merge with develop

.Rbuildignore

@@ -2,6 +2,7 @@
 ^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^.vscode$
 standalone
 deploy.sh
 extras/*
@@ -11,5 +12,6 @@ compare_versions
 docs/*
 _pkgdown.yml
 ^vignettes/articles$
+^vignettes/Videos.Rmd
 ^doc$
 ^Meta$

.gitignore

@@ -25,3 +25,8 @@ standalone/build/*
 /inst/shiny/DiagnosticsExplorer/rsconnect/*
 /doc/
 /Meta/
+/extras/
+/results/
+/.vscode/
+.project
+.cproject

DESCRIPTION

@@ -1,7 +1,6 @@
 Package: PatientLevelPrediction
 Type: Package
-Title: Developing patient level prediction using data in the OMOP Common Data
-    Model
+Title: Developing Patient Level Prediction Models Using the Observational Medical Outcomes Partnership Common Data Model
 Version: 6.3.9.9999
 Date: 2024-10-10
 Authors@R: c(
@@ -10,12 +9,12 @@ Authors@R: c(
     person("Martijn", "Schuemie", role = c("aut")),
     person("Marc", "Suchard", role = c("aut")),
     person("Patrick", "Ryan", role = c("aut")),
-    person("Peter", "Rijnbeek", role = c("aut"))
-    )
-Description: A user friendly way to create patient level prediction models using the OMOP common data model. Given a
+    person("Peter", "Rijnbeek", role = c("aut")),
+    person("Observational Health Data Science and Informatics", role = c("cph")))
+Description: A user friendly way to create patient level prediction models using the OMOP (ObservationalMedical Outcomes Partnership) common data model. Given a
     cohort of interest and an outcome of interest, the package can use data in the
     OMOP Common Data Model to build a large set of features. These features can then
-    be assessed to fit a predictive model using a number of machine learning algorithms.
+    be used to fit a predictive model with a number of machine learning algorithms.
     Several performance measures are implemented for model evaluation.
 License: Apache License 2.0
 URL: https://ohdsi.github.io/PatientLevelPrediction, https://github.com/OHDSI/PatientLevelPrediction
@@ -27,50 +26,41 @@ Imports:
     Andromeda,
     Cyclops (>= 3.0.0),
     DatabaseConnector (>= 6.0.0),
+    digest,
     dplyr,
     FeatureExtraction (>= 3.0.0),
-    ggplot2,
-    gridExtra,
     Matrix,
     memuse,
-    mgcv,
     ParallelLogger (>= 2.0.0),
-    polspline,
     pROC,
     PRROC,
-    reticulate (>= 1.30),
     rlang,
     SqlRender (>= 1.1.3),
-    survival,
     tidyr,
     utils
 Suggests:
-    AUC,
-    BigKnn (>= 1.0.0),
-    devtools,
-    Eunomia,
+    Eunomia (>= 2.0.0),
+    ggplot2,
+    gridExtra,
     IterativeHardThresholding,
     knitr,
-    markdown,
     Metrics,
+    mgcv,
     parallel,
-    plyr, 
-    pool,
+    polspline,
     readr,
     ResourceSelection,
     ResultModelManager (>= 0.2.0),
+    reticulate (>= 1.30),
     rmarkdown,
     RSQLite,
     scoring,
-    ShinyAppBuilder (>= 1.1.1),
+    OhdsiShinyAppBuilder (>= 1.0.0),
+    survival,
     survminer,
     testthat,
     withr,
     xgboost (> 1.3.2.1),
     lightgbm
-Remotes:
-    ohdsi/BigKnn,
-    ohdsi/ShinyAppBuilder,
-    ohdsi/ResultModelManager
 RoxygenNote: 7.3.2
 Encoding: UTF-8

NAMESPACE

@@ -22,6 +22,7 @@ export(createDatabaseSchemaSettings)
 export(createDefaultExecuteSettings)
 export(createDefaultSplitSetting)
 export(createExecuteSettings)
+export(createExistingSplitSettings)
 export(createFeatureEngineeringMapColumnsSettings)
 export(createFeatureEngineeringSettings)
 export(createGlmModel)
@@ -103,7 +104,6 @@ export(setCoxModel)
 export(setDecisionTree)
 export(setGradientBoostingMachine)
 export(setIterativeHardThresholding)
-export(setKNN)
 export(setLassoLogisticRegression)
 export(setLightGBM)
 export(setMLP)

NEWS.md

@@ -1,5 +1,7 @@
 PatientLevelPrediction develop
 ======================
+- Added existingSplit settings where users can split data bases on an 
+existing split
 - Fixed linting errors and R codestyle in docs to conform to HADES style
 - Remove links to pdf's, point to website instead.
 - Fix broken links in Readme and BuildingPredictiveModels vignette

PatientLevelPrediction.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 6acb9f49-7428-4e24-8a2a-6b10f35b95e2
 
 RestoreWorkspace: No
 SaveWorkspace: No