diff --git a/PredictingSevereInHospResults/data/Analysis_1/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_1/plpResult.rds deleted file mode 100644 index e07fa23c..00000000 Binary files a/PredictingSevereInHospResults/data/Analysis_1/plpResult.rds and /dev/null differ diff --git a/PredictingSevereInHospResults/data/Analysis_1/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_1001/plpLog.txt similarity index 100% rename from PredictingSevereInHospResults/data/Analysis_1/plpLog.txt rename to PredictingSevereInHospResults/data/Analysis_1001/plpLog.txt diff --git a/PredictingSevereInHospResults/data/Analysis_1001/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_1001/plpResult.rds new file mode 100644 index 00000000..5cc795c0 Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_1001/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/Analysis_1002/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_1002/plpLog.txt new file mode 100644 index 00000000..665a283f --- /dev/null +++ b/PredictingSevereInHospResults/data/Analysis_1002/plpLog.txt @@ -0,0 +1,44 @@ +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. diff --git a/PredictingSevereInHospResults/data/Analysis_1002/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_1002/plpResult.rds new file mode 100644 index 00000000..2ef09702 Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_1002/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/Analysis_2/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_2/plpResult.rds deleted file mode 100644 index 4dc90079..00000000 Binary files a/PredictingSevereInHospResults/data/Analysis_2/plpResult.rds and /dev/null differ diff --git a/PredictingSevereInHospResults/data/Analysis_2/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_2001/plpLog.txt similarity index 100% rename from PredictingSevereInHospResults/data/Analysis_2/plpLog.txt rename to PredictingSevereInHospResults/data/Analysis_2001/plpLog.txt diff --git a/PredictingSevereInHospResults/data/Analysis_2001/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_2001/plpResult.rds new file mode 100644 index 00000000..9277d563 Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_2001/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/Analysis_2002/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_2002/plpLog.txt new file mode 100644 index 00000000..ff3c35fe --- /dev/null +++ b/PredictingSevereInHospResults/data/Analysis_2002/plpLog.txt @@ -0,0 +1,44 @@ +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. diff --git a/PredictingSevereInHospResults/data/Analysis_2002/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_2002/plpResult.rds new file mode 100644 index 00000000..0cbcd1a8 Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_2002/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/Analysis_3/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_3/plpResult.rds deleted file mode 100644 index 7bc04d0a..00000000 Binary files a/PredictingSevereInHospResults/data/Analysis_3/plpResult.rds and /dev/null differ diff --git a/PredictingSevereInHospResults/data/Analysis_3/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_3001/plpLog.txt similarity index 100% rename from PredictingSevereInHospResults/data/Analysis_3/plpLog.txt rename to PredictingSevereInHospResults/data/Analysis_3001/plpLog.txt diff --git a/PredictingSevereInHospResults/data/Analysis_3001/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_3001/plpResult.rds new file mode 100644 index 00000000..15f9eca4 Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_3001/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/Analysis_3002/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_3002/plpLog.txt new file mode 100644 index 00000000..4fc593d3 --- /dev/null +++ b/PredictingSevereInHospResults/data/Analysis_3002/plpLog.txt @@ -0,0 +1,44 @@ +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. diff --git a/PredictingSevereInHospResults/data/Analysis_3002/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_3002/plpResult.rds new file mode 100644 index 00000000..220d153d Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_3002/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/Analysis_4/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_4/plpResult.rds deleted file mode 100644 index 83684807..00000000 Binary files a/PredictingSevereInHospResults/data/Analysis_4/plpResult.rds and /dev/null differ diff --git a/PredictingSevereInHospResults/data/Analysis_4/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_4001/plpLog.txt similarity index 100% rename from PredictingSevereInHospResults/data/Analysis_4/plpLog.txt rename to PredictingSevereInHospResults/data/Analysis_4001/plpLog.txt diff --git a/PredictingSevereInHospResults/data/Analysis_4001/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_4001/plpResult.rds new file mode 100644 index 00000000..b72b2273 Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_4001/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/Analysis_4002/plpLog.txt b/PredictingSevereInHospResults/data/Analysis_4002/plpLog.txt new file mode 100644 index 00000000..abeb3291 --- /dev/null +++ b/PredictingSevereInHospResults/data/Analysis_4002/plpLog.txt @@ -0,0 +1,44 @@ +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. diff --git a/PredictingSevereInHospResults/data/Analysis_4002/plpResult.rds b/PredictingSevereInHospResults/data/Analysis_4002/plpResult.rds new file mode 100644 index 00000000..e67748bc Binary files /dev/null and b/PredictingSevereInHospResults/data/Analysis_4002/plpResult.rds differ diff --git a/PredictingSevereInHospResults/data/settings.csv b/PredictingSevereInHospResults/data/settings.csv index 031a8e90..cd17508a 100644 --- a/PredictingSevereInHospResults/data/settings.csv +++ b/PredictingSevereInHospResults/data/settings.csv @@ -1,5 +1,9 @@ "outcomeId","cohortId","modelSettingsId","analysisId","devDatabase","populationSettingId","modelSettingId","covariateSettingId","modelSettingName","addExposureDaysToStart","riskWindowStart","addExposureDaysToEnd","riskWindowEnd","plpDataFolder","studyPopFile","plpResultFolder","cohortName","outcomeName" -5889,5891,1,1,"optumDod",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L1_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5889.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_1","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID27 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI requiring intensive services or resulting in death in 30d" -5889,5891,2,3,"optumDod",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L2_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5889.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_3","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID27 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI requiring intensive services or resulting in death in 30d" -5890,5891,1,2,"optumDod",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L1_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5890.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_2","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID28 v1] persons who die" -5890,5891,2,4,"optumDod",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L2_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5890.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_4","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID28 v1] persons who die" +5889,5891,1,1001,"optumDod",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L1_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5889.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_1","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID27 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI requiring intensive services or resulting in death in 30d" +5889,5891,2,3001,"optumDod",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L2_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5889.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_3","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID27 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI requiring intensive services or resulting in death in 30d" +5890,5891,1,2001,"optumDod",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L1_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5890.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_2","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID28 v1] persons who die" +5890,5891,2,4001,"optumDod",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/PlpData_L2_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/StudyPop_L1_T5891_O5890.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/optumDod/Analysis_4","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID28 v1] persons who die" +5889,5891,1,1002,"jmdc",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/PlpData_L1_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/StudyPop_L1_T5891_O5889.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_1","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID27 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI requiring intensive services or resulting in death in 30d" +5889,5891,2,3002,"jmdc",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/PlpData_L2_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/StudyPop_L1_T5891_O5889.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_3","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID27 V1] Hospitalizations with pneumonia or ARDS or sepsis or AKI requiring intensive services or resulting in death in 30d" +5890,5891,1,2002,"jmdc",1,1,1,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/PlpData_L1_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/StudyPop_L1_T5891_O5890.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_2","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID28 v1] persons who die" +5890,5891,2,4002,"jmdc",1,1,2,"Lasso Logistic Regression",0,0,0,30,"T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/PlpData_L2_T5891","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/StudyPop_L1_T5891_O5890.rds","T:/covid19Studies/covid19Results/SevereInHospitalizedPatientsResults/jmdc/Analysis_4","[COVID19 ID29 V1] Hospitalizations with pneumonia, age>=18","[COVID19 ID28 v1] persons who die"