From 35963ca3dc890daef8140678b7946decefc6a297 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Sat, 24 Feb 2024 18:51:37 +0100
Subject: [PATCH] vctrs fix

---
 DESCRIPTION |  2 +-
 NEWS.md     |  2 +-
 R/vctrs.R   | 30 ++++++++++++++++--------------
 R/zzz.R     |  8 ++++----
 4 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 73f0c3bf..0838f154 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9007
+Version: 2.1.1.9008
 Date: 2024-02-24
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index a0e8937c..6b0b1c92 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9007
+# AMR 2.1.1.9008
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
 
diff --git a/R/vctrs.R b/R/vctrs.R
index fb318c9d..e3737ff8 100755
--- a/R/vctrs.R
+++ b/R/vctrs.R
@@ -34,29 +34,31 @@
 
 # see https://github.com/tidyverse/dplyr/issues/5955 why this is required
 
-# S3: ab_selector
-vec_ptype2.ab_selector.default <- function (x, y, ..., x_arg = "", y_arg = "") {
+# S3: ab_selector ----
+# this does not need a .default method since it's used internally only
+vec_ptype2.character.ab_selector <- function(x, y, ...) {
   x
 }
-vec_ptype2.ab_selector.ab_selector <- function(x, y, ...) {
-  x
+vec_ptype2.ab_selector.character <- function(x, y, ...) {
+  y
 }
 vec_cast.character.ab_selector <- function(x, to, ...) {
   unclass(x)
 }
 
-# S3: ab_selector_any_all
-vec_ptype2.ab_selector_any_all.default <- function (x, y, ..., x_arg = "", y_arg = "") {
+# S3: ab_selector_any_all ----
+# this does not need a .default method since it's used internally only
+vec_ptype2.logical.ab_selector_any_all <- function(x, y, ...) {
   x
 }
-vec_ptype2.ab_selector_any_all.ab_selector_any_all <- function(x, y, ...) {
-  x
+vec_ptype2.ab_selector_any_all.logical <- function(x, y, ...) {
+  y
 }
 vec_cast.logical.ab_selector_any_all <- function(x, to, ...) {
   unclass(x)
 }
 
-# S3: ab
+# S3: ab ----
 vec_ptype2.ab.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
@@ -70,7 +72,7 @@ vec_cast.ab.character <- function(x, to, ...) {
   return_after_integrity_check(x, "antimicrobial drug code", as.character(AMR_env$AB_lookup$ab))
 }
 
-# S3: av
+# S3: av ----
 vec_ptype2.av.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
@@ -84,7 +86,7 @@ vec_cast.av.character <- function(x, to, ...) {
   return_after_integrity_check(x, "antiviral drug code", as.character(AMR_env$AV_lookup$av))
 }
 
-# S3: mo
+# S3: mo ----
 vec_ptype2.mo.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
@@ -99,7 +101,7 @@ vec_cast.mo.character <- function(x, to, ...) {
   return_after_integrity_check(x, "microorganism code", as.character(AMR_env$MO_lookup$mo))
 }
 
-# S3: disk
+# S3: disk ----
 vec_ptype2.disk.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
@@ -125,7 +127,7 @@ vec_cast.disk.character <- function(x, to, ...) {
   as.disk(x)
 }
 
-# S3: mic
+# S3: mic ----
 vec_ptype2.mic.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
@@ -157,7 +159,7 @@ vec_arith.mic <- function(op, x, y, ...) {
   vctrs::vec_arith(op, as.double(x), as.double(y))
 }
 
-# S3: sir
+# S3: sir ----
 vec_ptype2.sir.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
diff --git a/R/zzz.R b/R/zzz.R
index 054b0329..ea9d093e 100755
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -133,12 +133,12 @@ if (pkg_is_available("cli")) {
   # Support vctrs package for use in e.g. dplyr verbs
   # NOTE 2024-02-22 this is the right way - it should be 2 S3 classes in the second argument
   # S3: ab_selector
-  s3_register("vctrs::vec_ptype2", "ab_selector.default")
-  s3_register("vctrs::vec_ptype2", "ab_selector.ab_selector")
+  s3_register("vctrs::vec_ptype2", "character.ab_selector")
+  s3_register("vctrs::vec_ptype2", "ab_selector.character")
   s3_register("vctrs::vec_cast", "character.ab_selector")
   # S3: ab_selector_any_all
-  s3_register("vctrs::vec_ptype2", "ab_selector_any_all.default")
-  s3_register("vctrs::vec_ptype2", "ab_selector_any_all.ab_selector_any_all")
+  s3_register("vctrs::vec_ptype2", "logical.ab_selector_any_all")
+  s3_register("vctrs::vec_ptype2", "ab_selector_any_all.logical")
   s3_register("vctrs::vec_cast", "logical.ab_selector_any_all")
   # S3: ab
   s3_register("vctrs::vec_ptype2", "ab.default")