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AI improvements

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dr. M.S. (Matthijs) Berends
2018-12-07 12:04:55 +01:00
parent 87ad6da745
commit 8e8a9cd190
19 changed files with 199 additions and 140 deletions
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@@ -40,125 +40,125 @@ eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{info}{print progress}
\item{amcl}{column name of an antibiotic, see Details}
\item{amcl}{column name of an antibiotic, see Antibiotics}
\item{amik}{column name of an antibiotic, see Details}
\item{amik}{column name of an antibiotic, see Antibiotics}
\item{amox}{column name of an antibiotic, see Details}
\item{amox}{column name of an antibiotic, see Antibiotics}
\item{ampi}{column name of an antibiotic, see Details}
\item{ampi}{column name of an antibiotic, see Antibiotics}
\item{azit}{column name of an antibiotic, see Details}
\item{azit}{column name of an antibiotic, see Antibiotics}
\item{aztr}{column name of an antibiotic, see Details}
\item{aztr}{column name of an antibiotic, see Antibiotics}
\item{cefa}{column name of an antibiotic, see Details}
\item{cefa}{column name of an antibiotic, see Antibiotics}
\item{cfra}{column name of an antibiotic, see Details}
\item{cfra}{column name of an antibiotic, see Antibiotics}
\item{cfep}{column name of an antibiotic, see Details}
\item{cfep}{column name of an antibiotic, see Antibiotics}
\item{cfot}{column name of an antibiotic, see Details}
\item{cfot}{column name of an antibiotic, see Antibiotics}
\item{cfox}{column name of an antibiotic, see Details}
\item{cfox}{column name of an antibiotic, see Antibiotics}
\item{cfta}{column name of an antibiotic, see Details}
\item{cfta}{column name of an antibiotic, see Antibiotics}
\item{cftr}{column name of an antibiotic, see Details}
\item{cftr}{column name of an antibiotic, see Antibiotics}
\item{cfur}{column name of an antibiotic, see Details}
\item{cfur}{column name of an antibiotic, see Antibiotics}
\item{chlo}{column name of an antibiotic, see Details}
\item{chlo}{column name of an antibiotic, see Antibiotics}
\item{cipr}{column name of an antibiotic, see Details}
\item{cipr}{column name of an antibiotic, see Antibiotics}
\item{clar}{column name of an antibiotic, see Details}
\item{clar}{column name of an antibiotic, see Antibiotics}
\item{clin}{column name of an antibiotic, see Details}
\item{clin}{column name of an antibiotic, see Antibiotics}
\item{clox}{column name of an antibiotic, see Details}
\item{clox}{column name of an antibiotic, see Antibiotics}
\item{coli}{column name of an antibiotic, see Details}
\item{coli}{column name of an antibiotic, see Antibiotics}
\item{czol}{column name of an antibiotic, see Details}
\item{czol}{column name of an antibiotic, see Antibiotics}
\item{dapt}{column name of an antibiotic, see Details}
\item{dapt}{column name of an antibiotic, see Antibiotics}
\item{doxy}{column name of an antibiotic, see Details}
\item{doxy}{column name of an antibiotic, see Antibiotics}
\item{erta}{column name of an antibiotic, see Details}
\item{erta}{column name of an antibiotic, see Antibiotics}
\item{eryt}{column name of an antibiotic, see Details}
\item{eryt}{column name of an antibiotic, see Antibiotics}
\item{fosf}{column name of an antibiotic, see Details}
\item{fosf}{column name of an antibiotic, see Antibiotics}
\item{fusi}{column name of an antibiotic, see Details}
\item{fusi}{column name of an antibiotic, see Antibiotics}
\item{gent}{column name of an antibiotic, see Details}
\item{gent}{column name of an antibiotic, see Antibiotics}
\item{imip}{column name of an antibiotic, see Details}
\item{imip}{column name of an antibiotic, see Antibiotics}
\item{kana}{column name of an antibiotic, see Details}
