(v2.1.1.9048) vctrs update for sir

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9047
+Version: 2.1.1.9048
 Date: 2024-06-13
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9047
+# AMR 2.1.1.9048
 
 *(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!)*
 

R/aa_globals.R

@@ -161,6 +161,7 @@ globalVariables(c(
   "microorganisms",
   "microorganisms.codes",
   "mo",
+  "n",
   "name",
   "new",
   "numerator",
@@ -186,8 +187,10 @@ globalVariables(c(
   "total",
   "txt",
   "type",
+  "uti_index",
   "value",
   "varname",
+  "x",
   "xvar",
   "y",
   "year",

R/sir.R

@@ -362,10 +362,16 @@ as.sir.default <- function(x,
       x[x.bak == 2] <- "I"
       x[x.bak == 3] <- "R"
     }
-  } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "SDD", "I", "R", "N", NA_character_))) {
+  } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "I", "R", NA_character_))) {
     x[x.bak == "1"] <- "S"
     x[x.bak == "2"] <- "I"
     x[x.bak == "3"] <- "R"
+  } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "4", "5", "S", "SDD", "I", "R", "N", NA_character_))) {
+    x[x.bak == "1"] <- "S"
+    x[x.bak == "2"] <- "SDD"
+    x[x.bak == "3"] <- "I"
+    x[x.bak == "4"] <- "R"
+    x[x.bak == "5"] <- "N"
   } else if (!all(is.na(x)) && !identical(levels(x), c("S", "SDD", "I", "R", "N")) && !all(x %in% c("S", "SDD", "I", "R", "N", NA))) {
     if (all(x %unlike% "(S|I|R)", na.rm = TRUE)) {
       # check if they are actually MICs or disks
@@ -1133,7 +1139,7 @@ as_sir_method <- function(method_short,
     if (all(uti_current == FALSE, na.rm = TRUE)) {
       breakpoints_current <- breakpoints_current %pm>%
         # this will put UTI = FALSE first, then UTI = NA, then UTI = TRUE
-        pm_mutate(uti_index = ifelse(uti == FALSE, 1, 
+        pm_mutate(uti_index = ifelse(is.na(uti) & uti == FALSE, 1, 
                                      ifelse(is.na(uti), 2,
                                             3))) %pm>%
         # be as specific as possible (i.e. prefer species over genus):
@@ -1170,22 +1176,22 @@ as_sir_method <- function(method_short,
     } else {
       site <- paste0("body site '", site, "'")
     }
-    if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_coerced)) {
+    if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_current)) {
       # only UTI breakpoints available
       warning_("in `as.sir()`: interpretation of ", font_bold(ab_formatted), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms, thus assuming `uti = TRUE`. See `?as.sir`.")
       rise_warning <- TRUE
-    } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_coerced)) {
+    } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_current)) {
       # both UTI and Non-UTI breakpoints available
       msgs <- c(msgs, paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`."))
       breakpoints_current <- breakpoints_current %pm>%
         pm_filter(uti == FALSE)
-    } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_coerced)) {
+    } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
       # breakpoints for multiple body sites available
       msgs <- c(msgs, paste0("Multiple breakpoints available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, "."))
     }
 
     # first check if mo is intrinsic resistant
-    if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_coerced) %in% AMR_env$intrinsic_resistant) {
+    if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_current) %in% AMR_env$intrinsic_resistant) {
       msgs <- c(msgs, paste0("Intrinsic resistance applied for ", ab_formatted, " in ", mo_formatted, ""))
       new_sir <- rep(as.sir("R"), length(rows))
     } else if (nrow(breakpoints_current) == 0) {

R/vctrs.R

@@ -179,10 +179,13 @@ vec_arith.mic <- function(op, x, y, ...) {
 
 # S3: sir ----
 vec_ptype2.sir.default <- function (x, y, ..., x_arg = "", y_arg = "") {
-  x
+  NA_sir_[0]
 }
 vec_ptype2.sir.sir <- function(x, y, ...) {
-  x
+  NA_sir_[0]
+}
+vec_ptype2.character.sir <- function(x, y, ...) {
+  NA_sir_[0]
 }
 vec_cast.character.sir <- function(x, to, ...) {
   as.character(x)

