From 6adfde6b98d63deda9c4012d020e6bc12492b2b1 Mon Sep 17 00:00:00 2001
From: Henrik John <l.john@erasmusmc.nl>
Date: Tue, 27 Aug 2024 17:22:56 +0200
Subject: [PATCH] Pass embedding dimensions to model

---
 R/Estimator.R | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/R/Estimator.R b/R/Estimator.R
index 19f414e..850eab1 100644
--- a/R/Estimator.R
+++ b/R/Estimator.R
@@ -218,6 +218,7 @@ fitEstimator <- function(trainData,
       included = incs,
       covariateValue = 0,
       isNumeric = .data$columnId %in% cvResult$numericalIndex
+      # get mapping maybe here
     )
 
   comp <- start - Sys.time()
@@ -268,6 +269,7 @@ fitEstimator <- function(trainData,
       hyperParamSearch = hyperSummary
     ),
     covariateImportance = covariateRef
+    # also return mapping as part of covariateRef above, not necessary to do separately
   )
 
   class(result) <- "plpModel"
@@ -301,6 +303,7 @@ predictDeepEstimator <- function(plpModel,
       cohort = cohort,
       mapping = plpModel$covariateImportance %>%
         dplyr::select("columnId", "covariateId")
+      # check this if it is correclty passing the mapped data rather than creating a new mapping
     )
     data <- createDataset(mappedData, plpModel = plpModel)
   }
@@ -421,6 +424,7 @@ gridCvDeep <- function(mappedData,
   prediction$cohortStartDate <- as.Date(prediction$cohortStartDate,
     origin = "1970-01-01")
   numericalIndex <- dataset$get_numerical_features()
+  # get mapping as above
   
   # save torch code here
   if (!dir.exists(file.path(modelLocation))) {
@@ -434,6 +438,7 @@ gridCvDeep <- function(mappedData,
       finalParam = finalParam,
       paramGridSearch = paramGridSearch,
       numericalIndex = numericalIndex$to_list()
+      # add mapping here, two columns [covariateId, columnId]
     )
   )
 }
@@ -577,8 +582,9 @@ doCrossValidationImpl <- function(dataset,
     fillEstimatorSettings(modelSettings$estimatorSettings,
                           fitParams,
                           parameters)
-  currentModelParams$catFeatures <- dataset$get_cat_features()$max()
+  currentModelParams$catFeatures <- dataset$get_cat_features()$len()
   currentModelParams$numFeatures <- dataset$get_numerical_features()$len()
+  currentModelParams$cat2Features <- dataset$get_cat_2_features()$len()
   if (currentEstimatorSettings$findLR) {
     lr <- getLR(currentModelParams, currentEstimatorSettings, dataset)
     ParallelLogger::logInfo(paste0("Auto learning rate selected as: ", lr))
@@ -659,7 +665,8 @@ trainFinalModel <- function(dataset, finalParam, modelSettings, labels) {
   
     fitParams <- names(finalParam)[grepl("^estimator", names(finalParam))]
     
-    modelParams$catFeatures <- dataset$get_cat_features()$max()
+    modelParams$catFeatures <- dataset$get_cat_features()$len()
+    modelParams$cat2Features <- dataset$get_cat_2_features()$len()
     modelParams$numFeatures <- dataset$get_numerical_features()$len()
     modelParams$modelType <- modelSettings$modelType