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Merge pull request OHDSI#103 from mi-erasmusmc/master
added the shiny functionality to hfint2dm
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| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 4.2.5 | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_1 | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction CohortID: 19693 | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction OutcomeID: 19692 | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction Cohort size: 180552 | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction Covariates: 3 | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction Population size: 112989 | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction Cases: 1843 | ||
| 2021-01-06 05:42:56 [Main thread] WARN PatientLevelPrediction personSplitter deprecatedWarning: 'personSplitter' is deprecated. Use 'randomSplitter' instead. See help("Deprecated") | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class | ||
| 2021-01-06 05:42:56 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 28246 test cases and 84743 train cases (28248, 28248, 28247) | ||
| 2021-01-06 05:42:57 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
| 2021-01-06 05:42:58 [Main thread] INFO FeatureExtraction tidyCovariateData Removing 1 redundant covariates | ||
| 2021-01-06 05:42:58 [Main thread] INFO FeatureExtraction tidyCovariateData Removing 0 infrequent covariates | ||
| 2021-01-06 05:42:58 [Main thread] INFO FeatureExtraction tidyCovariateData Normalizing covariates | ||
| 2021-01-06 05:42:58 [Main thread] INFO FeatureExtraction tidyCovariateData Tidying covariates took 1.6 secs | ||
| 2021-01-06 05:42:58 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 05:42:59 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 05:43:00 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
| 2021-01-06 05:43:24 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
| 2021-01-06 05:43:24 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
| 2021-01-06 05:43:24 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 25.3 secs | ||
| 2021-01-06 05:43:29 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame | ||
| 2021-01-06 05:43:29 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set | ||
| 2021-01-06 05:43:29 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 05:43:30 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 05:43:30 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.536 secs | ||
| 2021-01-06 05:43:31 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 05:43:32 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 05:43:32 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 05:43:32 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 05:43:33 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.207 secs | ||
| 2021-01-06 05:43:33 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
| 2021-01-06 05:43:33 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 63.12 | ||
| 2021-01-06 05:43:33 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 3.07 | ||
| 2021-01-06 05:43:33 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
| 2021-01-06 05:43:36 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration in large- Mean predicted risk 0.0166 : observed risk 0.0163 | ||
| 2021-01-06 05:43:38 [Main thread] INFO PatientLevelPrediction evaluatePlp Weak calibration intercept: -0.0152 - gradient:1.0024 | ||
| 2021-01-06 05:43:38 [Main thread] INFO PatientLevelPrediction evaluatePlp Hosmer-Lemeshow calibration gradient: 1.33 intercept: -0.01 | ||
| 2021-01-06 05:43:41 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.03 | ||
| 2021-01-06 05:43:41 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
| 2021-01-06 05:43:41 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 64.08 | ||
| 2021-01-06 05:43:41 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 61.60 | ||
| 2021-01-06 05:43:41 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 66.56 | ||
| 2021-01-06 05:43:41 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 3.18 | ||
| 2021-01-06 05:43:41 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
| 2021-01-06 05:43:42 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration in large- Mean predicted risk 0.0166 : observed risk 0.0163 | ||
| 2021-01-06 05:43:42 [Main thread] INFO PatientLevelPrediction evaluatePlp Weak calibration intercept: -0.0191 - gradient:1.0031 | ||
| 2021-01-06 05:43:42 [Main thread] INFO PatientLevelPrediction evaluatePlp Hosmer-Lemeshow calibration gradient: 1.42 intercept: -0.01 | ||
| 2021-01-06 05:43:43 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.03 | ||
| 2021-01-06 05:43:44 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2021-01-06 05:43:44 | ||
| 2021-01-06 05:43:44 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
| 2021-01-06 05:43:46 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2021-01-06 05:43:46 | ||
| 2021-01-06 05:43:46 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
