fix add manual ab

.github/workflows/check-devel.yaml

@@ -33,6 +33,10 @@ on:
     branches: '**'
   push:
     branches: '**'
+  schedule:
+    # run a schedule everyday at 1 AM.
+    # this is to check that all dependencies are still available (see R/zzz.R)
+    cron:  '0 1 * * *'
 
 name: check-devel
 

.github/workflows/check-release.yaml

@@ -34,7 +34,7 @@ on:
   schedule:
     # run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)
-    - cron:  '0 1 * * *'
+    cron:  '0 1 * * *'
 
 name: check-release
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9018
-Date: 2022-10-15
+Version: 1.8.2.9019
+Date: 2022-10-18
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9018
+# AMR 1.8.2.9019
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 

R/add_custom_antimicrobials.R

@@ -112,13 +112,19 @@ add_custom_antimicrobials <- function(x) {
   AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
   class(AMR_env$AB_lookup$ab) <- "character"
 
-  bind_rows <- import_fn("bind_rowtts", "dplyr", error_on_fail = FALSE)
+  bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
   if (is.null(bind_rows)) {
     # do the binding in base R
     new_df <- AMR_env$AB_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
     rownames(new_df) <- NULL
+    list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
+    for (l in which(list_cols)) {
+      # prevent binding NULLs in lists, replace with NA
+      new_df[, l] <- as.list(NA_character_)
+    }
     for (col in colnames(x)) {
-      new_df[, col] <- x[, col, drop = TRUE]
+      # assign new values
+      new_df[, col] <-  x[, col, drop = TRUE]
     }
     AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
   } else {

inst/tinytest/test-zzz.R

@@ -34,6 +34,7 @@
 import_functions <- c(
   "%chin%" = "data.table",
   "anti_join" = "dplyr",
+  "bind_rows" = "dplyr",
   "chmatch" = "data.table",
   "cur_column" = "dplyr",
   "full_join" = "dplyr",
@@ -54,8 +55,8 @@ import_functions <- c(
   "semi_join" = "dplyr",
   "showQuestion" = "rstudioapi"
 )
-# functions that are called directly
 
+# functions that are called directly with ::
 call_functions <- c(
   # cleaner
   "freq.default" = "cleaner",
@@ -104,6 +105,7 @@ extended_functions <- c(
   "get_skimmers" = "skimr",
   "type_sum" = "tibble",
   "vec_cast" = "vctrs",
+  "vec_math" = "vctrs",
   "vec_ptype2" = "vctrs"
 )