Snakecase functions are deprecated in CDMConnector 1.7.0

data-raw/test_db/create_test_db.R

@@ -21,7 +21,7 @@ schema <- "main"
 withr::with_envvar(
   new = c(EUNOMIA_DATA_FOLDER = dir),
   {
-    invisible(CDMConnector::eunomia_dir(dataset_name = name, cdm_version = version))
+    invisible(CDMConnector::eunomiaDir(datasetName = name, cdmVersion = version))
   }
 )
 
@@ -103,7 +103,7 @@ write_table(dummy_observations, con, "observation", schema = schema)
 
 ## Verify integrity, turn warnings into error
 tryCatch(
-  cdm <- CDMConnector::cdm_from_con(con, cdm_schema = schema, write_schema = schema),
+  cdm <- CDMConnector::cdmFromCon(con, cdmSchema = schema, writeSchema = schema),
   warning = function(cnd) {
     msg <- sprintf("CDM integrity check produced warnings: %s", conditionMessage(cnd))
     rlang::abort(msg, call = NULL)

data-raw/test_db/dummy/add_dummy_bundle_concepts.R

@@ -9,11 +9,11 @@ here::i_am("data-raw/test_db/dummy/add_dummy_bundle_concepts.R")
 db_path <- here::here("data-raw/test_db/eunomia/synthea-allergies-10k_5.3_1.0.duckdb")
 
 con <- connect_to_db(db_path)
-eunomia_cdm <- CDMConnector::cdm_from_con(
+eunomia_cdm <- CDMConnector::cdmFromCon(
   con = con,
-  cdm_schema = "main",
-  write_schema = "main",
-  cdm_name = "synthea-allergies-10k"
+  cdmSchema = "main",
+  writeSchema = "main",
+  cdmName = "synthea-allergies-10k"
 )
 eunomia_concepts <- eunomia_cdm$concept |> dplyr::pull(concept_id)
 

preprocessing/R/concepts.R

@@ -1,6 +1,6 @@
 #' Generate the `omopcat_concepts` table
 #'
-#' @param cdm A [`CDMConnector`] object, e.g. from [`CDMConnector::cdm_from_con()`]
+#' @param cdm A [`CDMConnector`] object, e.g. from [`CDMConnector::cdmFromCon()`]
 #' @param concept_ids A vector of concept IDs
 #'
 #' @return A `data.frame` with the monthly counts

preprocessing/R/monthly_counts.R

@@ -1,6 +1,6 @@
 #' Generate the 'omopcat_monthly_counts' table
 #'
-#' @param cdm A [`CDMConnector`] object, e.g. from [`CDMConnector::cdm_from_con()`]
+#' @param cdm A [`CDMConnector`] object, e.g. from [`CDMConnector::cdmFromCon()`]
 #' @param threshold Threshold value below which values will be replaced by `replacement`
 #' @param replacement Value with which values below `threshold` will be replaced
 #' @param level At which resolution the counts should be summarised.

preprocessing/R/preprocess.R

@@ -104,7 +104,7 @@ preprocess <- function(out_path = Sys.getenv("PREPROCESS_OUT_PATH")) {
 #' configured through the relevant environment variables.
 #'
 #' When not in production, creates a CDM from one of the CDMConnector example
-#' datasets (`"GiBleed"` by default), using [`CDMConnector::eunomia_dir()`].
+#' datasets (`"GiBleed"` by default), using [`CDMConnector::eunomiaDir()`].
 #' This is intended for use in testing and development.
 #'
 #' @param .envir Passed on to [`connect_to_db()`], controls the scope in which the database
@@ -124,16 +124,16 @@ preprocess <- function(out_path = Sys.getenv("PREPROCESS_OUT_PATH")) {
     )
   } else {
     name <- Sys.getenv("DB_NAME", unset = "GiBleed")
-    duckdb_path <- CDMConnector::eunomia_dir(dataset_name = name)
+    duckdb_path <- CDMConnector::eunomiaDir(datasetName = name)
     rlang::check_installed("duckdb")
     con <- connect_to_db(duckdb::duckdb(duckdb_path), .envir = .envir)
   }
 
   # Load the data in a CDMConnector object
-  CDMConnector::cdm_from_con(
+  CDMConnector::cdmFromCon(
     con = con,
-    cdm_schema = Sys.getenv("DB_CDM_SCHEMA", unset = "main"),
-    write_schema = Sys.getenv("DB_CDM_SCHEMA", unset = "main"),
-    cdm_name = name
+    cdmSchema = Sys.getenv("DB_CDM_SCHEMA", unset = "main"),
+    writeSchema = Sys.getenv("DB_CDM_SCHEMA", unset = "main"),
+    cdmName = name
   )
 }

preprocessing/R/summary_stats.R

@@ -1,6 +1,6 @@
 #' Generate the `omopcat_summary_stats` table
 #'
-#' @param cdm A [`CDMConnector`] object, e.g. from [`CDMConnector::cdm_from_con()`]
+#' @param cdm A [`CDMConnector`] object, e.g. from [`CDMConnector::cdmFromCon()`]
 #' @param threshold Threshold value below which values will be replaced by `replacement`
 #' @param replacement Value with which values below `threshold` will be replaced
 #'