Skip to content

Commit

Permalink
adding JMDC results
Browse files Browse the repository at this point in the history
  • Loading branch information
jreps committed Mar 29, 2020
1 parent 2681a78 commit 769b7f4
Show file tree
Hide file tree
Showing 21 changed files with 184 additions and 4 deletions.
Binary file not shown.
Binary file not shown.
44 changes: 44 additions & 0 deletions PredictingSevereInHospResults/data/Analysis_1002/plpLog.txt
Original file line number Diff line number Diff line change
@@ -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.
Binary file not shown.
Binary file not shown.
Binary file not shown.
44 changes: 44 additions & 0 deletions PredictingSevereInHospResults/data/Analysis_2002/plpLog.txt
Original file line number Diff line number Diff line change
@@ -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.
Binary file not shown.
Binary file not shown.
Binary file not shown.
44 changes: 44 additions & 0 deletions PredictingSevereInHospResults/data/Analysis_3002/plpLog.txt
Original file line number Diff line number Diff line change
@@ -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.
Binary file not shown.
Binary file not shown.
Binary file not shown.
44 changes: 44 additions & 0 deletions PredictingSevereInHospResults/data/Analysis_4002/plpLog.txt
Original file line number Diff line number Diff line change
@@ -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.
Binary file not shown.
Loading

0 comments on commit 769b7f4

Please sign in to comment.