| 2021-01-06 05:43:49 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\./results/ccae/Analysis_1\plpResult | ||
| 2021-01-06 05:43:49 [Main thread] INFO PatientLevelPrediction Log saved to ./results/ccae/Analysis_1/plplog.txt | ||
| 2021-01-06 05:43:49 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 4.0.2 | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_10 | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction CohortID: 13897 | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction OutcomeID: 11696 | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction Cohort size: 5015 | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction Covariates: 13219 | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction Population size: 3567 | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction Cases: 53 | ||
| 2020-07-08 09:50:16 [Main thread] WARN PatientLevelPrediction personSplitter deprecatedWarning: 'personSplitter' is deprecated. Use 'randomSplitter' instead. See help("Deprecated") | ||
| 2020-07-08 09:50:16 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class | ||
| 2020-07-08 09:50:17 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 891 test cases and 2676 train cases (893, 892, 891) | ||
| 2020-07-08 09:50:17 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
| 2020-07-08 09:50:19 [Main thread] INFO FeatureExtraction tidyCovariateData Removing 11 redundant covariates | ||
| 2020-07-08 09:50:19 [Main thread] INFO FeatureExtraction tidyCovariateData Removing 6146 infrequent covariates | ||
| 2020-07-08 09:50:19 [Main thread] INFO FeatureExtraction tidyCovariateData Normalizing covariates | ||
| 2020-07-08 09:50:21 [Main thread] INFO FeatureExtraction tidyCovariateData Tidying covariates took 4.12 secs | ||
| 2020-07-08 09:50:21 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2020-07-08 09:50:22 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2020-07-08 09:50:23 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
| 2020-07-08 09:50:26 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
| 2020-07-08 09:50:26 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
| 2020-07-08 09:50:26 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 5.56 secs | ||
| 2020-07-08 09:50:27 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame | ||
| 2020-07-08 09:50:27 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set | ||
| 2020-07-08 09:50:27 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2020-07-08 09:50:28 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2020-07-08 09:50:28 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.165 secs | ||
| 2020-07-08 09:50:28 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2020-07-08 09:50:29 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2020-07-08 09:50:29 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 0.089 secs | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 80.15 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 71.69 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 88.62 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 10.96 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 2.52 intercept: -0.02 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.12 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 58.27 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 40.77 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 75.78 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 2.12 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.01 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration gradient: 0.88 intercept: 0.00 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.03 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2020-07-08 09:50:30 | ||
| 2020-07-08 09:50:30 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
| 2020-07-08 09:50:42 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2020-07-08 09:50:42 | ||
| 2020-07-08 09:50:42 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
| 2020-07-08 09:50:43 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\./hfint2dm07072020Results/jmdc/Analysis_10\plpResult | ||
| 2020-07-08 09:50:43 [Main thread] INFO PatientLevelPrediction Log saved to ./hfint2dm07072020Results/jmdc/Analysis_10/plplog.txt | ||
| 2020-07-08 09:50:43 [Main thread] INFO PatientLevelPrediction Run finished successfully. | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 4.2.5 | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_2 | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction CohortID: 19693 | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction OutcomeID: 19692 | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction Cohort size: 213363 | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction Covariates: 92383 | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction Population size: 159633 | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction Cases: 3690 | ||
| 2021-01-06 11:39:13 [Main thread] WARN PatientLevelPrediction personSplitter deprecatedWarning: 'personSplitter' is deprecated. Use 'randomSplitter' instead. See help("Deprecated") | ||
