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 22:49:18 | ||
2020-03-28 22:49:18 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
2020-03-28 22:49:18 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 22:49:18 | ||
2020-03-28 22:49:18 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_3\plpResult | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_3/plplog.txt | ||
2020-03-28 22:49:19 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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PredictingSevereInHospResults/data/Analysis_4002/plpLog.txt
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2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.15 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_4 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction CohortID: 5891 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction OutcomeID: 5890 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Cohort size: 21544 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Covariates: 15 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Population size: 21544 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Cases: 538 | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction splitSeed: -7473021 | ||
2020-03-28 22:51:36 [Main thread] WARN PatientLevelPrediction personSplitter This function is deprecated. Use 'randomSplitter' instead. | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 5385 test cases and 16159 train cases (5387, 5387, 5385) | ||
2020-03-28 22:51:36 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
2020-03-28 22:51:37 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
2020-03-28 22:51:37 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
2020-03-28 22:51:37 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
2020-03-28 22:51:37 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 0.737 secs | ||
2020-03-28 22:51:37 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame | ||
2020-03-28 22:51:37 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.276 secs | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.111 secs | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 65.03 | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 62.47 | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 67.59 | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 4.16 | ||
2020-03-28 22:51:38 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.07 intercept: -0.00 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.04 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 65.31 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 61.21 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 69.42 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 3.94 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.07 intercept: -0.00 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.04 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-03-28 22:51:39 | ||
2020-03-28 22:51:39 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
2020-03-28 22:51:40 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-03-28 22:51:40 | ||
2020-03-28 22:51:40 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
2020-03-28 22:51:41 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_4\plpResult | ||
2020-03-28 22:51:41 [Main thread] INFO PatientLevelPrediction Log saved to T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_4/plplog.txt | ||
2020-03-28 22:51:41 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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