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OHDSI / PatientLevelPrediction

An R package for performing patient level prediction in an observational database in the OMOP Common Data Model.
https://ohdsi.github.io/PatientLevelPrediction
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cyclops status not returned when model does not converge #130

Closed fdefalco closed 5 years ago

fdefalco commented 5 years ago

When running lasso logistic regression model if the model does not complete successfully no message is returned.

R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] shinydashboard_0.7.1 shinycssloaders_0.2.0 plotly_4.9.0
[4] ggplot2_3.1.1 shiny_1.3.2 FJD20190430_0.0.1
[7] DatabaseConnector_2.4.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 lattice_0.20-38
[3] tidyr_0.8.3 SqlRender_1.6.1
[5] assertthat_0.2.1 digest_0.6.18
[7] foreach_1.4.4 mime_0.6
[9] R6_2.4.0 plyr_1.8.4
[11] httr_1.4.0 pillar_1.3.1
[13] rlang_0.3.4 lazyeval_0.2.2
[15] uuid_0.1-2 rstudioapi_0.10
[17] data.table_1.12.2 PatientLevelPrediction_3.0.4 [19] DT_0.5 Matrix_1.2-16
[21] urltools_1.7.3 splines_3.5.0
[23] htmlwidgets_1.3 bit_1.1-14
[25] triebeard_0.3.0 munsell_0.5.0
[27] compiler_3.5.0 httpuv_1.5.1
[29] pkgconfig_2.0.2 base64enc_0.1-3
[31] FeatureExtraction_2.2.2 htmltools_0.3.6
[33] tidyselect_0.2.5 tibble_2.1.1
[35] ff_2.2-14 codetools_0.2-16
[37] viridisLite_0.3.0 withr_2.1.2
[39] crayon_1.3.4 dplyr_0.8.0.1
[41] later_0.8.0 MASS_7.3-51.1
[43] grid_3.5.0 jsonlite_1.6
[45] xtable_1.8-4 gtable_0.3.0
[47] DBI_1.0.0.9001 magrittr_1.5
[49] scales_1.0.0 zip_2.0.1
[51] promises_1.0.1 xml2_1.2.0
[53] fastmatch_1.1-0 ffbase_0.12.7
[55] iterators_1.0.10 tools_3.5.0
[57] glue_1.3.1 officer_0.3.3
[59] ParallelLogger_1.1.0 purrr_0.3.2
[61] crosstalk_1.0.0 Cyclops_2.0.2
[63] rsconnect_0.8.13 survival_2.43-3
[65] yaml_2.2.0 colorspace_1.4-1
[67] rJava_0.9-11

2019-04-30 16:07:53 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction Patient-Level Prediction Package version 3.0.4 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction AnalysisID: Analysis_2 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction CohortID: 5645 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction OutcomeID: 5649 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction Cohort size: 999472 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction Covariates: 117097 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction Population size: 351153 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction Cases: 622 2019-04-30 16:07:54 [Main thread] INFO PatientLevelPrediction splitSeed: -3508226 2019-04-30 16:07:55 [Main thread] INFO PatientLevelPrediction personSplitter Creating a 25% test and 75% train (into 3 folds) stratified split by person 2019-04-30 16:07:55 [Main thread] INFO PatientLevelPrediction personSplitter Data split into 87788 test cases and 263365 train cases (87789, 87789, 87787) 2019-04-30 16:07:56 [Main thread] INFO PatientLevelPrediction Training Lasso Logistic Regression model

Spoke with Jenna and it appears to be a status variable that needs to be logged.

jreps commented 5 years ago

Adding logging for this to commit: a5a302b05cb163c37f0371f84c2497c7e7e7f34f