| 2021-01-06 11:39:13 [Main thread] INFO PatientLevelPrediction randomSplitter Creating a 25% test and 75% train (into 3 folds) random stratified split by class | ||
| 2021-01-06 11:39:14 [Main thread] INFO PatientLevelPrediction randomSplitter Data split into 39907 test cases and 119726 train cases (39909, 39909, 39908) | ||
| 2021-01-06 11:39:14 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model | ||
| 2021-01-06 11:46:53 [Main thread] INFO FeatureExtraction tidyCovariateData Removing 1 redundant covariates | ||
| 2021-01-06 11:46:53 [Main thread] INFO FeatureExtraction tidyCovariateData Removing 81159 infrequent covariates | ||
| 2021-01-06 11:46:53 [Main thread] INFO FeatureExtraction tidyCovariateData Normalizing covariates | ||
| 2021-01-06 11:52:17 [Main thread] INFO FeatureExtraction tidyCovariateData Tidying covariates took 13 mins | ||
| 2021-01-06 11:52:17 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 11:53:26 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 11:54:28 [Main thread] INFO PatientLevelPrediction fitGLMModel Running Cyclops | ||
| 2021-01-06 12:07:23 [Main thread] INFO PatientLevelPrediction fitGLMModel Done. | ||
| 2021-01-06 12:07:23 [Main thread] INFO PatientLevelPrediction fitGLMModel GLM fit status: OK | ||
| 2021-01-06 12:07:23 [Main thread] INFO PatientLevelPrediction fitGLMModel Fitting model took 15.1 mins | ||
| 2021-01-06 12:08:48 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Creating variable importance data frame | ||
| 2021-01-06 12:08:48 [Main thread] INFO PatientLevelPrediction fitLassoLogisticRegression Getting predictions on train set | ||
| 2021-01-06 12:08:48 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 12:10:03 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 12:10:21 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 17.6 secs | ||
| 2021-01-06 12:10:22 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 12:13:02 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 12:13:34 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Starting to limit covariate data to population... | ||
| 2021-01-06 12:13:55 [Main thread] INFO PatientLevelPrediction limitCovariatesToPopulation Finished limiting covariate data to population... | ||
| 2021-01-06 12:14:01 [Main thread] INFO PatientLevelPrediction predictProbabilities Prediction took 5.64 secs | ||
| 2021-01-06 12:14:01 [Main thread] INFO PatientLevelPrediction Train set evaluation | ||
| 2021-01-06 12:14:02 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 83.69 | ||
| 2021-01-06 12:14:02 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 16.18 | ||
| 2021-01-06 12:14:02 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
| 2021-01-06 12:14:06 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration in large- Mean predicted risk 0.0231 : observed risk 0.0231 | ||
| 2021-01-06 12:14:08 [Main thread] INFO PatientLevelPrediction evaluatePlp Weak calibration intercept: -1e-04 - gradient:1.0147 | ||
| 2021-01-06 12:14:09 [Main thread] INFO PatientLevelPrediction evaluatePlp Hosmer-Lemeshow calibration gradient: 1.15 intercept: -0.00 | ||
| 2021-01-06 12:14:12 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.16 | ||
| 2021-01-06 12:14:12 [Main thread] INFO PatientLevelPrediction Test set evaluation | ||
| 2021-01-06 12:14:13 [Main thread] INFO PatientLevelPrediction evaluatePlp AUC: 81.25 | ||
| 2021-01-06 12:14:13 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% lower AUC: 79.84 | ||
| 2021-01-06 12:14:13 [Main thread] INFO PatientLevelPrediction evaluatePlp 95% upper AUC: 82.67 | ||
| 2021-01-06 12:14:13 [Main thread] INFO PatientLevelPrediction evaluatePlp AUPRC: 14.46 | ||
| 2021-01-06 12:14:13 [Main thread] INFO PatientLevelPrediction evaluatePlp Brier: 0.02 | ||
| 2021-01-06 12:14:14 [Main thread] INFO PatientLevelPrediction evaluatePlp Calibration in large- Mean predicted risk 0.023 : observed risk 0.0231 | ||
| 2021-01-06 12:14:15 [Main thread] INFO PatientLevelPrediction evaluatePlp Weak calibration intercept: 0.006 - gradient:1.0031 | ||
| 2021-01-06 12:14:15 [Main thread] INFO PatientLevelPrediction evaluatePlp Hosmer-Lemeshow calibration gradient: 1.03 intercept: -0.00 | ||
| 2021-01-06 12:14:16 [Main thread] INFO PatientLevelPrediction evaluatePlp Average Precision: 0.15 | ||
| 2021-01-06 12:14:17 [Main thread] INFO PatientLevelPrediction Calculating covariate summary @ 2021-01-06 12:14:17 | ||
| 2021-01-06 12:14:17 [Main thread] INFO PatientLevelPrediction This can take a while... | ||
| 2021-01-06 12:26:40 [Main thread] INFO PatientLevelPrediction Finished covariate summary @ 2021-01-06 12:26:40 | ||
| 2021-01-06 12:26:40 [Main thread] INFO PatientLevelPrediction Saving PlpResult | ||
| 2021-01-06 12:26:47 [Main thread] INFO PatientLevelPrediction plpResult saved to ..\./results/panther/Analysis_2\plpResult | ||
| 2021-01-06 12:26:47 [Main thread] INFO PatientLevelPrediction Log saved to ./results/panther/Analysis_2/plplog.txt | ||
| 2021-01-06 12:26:47 [Main thread] INFO PatientLevelPrediction Run finished successfully. |
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