From 2dcb419b641ff1e2c35a8f24f08a44e434c09fd0 Mon Sep 17 00:00:00 2001 From: catalamarti Date: Fri, 7 Mar 2025 13:12:02 +0000 Subject: [PATCH 1/3] dont use get --- R/getRoutes.R | 2 +- R/stratifyByRoute.R | 2 +- R/subsetOnRouteCategory.R | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/getRoutes.R b/R/getRoutes.R index c32b8da..e1996ad 100644 --- a/R/getRoutes.R +++ b/R/getRoutes.R @@ -31,7 +31,7 @@ getRouteCategories <- function(cdm) { # relate does form concept id with the classification established by # doseFormToRoute - doseRouteData <- get("doseFormToRoute") + doseRouteData <- doseFormToRoute routeCategory <- cdm$concept_relationship |> # get dose form available in the cdm diff --git a/R/stratifyByRoute.R b/R/stratifyByRoute.R index 98a371f..328a4c5 100644 --- a/R/stratifyByRoute.R +++ b/R/stratifyByRoute.R @@ -43,7 +43,7 @@ stratifyByRouteCategory <- function(x, cdm, keepOriginal = FALSE){ } checkmate::assertLogical(keepOriginal, len = 1) - doseRouteData <- get("doseFormToRoute") + doseRouteData <- doseFormToRoute tableCodelist <- paste0(omopgenerics::uniqueTableName(), omopgenerics::uniqueId()) diff --git a/R/subsetOnRouteCategory.R b/R/subsetOnRouteCategory.R index d460677..3fc0add 100644 --- a/R/subsetOnRouteCategory.R +++ b/R/subsetOnRouteCategory.R @@ -44,7 +44,7 @@ subsetOnRouteCategory <- function(x, cdm, routeCategory){ cli::cli_abort("routeCategory must be a character vector") } - doseRouteData <- get("doseFormToRoute") + doseRouteData <- doseFormToRoute tableCodelist <- paste0(omopgenerics::uniqueTableName(), omopgenerics::uniqueId()) From 16d6409fc4f942b10000e968348c29eeb05bc86d Mon Sep 17 00:00:00 2001 From: catalamarti Date: Fri, 7 Mar 2025 13:17:09 +0000 Subject: [PATCH 2/3] use :: --- R/getRoutes.R | 2 +- R/stratifyByRoute.R | 2 +- R/subsetOnRouteCategory.R | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/getRoutes.R b/R/getRoutes.R index e1996ad..3f72451 100644 --- a/R/getRoutes.R +++ b/R/getRoutes.R @@ -31,7 +31,7 @@ getRouteCategories <- function(cdm) { # relate does form concept id with the classification established by # doseFormToRoute - doseRouteData <- doseFormToRoute + doseRouteData <- CodelistGenerator::doseFormToRoute routeCategory <- cdm$concept_relationship |> # get dose form available in the cdm diff --git a/R/stratifyByRoute.R b/R/stratifyByRoute.R index 328a4c5..45ef32e 100644 --- a/R/stratifyByRoute.R +++ b/R/stratifyByRoute.R @@ -43,7 +43,7 @@ stratifyByRouteCategory <- function(x, cdm, keepOriginal = FALSE){ } checkmate::assertLogical(keepOriginal, len = 1) - doseRouteData <- doseFormToRoute + doseRouteData <- CodelistGenerator::doseFormToRoute tableCodelist <- paste0(omopgenerics::uniqueTableName(), omopgenerics::uniqueId()) diff --git a/R/subsetOnRouteCategory.R b/R/subsetOnRouteCategory.R index 3fc0add..b3aa545 100644 --- a/R/subsetOnRouteCategory.R +++ b/R/subsetOnRouteCategory.R @@ -44,7 +44,7 @@ subsetOnRouteCategory <- function(x, cdm, routeCategory){ cli::cli_abort("routeCategory must be a character vector") } - doseRouteData <- doseFormToRoute + doseRouteData <- CodelistGenerator::doseFormToRoute tableCodelist <- paste0(omopgenerics::uniqueTableName(), omopgenerics::uniqueId()) From e0f298de3f647e90db997619a4354129c400d83e Mon Sep 17 00:00:00 2001 From: catalamarti Date: Fri, 7 Mar 2025 13:19:04 +0000 Subject: [PATCH 3/3] add development version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 05b76de..5feabd0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: CodelistGenerator Title: Identify Relevant Clinical Codes and Evaluate Their Use -Version: 3.4.0 +Version: 3.4.0.900 Authors@R: c( person("Edward", "Burn", email = "edward.burn@ndorms.ox.ac.uk", role = c("aut", "cre"),