P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 17:02:03 +02:00
Code Releases Activity

test syntax fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-01 20:50:10 +01:00
parent 5476fecc73
commit e601fd259a
6 changed files with 11 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
man/EUCAST.Rd
View File

@ -46,7 +46,7 @@ interpretive_reading(...)
\arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
\item{col_mo}{column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress}
@ -56,7 +56,7 @@ interpretive_reading(...)
\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
\item{col_bactid}{deprecated, use \code{col_mo} instead.}
\item{...}{parameters that are passed on to \code{EUCAST_rules}}
}
@ -162,7 +162,7 @@ a
# 4 Klebsiella pneumoniae - - - - - S S
# 5 Pseudomonas aeruginosa - - - - - S S
b <- EUCAST_rules(a) # 18 results are forced as R or S
b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
b
# mo vanc amox coli cfta cfur peni cfox

4
man/MDRO.Rd
View File

@ -36,7 +36,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
\item{col_mo}{column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress}
@ -160,7 +160,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
\item{col_bactid}{deprecated, use \code{col_mo} instead.}
\item{...}{parameters that are passed on to methods}
}

2
man/first_isolate.Rd
View File

@ -23,7 +23,7 @@ first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.}

2
man/key_antibiotics.Rd
View File

@ -20,7 +20,7 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
\arguments{
\item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive}