Dependancies (#518)

* use rlang::check_installed instead of ensure_installed * move mgcv to suggests, guard mgcv use behing check_installed, lint smoothCalibration * move survival packages to suggest and add guard * add guards for survival functionality and move packages to suggest * reticulate in suggest and behind guard * tests pass without suggested packages or python * remove BigKnn and fix mentions of ShinyAppBuilder * remove unused suggested packages
OHDSI · Jan 10, 2025 · baa52d0 · baa52d0
1 parent 19d59ba
commit baa52d0
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diff --git a/.Rbuildignore b/.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$
diff --git a/.cproject b/.cproject
diff --git a/.gitignore b/.gitignore
@@ -25,3 +25,5 @@ standalone/build/*
 /inst/shiny/DiagnosticsExplorer/rsconnect/*
 /doc/
 /Meta/
+.project
+.cproject
diff --git a/.project b/.project
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,48 +30,38 @@ Imports:
     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
diff --git a/NAMESPACE b/NAMESPACE
@@ -102,7 +102,6 @@ export(setCoxModel)
 export(setDecisionTree)
 export(setGradientBoostingMachine)
 export(setIterativeHardThresholding)
-export(setKNN)
 export(setLassoLogisticRegression)
 export(setLightGBM)
 export(setMLP)

diff --git a/PatientLevelPrediction.Rproj b/PatientLevelPrediction.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 6acb9f49-7428-4e24-8a2a-6b10f35b95e2
 
 RestoreWorkspace: No
 SaveWorkspace: No