Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
Added uti (as abbreviation of urinary tract infections) as parameter to as.rsi(), so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
Info printing in functions eucast_rules(), first_isolate(), mdro() and resistance_predict() will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)
eucast_rules( x, col_mo = NULL, - info = TRUE, + info = interactive(), rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE, ... diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index 7d98a1fc..a104e387 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 60d8f6ea..26ddd36f 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -79,7 +79,7 @@ @@ -241,7 +241,7 @@ type = "keyantibiotics", ignore_I = TRUE, points_threshold = 2, - info = TRUE, + info = interactive(), include_unknown = FALSE, ... ) diff --git a/docs/reference/index.html b/docs/reference/index.html index 6b1c899b..f7c2ee1e 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ @@ -451,6 +451,12 @@Data set with 2,000 example isolates
+ + + ++ Data set with unclean data
+ diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index 084d51a3..95ac9936 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -79,7 +79,7 @@ @@ -229,7 +229,7 @@ x, guideline = "CMI2012", col_mo = NULL, - info = TRUE, + info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE, verbose = FALSE, diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index 6a25eb11..58fef3c2 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -79,7 +79,7 @@ @@ -236,7 +236,7 @@ model = NULL, I_as_S = TRUE, preserve_measurements = TRUE, - info = TRUE, + info = interactive(), ... ) @@ -251,7 +251,7 @@ model = NULL, I_as_S = TRUE, preserve_measurements = TRUE, - info = TRUE, + info = interactive(), ... ) diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index e2a6b4d1..c1b1f37b 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -19,7 +19,7 @@ Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility test eucast_rules( x, col_mo = NULL, - info = TRUE, + info = interactive(), rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE, ... diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index a3b30774..cd9f51c9 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -27,7 +27,7 @@ first_isolate( type = "keyantibiotics", ignore_I = TRUE, points_threshold = 2, - info = TRUE, + info = interactive(), include_unknown = FALSE, ... ) diff --git a/man/mdro.Rd b/man/mdro.Rd index 727dc191..a7f3e9be 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -22,7 +22,7 @@ mdro( x, guideline = "CMI2012", col_mo = NULL, - info = TRUE, + info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE, verbose = FALSE, diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index 6f07acab..3356f1b3 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -18,7 +18,7 @@ resistance_predict( model = NULL, I_as_S = TRUE, preserve_measurements = TRUE, - info = TRUE, + info = interactive(), ... ) @@ -33,7 +33,7 @@ rsi_predict( model = NULL, I_as_S = TRUE, preserve_measurements = TRUE, - info = TRUE, + info = interactive(), ... ) diff --git a/tests/testthat/test-disk.R b/tests/testthat/test-disk.R index 850426e3..f463319f 100755 --- a/tests/testthat/test-disk.R +++ b/tests/testthat/test-disk.R @@ -31,5 +31,9 @@ test_that("disk works", { expect_silent(as.disk(levels(as.disk(15)))) expect_warning(as.disk("INVALID VALUE")) + + expect_output(print(as.disk(12))) + library(tibble) + expect_output(print(tibble(d = as.disk(12)))) }) diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R index 531791a3..5d5ca8b5 100755 --- a/tests/testthat/test-eucast_rules.R +++ b/tests/testthat/test-eucast_rules.R @@ -110,9 +110,9 @@ test_that("EUCAST rules work", { "S") # also test norf - expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S")))) + expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE))) # check verbose output - expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE))) + expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, info = TRUE))) }) diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R index 5adf13b0..73c5cf6a 100755 --- a/tests/testthat/test-first_isolate.R +++ b/tests/testthat/test-first_isolate.R @@ -141,7 +141,8 @@ test_that("first isolates work", { mutate(first = first_isolate(., "date", "patient_id", col_mo = "mo", col_specimen = "specimen", - filter_specimen = "something_unexisting"))) + filter_specimen = "something_unexisting", + info = TRUE))) # printing of exclusion message expect_message(example_isolates %>% @@ -149,7 +150,8 @@ test_that("first isolates work", { col_mo = "mo", col_patient_id = "patient_id", col_testcode = "gender", - testcodes_exclude = "M")) + testcodes_exclude = "M", + info = TRUE)) # errors expect_error(first_isolate("date", "patient_id", col_mo = "mo"))