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| Version: 1.0 | ||
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| RestoreWorkspace: Default | ||
| SaveWorkspace: Default | ||
| AlwaysSaveHistory: Default | ||
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| Encoding: UTF-8 | ||
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| RnwWeave: Sweave | ||
| LaTeX: pdfLaTeX |
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| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.5 | ||
| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_1 | ||
| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction CohortID: 3 | ||
| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction OutcomeID: 1 | ||
| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction Cohort size: 500000 | ||
| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction Covariates: 74348 | ||
| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction Population size: 351028 | ||
| 2019-06-03 22:53:09 [Main thread] INFO PatientLevelPrediction Cases: 2601 | ||
| 2019-06-03 22:53:10 [Main thread] INFO PatientLevelPrediction personSplitter Creating a 25% test and 75% train (into 3 folds) stratified split by person | ||
| 2019-06-03 22:53:10 [Main thread] INFO PatientLevelPrediction personSplitter Data split into 87757 test cases and 263271 train cases (87758, 87757, 87756) | ||
| 2019-06-03 22:53:11 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
| 2019-06-03 22:56:44 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
| 2019-06-03 23:09:24 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
| 2019-06-03 23:09:24 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
| 2019-06-03 23:09:24 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 13.8 mins | ||
| 2019-06-03 23:10:00 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 11.9 secs | ||
| 2019-06-03 23:10:48 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 4.04 secs | ||
| 2019-06-03 23:10:48 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
| 2019-06-03 23:10:51 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 78.08 | ||
| 2019-06-03 23:10:51 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 4.35 | ||
| 2019-06-03 23:10:51 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01 | ||
| 2019-06-03 23:11:25 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.21 intercept: -0.00 | ||
| 2019-06-03 23:11:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.04 | ||
| 2019-06-03 23:11:30 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
| 2019-06-03 23:11:31 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 74.49 | ||
| 2019-06-03 23:11:31 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 72.54 | ||
| 2019-06-03 23:11:31 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 76.44 | ||
| 2019-06-03 23:11:31 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 3.09 | ||
| 2019-06-03 23:11:31 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01 | ||
| 2019-06-03 23:12:04 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.07 intercept: -0.00 | ||
| 2019-06-03 23:12:05 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.03 | ||
| 2019-06-03 23:12:06 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2019-06-03 23:12:06 | ||
| 2019-06-03 23:12:06 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
| 2019-06-03 23:16:31 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2019-06-03 23:16:31 | ||
| 2019-06-03 23:16:31 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
| 2019-06-03 23:16:37 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/atlasResults/testingDocResults/Analysis_1\plpResult | ||
| 2019-06-03 23:16:37 [Main thread] INFO PatientLevelPrediction Log saved to T:/atlasResults/testingDocResults/Analysis_1/plplog.txt | ||
| 2019-06-03 23:16:37 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.5 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_2 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction CohortID: 4 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction OutcomeID: 1 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction Cohort size: 216387 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction Covariates: 63216 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction Population size: 152994 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction Cases: 788 | ||
| 2019-06-04 00:20:16 [Main thread] INFO PatientLevelPrediction personSplitter Creating a 25% test and 75% train (into 3 folds) stratified split by person | ||
| 2019-06-04 00:20:17 [Main thread] INFO PatientLevelPrediction personSplitter Data split into 38248 test cases and 114746 train cases (38249, 38249, 38248) | ||
| 2019-06-04 00:20:17 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
| 2019-06-04 00:21:45 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
| 2019-06-04 00:25:21 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
| 2019-06-04 00:25:21 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
| 2019-06-04 00:25:21 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 4.03 mins | ||
| 2019-06-04 00:25:35 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 4.19 secs | ||
| 2019-06-04 00:25:55 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 1.26 secs | ||
| 2019-06-04 00:25:55 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
| 2019-06-04 00:25:55 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 79.85 | ||
| 2019-06-04 00:25:55 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 78.05 | ||
| 2019-06-04 00:25:55 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 81.65 | ||
| 2019-06-04 00:25:55 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 4.09 | ||
| 2019-06-04 00:25:55 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01 | ||
| 2019-06-04 00:26:11 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.28 intercept: -0.00 | ||
| 2019-06-04 00:26:14 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.04 | ||
| 2019-06-04 00:26:14 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
| 2019-06-04 00:26:14 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 73.51 | ||
| 2019-06-04 00:26:14 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 70.07 | ||
| 2019-06-04 00:26:14 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 76.94 | ||
| 2019-06-04 00:26:14 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 1.76 | ||
| 2019-06-04 00:26:14 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01 | ||
| 2019-06-04 00:26:28 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.84 intercept: 0.00 | ||
| 2019-06-04 00:26:29 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.02 | ||
| 2019-06-04 00:26:29 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2019-06-04 00:26:29 | ||
| 2019-06-04 00:26:29 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
| 2019-06-04 00:28:18 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2019-06-04 00:28:18 | ||
| 2019-06-04 00:28:18 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
| 2019-06-04 00:28:21 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/atlasResults/testingDocResults/Analysis_2\plpResult | ||
| 2019-06-04 00:28:21 [Main thread] INFO PatientLevelPrediction Log saved to T:/atlasResults/testingDocResults/Analysis_2/plplog.txt | ||