\item{kana}{column name of an antibiotic, see Antibiotics}
\item{levo}{column name of an antibiotic, see Details}
\item{levo}{column name of an antibiotic, see Antibiotics}
\item{linc}{column name of an antibiotic, see Details}
\item{linc}{column name of an antibiotic, see Antibiotics}
\item{line}{column name of an antibiotic, see Details}
\item{line}{column name of an antibiotic, see Antibiotics}
\item{mero}{column name of an antibiotic, see Details}
\item{mero}{column name of an antibiotic, see Antibiotics}
\item{metr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
\item{metr}{column name of an antibiotic, see Antibiotics}
\item{mino}{column name of an antibiotic, see Details}
\item{mino}{column name of an antibiotic, see Antibiotics}
\item{moxi}{column name of an antibiotic, see Details}
\item{moxi}{column name of an antibiotic, see Antibiotics}
\item{nali}{column name of an antibiotic, see Details}
\item{nali}{column name of an antibiotic, see Antibiotics}
\item{neom}{column name of an antibiotic, see Details}
\item{neom}{column name of an antibiotic, see Antibiotics}
\item{neti}{column name of an antibiotic, see Details}
\item{neti}{column name of an antibiotic, see Antibiotics}
\item{nitr}{column name of an antibiotic, see Details}
\item{nitr}{column name of an antibiotic, see Antibiotics}
\item{novo}{column name of an antibiotic, see Details}
\item{novo}{column name of an antibiotic, see Antibiotics}
\item{norf}{column name of an antibiotic, see Details}
\item{norf}{column name of an antibiotic, see Antibiotics}
\item{oflo}{column name of an antibiotic, see Details}
\item{oflo}{column name of an antibiotic, see Antibiotics}
\item{peni}{column name of an antibiotic, see Details}
\item{peni}{column name of an antibiotic, see Antibiotics}
\item{pipe}{column name of an antibiotic, see Details}
\item{pipe}{column name of an antibiotic, see Antibiotics}
\item{pita}{column name of an antibiotic, see Details}
\item{pita}{column name of an antibiotic, see Antibiotics}
\item{poly}{column name of an antibiotic, see Details}
\item{poly}{column name of an antibiotic, see Antibiotics}
\item{qida}{column name of an antibiotic, see Details}
\item{qida}{column name of an antibiotic, see Antibiotics}
\item{rifa}{column name of an antibiotic, see Details}
\item{rifa}{column name of an antibiotic, see Antibiotics}
\item{roxi}{column name of an antibiotic, see Details}
\item{roxi}{column name of an antibiotic, see Antibiotics}
\item{siso}{column name of an antibiotic, see Details}
\item{siso}{column name of an antibiotic, see Antibiotics}
\item{teic}{column name of an antibiotic, see Details}
\item{teic}{column name of an antibiotic, see Antibiotics}
\item{tetr}{column name of an antibiotic, see Details}
\item{tetr}{column name of an antibiotic, see Antibiotics}
\item{tica}{column name of an antibiotic, see Details}
\item{tica}{column name of an antibiotic, see Antibiotics}
\item{tige}{column name of an antibiotic, see Details}
\item{tige}{column name of an antibiotic, see Antibiotics}
\item{tobr}{column name of an antibiotic, see Details}
\item{tobr}{column name of an antibiotic, see Antibiotics}
\item{trim}{column name of an antibiotic, see Details}
\item{trim}{column name of an antibiotic, see Antibiotics}
\item{trsu}{column name of an antibiotic, see Details}
\item{trsu}{column name of an antibiotic, see Antibiotics}
\item{vanc}{column name of an antibiotic, see Details}
\item{vanc}{column name of an antibiotic, see Antibiotics}
\item{col_bactid}{deprecated, use \code{col_mo} instead.}
@@ -175,6 +175,8 @@ When \code{country} will be left blank, guidelines will be taken from EUCAST Exp
}
\section{Antibiotics}{
To define antibiotics column names, input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
\strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}),