small improvement for is.rsi.eligible, more unit tests

tests/testthat/test-mdro.R

@@ -4,7 +4,12 @@ context("mdro.R")
 test_that("MDRO works", {
   library(dplyr)
 
-  outcome <- suppressWarnings(MDRO(septic_patients, "EUCAST", info = TRUE))
+  expect_error(suppressWarnings(MDRO(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
+  expect_error(suppressWarnings(MDRO(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
+  expect_error(suppressWarnings(MDRO(septic_patients, country = c("de", "nl"), info = TRUE)))
+  expect_error(suppressWarnings(MDRO(septic_patients, col_mo = "invalid", info = TRUE)))
+
+  outcome <- suppressWarnings(MDRO(septic_patients))
   outcome <- suppressWarnings(EUCAST_exceptional_phenotypes(septic_patients, info = TRUE))
   # check class
   expect_equal(outcome %>% class(), c('ordered', 'factor'))

tests/testthat/test-mo.R

@@ -22,6 +22,11 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo("L. pneumophila")), "LEGPNE")
   expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
   expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
+  expect_equal(as.character(as.mo("Strepto")), "STC") # not Streptobacillus
+  expect_equal(as.character(as.mo("Streptococcus")), "STC") # not Peptostreptoccus
+
+  expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("STCGRA", "STCGRB"))
+
 
   expect_equal(as.character(as.mo("S. pyo")), "STCPYO") # not Actinomyces pyogenes
 
@@ -31,7 +36,7 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo("Gram negative rods")), "GNR")
 
   # GLIMS
-  expect_equal(as.character(as.mo("shiboy")), "SHIBOY")
+  expect_equal(as.character(as.mo("bctfgr")), "BACFRA")
 
   expect_equal(as.character(as.mo("MRSE")), "STAEPI")
   expect_equal(as.character(as.mo("VRE")), "ENC")