(v0.7.1.9102) lintr

man/bug_drug_combinations.Rd

@@ -67,7 +67,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 \donttest{
 x <- bug_drug_combinations(example_isolates)
 x
-format(x)
+format(x, translate_ab = "name (atc)")
 
 # Use FUN to change to transformation of microorganism codes
 x <- bug_drug_combinations(example_isolates, 

man/first_isolate.Rd

@@ -150,39 +150,11 @@ B <- example_isolates \%>\%
 # set key antibiotics to a new variable
 x$keyab <- key_antibiotics(x)
 
-x$first_isolate <-
-  first_isolate(x)
+x$first_isolate <- first_isolate(x)
 
-x$first_isolate_weighed <-
-  first_isolate(x,
-                col_keyantibiotics = 'keyab')
+x$first_isolate_weighed <- first_isolate(x, col_keyantibiotics = 'keyab')
 
-x$first_blood_isolate <-
-  first_isolate(x,
-                specimen_group = 'Blood')
-
-x$first_blood_isolate_weighed <-
-  first_isolate(x,
-                specimen_group = 'Blood',
-                col_keyantibiotics = 'keyab')
-
-x$first_urine_isolate <-
-  first_isolate(x,
-                specimen_group = 'Urine')
-
-x$first_urine_isolate_weighed <-
-  first_isolate(x,
-                specimen_group = 'Urine',
-                col_keyantibiotics = 'keyab')
-
-x$first_resp_isolate <-
-  first_isolate(x,
-                specimen_group = 'Respiratory')
-
-x$first_resp_isolate_weighed <-
-  first_isolate(x,
-                specimen_group = 'Respiratory',
-                col_keyantibiotics = 'keyab')
+x$first_blood_isolate <- first_isolate(x, specimen_group = "Blood")
 }
 }
 \seealso{