| 2019-06-04 00:28:21 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.5 | ||
| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_3 | ||
| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction CohortID: 3 | ||
| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction OutcomeID: 2 | ||
| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction Cohort size: 500000 | ||
| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction Covariates: 74348 | ||
| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction Population size: 350460 | ||
| 2019-06-04 00:38:38 [Main thread] INFO PatientLevelPrediction Cases: 591 | ||
| 2019-06-04 00:38:39 [Main thread] INFO PatientLevelPrediction personSplitter Creating a 25% test and 75% train (into 3 folds) stratified split by person | ||
| 2019-06-04 00:38:39 [Main thread] INFO PatientLevelPrediction personSplitter Data split into 87615 test cases and 262845 train cases (87616, 87615, 87614) | ||
| 2019-06-04 00:38:40 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
| 2019-06-04 00:42:18 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
| 2019-06-04 00:49:27 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
| 2019-06-04 00:49:27 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
| 2019-06-04 00:49:27 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 8.26 mins | ||
| 2019-06-04 00:49:59 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 7.21 secs | ||
| 2019-06-04 00:50:45 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 2.56 secs | ||
| 2019-06-04 00:50:45 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
| 2019-06-04 00:50:47 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 66.79 | ||
| 2019-06-04 00:50:47 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 64.08 | ||
| 2019-06-04 00:50:47 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 69.50 | ||
| 2019-06-04 00:50:47 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 0.44 | ||
| 2019-06-04 00:50:47 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.00 | ||
| 2019-06-04 00:51:20 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.79 intercept: -0.00 | ||
| 2019-06-04 00:51:25 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.00 | ||
| 2019-06-04 00:51:25 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
| 2019-06-04 00:51:26 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 60.52 | ||
| 2019-06-04 00:51:26 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 55.83 | ||
| 2019-06-04 00:51:26 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 65.21 | ||
| 2019-06-04 00:51:26 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 0.25 | ||
| 2019-06-04 00:51:26 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.00 | ||
| 2019-06-04 00:51:59 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.02 intercept: -0.00 | ||
| 2019-06-04 00:52:01 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.00 | ||
| 2019-06-04 00:52:01 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2019-06-04 00:52:01 | ||
| 2019-06-04 00:52:01 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
| 2019-06-04 00:56:23 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2019-06-04 00:56:23 | ||
| 2019-06-04 00:56:23 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
| 2019-06-04 00:56:29 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/atlasResults/testingDocResults/Analysis_3\plpResult | ||
| 2019-06-04 00:56:29 [Main thread] INFO PatientLevelPrediction Log saved to T:/atlasResults/testingDocResults/Analysis_3/plplog.txt | ||
| 2019-06-04 00:56:29 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.5 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_4 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction CohortID: 4 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction OutcomeID: 2 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction Cohort size: 216387 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction Covariates: 63216 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction Population size: 152819 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction Cases: 164 | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction personSplitter Creating a 25% test and 75% train (into 3 folds) stratified split by person | ||
| 2019-06-04 01:36:46 [Main thread] INFO PatientLevelPrediction personSplitter Data split into 38205 test cases and 114614 train cases (38205, 38205, 38204) | ||
| 2019-06-04 01:36:47 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
| 2019-06-04 01:38:10 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
| 2019-06-04 01:41:39 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
| 2019-06-04 01:41:39 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
| 2019-06-04 01:41:39 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 3.89 mins | ||
| 2019-06-04 01:41:51 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 2.85 secs | ||
| 2019-06-04 01:42:12 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 1.09 secs | ||
| 2019-06-04 01:42:12 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
| 2019-06-04 01:42:12 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 70.08 | ||
| 2019-06-04 01:42:12 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 65.13 | ||
| 2019-06-04 01:42:12 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 75.03 | ||
| 2019-06-04 01:42:12 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 0.91 | ||
| 2019-06-04 01:42:12 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.00 | ||
| 2019-06-04 01:42:26 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.81 intercept: -0.00 | ||
| 2019-06-04 01:42:29 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.01 | ||
| 2019-06-04 01:42:29 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
| 2019-06-04 01:42:29 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 64.35 | ||
| 2019-06-04 01:42:29 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 55.62 | ||
| 2019-06-04 01:42:29 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 73.09 | ||
| 2019-06-04 01:42:29 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 0.18 | ||
| 2019-06-04 01:42:29 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.00 | ||
| 2019-06-04 01:42:43 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 1.09 intercept: -0.00 | ||
| 2019-06-04 01:42:44 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.00 | ||
| 2019-06-04 01:42:44 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2019-06-04 01:42:44 | ||
| 2019-06-04 01:42:44 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
| 2019-06-04 01:44:33 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2019-06-04 01:44:33 | ||
| 2019-06-04 01:44:33 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
| 2019-06-04 01:44:36 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\T:/atlasResults/testingDocResults/Analysis_4\plpResult | ||
| 2019-06-04 01:44:36 [Main thread] INFO PatientLevelPrediction Log saved to T:/atlasResults/testingDocResults/Analysis_4/plplog.txt | ||
| 2019-06-04 01:44:36 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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