fixes

inst/tinytest/test-first_isolate.R

@@ -214,7 +214,7 @@ expect_equal(
   1108
 )
 
-# empty rsi results
+# empty sir results
 expect_equal(
   sum(first_isolate(example_isolates, include_untested_sir = FALSE)),
   1366

inst/tinytest/test-rsi.R

@@ -69,7 +69,7 @@ expect_error(as.sir.mic(as.mic(16)))
 expect_error(as.sir.disk(as.disk(16)))
 expect_error(get_guideline("this one does not exist"))
 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
-  # 40 rsi columns
+  # 40 sir columns
   expect_equal(
     example_isolates %>%
       mutate_at(vars(PEN:RIF), as.character) %>%
@@ -218,7 +218,7 @@ expect_inherits(
 expect_inherits(
   suppressWarnings(as.sir(data.frame(
     mo = "Escherichia coli",
-    amoxi = c("R", "S", "I", "invalid")
+    amoxi = c("S", "I", "R", "invalid")
   ))$amoxi),
   "sir"
 )

inst/tinytest/test-vctrs.R

@@ -33,7 +33,7 @@ if (AMR:::pkg_is_available("dplyr", also_load = FALSE)) {
                         mo = as.mo("Escherichia coli"),
                         mic = as.mic(2),
                         disk = as.disk(20),
-                        rsi = as.sir("S"))
+                        sir = as.sir("S"))
   check1 <- lapply(test, class)
   test[1, "ab"] <- "GEN"
   test[1, "mo"] <- "B_KLBSL_PNMN"