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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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14
man/bug_drug_combinations.Rd
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@ -45,7 +45,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
\item{remove_intrinsic_resistant}{logical to indicate that rows with 100\% resistance for all tested antimicrobials must be removed from the table}
\item{remove_intrinsic_resistant}{logical to indicate that rows and columns with 100\% resistance for all tested antimicrobials must be removed from the table}
\item{decimal.mark}{the character to be used to indicate the numeric
decimal point.}
@ -83,12 +83,12 @@ x
format(x, translate_ab = "name (atc)")
# Use FUN to change to transformation of microorganism codes
x <- bug_drug_combinations(example_isolates,
FUN = mo_gramstain)
bug_drug_combinations(example_isolates,
FUN = mo_gramstain)
x <- bug_drug_combinations(example_isolates,
FUN = function(x) ifelse(x == as.mo("E. coli"),
"E. coli",
"Others"))
bug_drug_combinations(example_isolates,
FUN = function(x) ifelse(x == as.mo("E. coli"),
"E. coli",
"Others"))
}
}