mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:46:11 +01:00
220 lines
5.0 KiB
R
220 lines
5.0 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/deprecated.R
|
|
\name{AMR-deprecated}
|
|
\alias{AMR-deprecated}
|
|
\alias{p_symbol}
|
|
\alias{filter_first_weighted_isolate}
|
|
\alias{key_antibiotics}
|
|
\alias{key_antibiotics_equal}
|
|
\alias{filter_ab_class}
|
|
\alias{filter_aminoglycosides}
|
|
\alias{filter_betalactams}
|
|
\alias{filter_carbapenems}
|
|
\alias{filter_cephalosporins}
|
|
\alias{filter_1st_cephalosporins}
|
|
\alias{filter_2nd_cephalosporins}
|
|
\alias{filter_3rd_cephalosporins}
|
|
\alias{filter_4th_cephalosporins}
|
|
\alias{filter_5th_cephalosporins}
|
|
\alias{filter_fluoroquinolones}
|
|
\alias{filter_glycopeptides}
|
|
\alias{filter_macrolides}
|
|
\alias{filter_oxazolidinones}
|
|
\alias{filter_penicillins}
|
|
\alias{filter_tetracyclines}
|
|
\title{Deprecated Functions}
|
|
\usage{
|
|
p_symbol(p, emptychar = " ")
|
|
|
|
filter_first_weighted_isolate(
|
|
x = NULL,
|
|
col_date = NULL,
|
|
col_patient_id = NULL,
|
|
col_mo = NULL,
|
|
...
|
|
)
|
|
|
|
key_antibiotics(
|
|
x = NULL,
|
|
col_mo = NULL,
|
|
universal_1 = guess_ab_col(x, "amoxicillin"),
|
|
universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
|
|
universal_3 = guess_ab_col(x, "cefuroxime"),
|
|
universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
|
|
universal_5 = guess_ab_col(x, "ciprofloxacin"),
|
|
universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
|
|
GramPos_1 = guess_ab_col(x, "vancomycin"),
|
|
GramPos_2 = guess_ab_col(x, "teicoplanin"),
|
|
GramPos_3 = guess_ab_col(x, "tetracycline"),
|
|
GramPos_4 = guess_ab_col(x, "erythromycin"),
|
|
GramPos_5 = guess_ab_col(x, "oxacillin"),
|
|
GramPos_6 = guess_ab_col(x, "rifampin"),
|
|
GramNeg_1 = guess_ab_col(x, "gentamicin"),
|
|
GramNeg_2 = guess_ab_col(x, "tobramycin"),
|
|
GramNeg_3 = guess_ab_col(x, "colistin"),
|
|
GramNeg_4 = guess_ab_col(x, "cefotaxime"),
|
|
GramNeg_5 = guess_ab_col(x, "ceftazidime"),
|
|
GramNeg_6 = guess_ab_col(x, "meropenem"),
|
|
warnings = TRUE,
|
|
...
|
|
)
|
|
|
|
key_antibiotics_equal(
|
|
y,
|
|
z,
|
|
type = "keyantimicrobials",
|
|
ignore_I = TRUE,
|
|
points_threshold = 2,
|
|
info = FALSE,
|
|
na.rm = TRUE,
|
|
...
|
|
)
|
|
|
|
filter_ab_class(
|
|
x,
|
|
ab_class,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_aminoglycosides(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_betalactams(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_carbapenems(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_cephalosporins(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_1st_cephalosporins(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_2nd_cephalosporins(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_3rd_cephalosporins(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_4th_cephalosporins(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_5th_cephalosporins(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_fluoroquinolones(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_glycopeptides(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_macrolides(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_oxazolidinones(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_penicillins(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
|
|
filter_tetracyclines(
|
|
x,
|
|
result = NULL,
|
|
scope = "any",
|
|
only_rsi_columns = FALSE,
|
|
...
|
|
)
|
|
}
|
|
\description{
|
|
These functions are so-called '\link{Deprecated}'. \strong{They will be removed in a future release.} Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
|
|
}
|
|
\details{
|
|
All antibiotic class selectors (such as \code{\link[=carbapenems]{carbapenems()}}, \code{\link[=aminoglycosides]{aminoglycosides()}}) can now be used for filtering as well, making all their accompanying \verb{filter_*()} functions redundant (such as \code{\link[=filter_carbapenems]{filter_carbapenems()}}, \code{\link[=filter_aminoglycosides]{filter_aminoglycosides()}}).
|
|
}
|
|
\section{Retired Lifecycle}{
|
|
|
|
\if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
|
|
The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
|
|
}
|
|
|
|
\section{Read more on Our Website!}{
|
|
|
|
On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
|
}
|
|
|
|
\keyword{internal}
|