R/zzz.R

@@ -176,6 +176,7 @@ AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %o
   # S3: sir
   s3_register("vctrs::vec_ptype2", "sir.default")
   s3_register("vctrs::vec_ptype2", "sir.sir")
+  s3_register("vctrs::vec_ptype2", "character.sir")
   s3_register("vctrs::vec_cast", "character.sir")
   s3_register("vctrs::vec_cast", "sir.character")
 

data-raw/ab.md5

@@ -1 +1 @@
-3e7a1cbb21b49cdc7626ea3016a017cc
+4e536434d1301bedaec0e856c74cded8

data-raw/antibiotics.txt

@@ -9,7 +9,7 @@
 "AMC"	23665637	"Amoxicillin/clavulanic acid"	"Beta-lactams/penicillins"	"J01CR02"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/c,amcl,aml,aug,xl"	"amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,augmentan,augmentin,augmentin xr,augmentine,auspilic,clamentin,clamobit,clavamox,clavinex,clavoxilin plus,clavulin,clavumox,coamoxiclav,eumetinex,kmoxilin,spectramox,spektramox,synulox,viaclav,xiclav"	1.5	"g"	3	"g"	""
 "AXS"	465441	"Amoxicillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					"55614-2,55615-9,55616-7"
 "AMB"	5280965	"Amphotericin B"	"Antifungals/antimycotics"	"A01AB04,A07AA07,G01AA03,J02AA01"	"Antimycotics for systemic use"	"Antibiotics"	"amf,amfb,amph"	"abelcet,abelecet,ambisome,amfotericina b,amphocin,amphomoronal,amphortericin b,amphotec,amphotericin,amphotericin b,amphotericine b,amphotericinum b,amphozone,anfotericine b,fungilin,fungisome,fungisone,fungizone,halizon"	40	"mg"	210	"mg"	"16370-9,18863-1,23-2,24-0,25-7,26-5,3353-0,3354-8,40707-2,40757-7,49859-2,6978-1"
-"AMH"		"Amphotericin B-high"	"Aminoglycosides"	"NA"			"amfo b high,amhl,ampho b high,amphotericin high"	""					""
+"AMH"		"Amphotericin B-high"	"Antifungals/antimycotics"	"NA"			"amfo b high,amhl,ampho b high,amphotericin high"	""					""
 "AMP"	6249	"Ampicillin"	"Beta-lactams/penicillins"	"J01CA01,S01AA19"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"am,amp,ampi"	"acillin,adobacillin,amblosin,amcill,amfipen,amfipen v,amipenix s,ampichel,ampicil,ampicilina,ampicillin,ampicillin a,ampicillin acid,ampicillin anhydrate,ampicillin anhydrous,ampicillin base,ampicillin hydrate,ampicillin sodium,ampicillina,ampicilline,ampicillinum,ampicin,ampifarm,ampikel,ampimed,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,anhydrous ampicillin,austrapen,binotal,bonapicillin,britacil,campicillin,copharcilin,delcillin,deripen,divercillin,doktacillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,olin kid,omnipen,orbicilina,pen a oral,pen ampil,penbristol,penbritin,penbritin paediatric,penbritin syrup,penbrock,penicline,penimic,pensyn,pentrex,pentrexl,pentrexyl,pentritin,pfizerpen a,polycillin,polyflex,ponecil,princillin,principen,qidamp,racenacillin,redicilin,rosampline,roscillin,semicillin,semicillin r,servicillin,sumipanto,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,viccillin s,vidocillin,wypicil"	2	"g"	6	"g"	"101477-8,101478-6,18864-9,18865-6,20374-5,21066-6,23618-2,27-3,28-1,29-9,30-7,31-5,32-3,33-1,3355-5,33562-0,33919-2,34-9,43883-8,43884-6,6979-9,6980-7,87604-5"
 "SAM"	119561	"Ampicillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR01"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/s,ab,ams,amsu,apsu,sam"	"sulacillin"			6	"g"	"101478-6,18865-6,20374-5,23618-2,31-5,32-3,33-1,34-9,6980-7"
 "AMR"	73341	"Amprolium"	"Other antibacterials"	"QP51BX02"			""	"amprocidum,amprol,amprolio,amprolium,amprolium chloride,amprovine,thiacoccid"					""

inst/tinytest/test-sir.R

@@ -92,6 +92,12 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
                 mutate(MEM = as.sir(ifelse(AMC == "S", "S", MEM))) %>% 
                 pull(MEM) %>% 
                 is.sir())
+
+  expect_true(example_isolates %>% 
+                select(AMC, MEM) %>% 
+                mutate(MEM = if_else(AMC == "S", "S", MEM)) %>% 
+                pull(MEM) %>% 
+                is.sir())
 }
 if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
   expect_inherits(