patient ID in first isolate

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9150
+Version: 1.8.2.9151
 Date: 2023-03-11
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9150
+# AMR 1.8.2.9151
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/first_isolate.R

@@ -350,7 +350,7 @@ first_isolate <- function(x = NULL,
   x$newvar_mo <- as.mo(x[, col_mo, drop = TRUE])
   x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
   x$newvar_date <- x[, col_date, drop = TRUE]
-  x$newvar_patient_id <- x[, col_patient_id, drop = TRUE]
+  x$newvar_patient_id <- as.character(x[, col_patient_id, drop = TRUE])
 
   if (is.null(col_testcode)) {
     testcodes_exclude <- NULL
@@ -378,7 +378,7 @@ first_isolate <- function(x = NULL,
     }
   }
   if (!is.null(col_keyantimicrobials)) {
-    x$newvar_key_ab <- x[, col_keyantimicrobials, drop = TRUE]
+    x$newvar_key_ab <- as.character(x[, col_keyantimicrobials, drop = TRUE])
   }
 
   if (is.null(testcodes_exclude)) {

R/proportion.R

@@ -303,13 +303,14 @@ sir_confidence_interval <- function(...,
   }
   if (isTRUE(as_percent)) {
     out <- percentage(out, digits = 1)
-  } else {
-    out <- round(out, digits = 3)
   }
   if (!isFALSE(collapse) && length(out) > 1) {
+    if (is.numeric(out)) {
+      out <- round(out, digits = 3)
+    }
     out <- paste(out, collapse = ifelse(isTRUE(collapse), "-", collapse))
   }
-  
+
   if (n < minimum) {
     warning_("Introducing NA: ",
              ifelse(n == 0, "no", paste("only", n)),