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mdro and 1st isolate improvements

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dr. M.S. (Matthijs) Berends
2018-10-23 11:15:05 +02:00
parent 299c5bea43
commit 7997de6a6d
8 changed files with 138 additions and 95 deletions
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21
man/first_isolate.Rd
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@ -7,22 +7,23 @@
Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
}
\usage{
first_isolate(tbl, col_date, col_patient_id, col_mo = NA,
col_testcode = NA, col_specimen = NA, col_icu = NA,
col_keyantibiotics = NA, episode_days = 365,
testcodes_exclude = "", icu_exclude = FALSE, filter_specimen = NA,
output_logical = TRUE, type = "keyantibiotics", ignore_I = TRUE,
points_threshold = 2, info = TRUE, col_bactid = NA,
col_genus = NA, col_species = NA)
first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, col_testcode = NULL, col_specimen = NULL,
col_icu = NULL, col_keyantibiotics = NULL, episode_days = 365,
testcodes_exclude = NULL, icu_exclude = FALSE,
filter_specimen = NULL, output_logical = TRUE,
type = "keyantibiotics", ignore_I = TRUE, points_threshold = 2,
info = TRUE, col_bactid = NULL, col_genus = NULL,
col_species = NULL)
}
\arguments{
\item{tbl}{a \code{data.frame} containing isolates.}
\item{col_date}{column name of the result date (or date that is was received on the lab)}
\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}}
\item{col_patient_id}{column name of the unique IDs of the patients}
\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}}. 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}. If this column has another class than \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.}

9
man/freq.Rd
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@ -10,11 +10,12 @@
frequency_tbl(x, ..., sort.count = TRUE,
nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
markdown = !interactive(), digits = 2, quote = FALSE,
header = !markdown, sep = " ")
header = !markdown, na = "<NA>", sep = " ")
freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
digits = 2, quote = FALSE, header = !markdown, sep = " ")
digits = 2, quote = FALSE, header = !markdown, na = "<NA>",
sep = " ")
top_freq(f, n)
@ -30,7 +31,7 @@ top_freq(f, n)
\item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0}, \code{nmax = Inf}, \code{nmax = NULL} or \code{nmax = NA} to print all rows.}
\item{na.rm}{a logical value indicating whether \code{NA} values should be removed from the frequency table. The header will always print the amount of \code{NA}s.}
\item{na.rm}{a logical value indicating whether \code{NA} values should be removed from the frequency table. The header (if set) will always print the amount of \code{NA}s.}
\item{row.names}{a logical value indicating whether row indices should be printed as \code{1:nrow(x)}}
@ -42,6 +43,8 @@ top_freq(f, n)
\item{header}{a logical value indicating whether an informative header should be printed}
\item{na}{a character string to should be used to show empty (\code{NA}) values (only useful when \code{na.rm = FALSE})}
\item{sep}{a character string to separate the terms when selecting multiple columns}
\item{f}{a frequency table}

2
man/key_antibiotics.Rd
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@ -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}}. 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}. If this column has another class than \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}