fix notes

OHDSI · Jan 13, 2025 · bf0c6c4 · bf0c6c4
1 parent 7169aba
commit bf0c6c4
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/R/Imputation.R b/R/Imputation.R
@@ -117,7 +117,7 @@ simpleImpute <- function(trainData, featureEngineeringSettings, done = FALSE) {
       numericData$imputedValues <- numericData$covariates %>%
           dplyr::group_by(.data$covariateId) %>%
           dplyr::collect() %>% # median not possible in sql
-          dplyr::summarise(imputedValues = median(.data$covariateValue, na.rm = TRUE))
+          dplyr::summarise(imputedValues = stats::median(.data$covariateValue, na.rm = TRUE))
     }
 
     allRowIds <- outputData$labels$rowId
@@ -460,7 +460,7 @@ pmmFit <- function(data, k = 5) {
     dplyr::pull(.data$y), alpha = 1, nfolds = 3)
 
   # predict on both XObs and XMiss
-  predsObs <- predict(fit, xObs, fit$lambda.min)
+  predsObs <- stats::predict(fit, xObs, fit$lambda.min)
   data$xMiss <- data$xMiss %>%
     dplyr::left_join(
       data$xMiss %>%

diff --git a/R/PreprocessingData.R b/R/PreprocessingData.R
@@ -192,7 +192,7 @@ robustNormalize <- function(trainData, featureEngineeringSettings, normalized =
       dplyr::summarise(
         q25 = dplyr::sql("lower_quartile(covariateValue)"),
         q75 = dplyr::sql("upper_quartile(covariateValue)"),
-        median = median(.data$covariateValue, na.rm = TRUE)
+        median = stats::median(.data$covariateValue, na.rm = TRUE)
       ) %>%
       dplyr::mutate(iqr = .data$q75 - .data$q25) %>%
       dplyr::select(-c("q75", "q25")) %>%

diff --git a/tests/testthat/test-imputation.R b/tests/testthat/test-imputation.R
@@ -15,7 +15,8 @@ createMissingData <- function(trainData, missingness) {
                                      covariateValue = covariateValue))
   Andromeda::appendToTable((missingData$covariateData$covariateRef),
                           data.frame(covariateId = 666,
-                                     covariateName = "fakeMissingVariable" = 666,
+                                     covariateName = "fakeMissingVariable",
+                                     analysisId = 666,
                                      conceptId = 666))
   Andromeda::appendToTable(missingData$covariateData$analysisRef,
                          data.frame(analysisId = 666,