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 7d98a1fc7..a104e387d 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 60d8f6eae..26ddd36fd 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 6b1c899bb..f7c2ee1e4 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 084d51a3f..95ac99366 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 6a25eb111..58fef3c23 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 e2a6b4d1d..c1b1f37b0 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 a3b30774d..cd9f51c97 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 727dc1916..a7f3e9be2 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 6f07acabc..3356f1b38 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 850426e38..f463319fc 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 531791a33..5d5ca8b5b 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 5adf13b03..73c5cf6a7 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"))