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fix first isolate

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dr. M.S. (Matthijs) Berends
2023-02-10 13:13:17 +01:00
parent 1a0dc4bf46
commit 70a7ba0206
13 changed files with 222 additions and 56 deletions
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2
man/antibiotic_class_selectors.Rd
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@ -110,7 +110,7 @@ not_intrinsic_resistant(
\item{filter}{an \link{expression} to be evaluated in the \link{antibiotics} data set, such as \code{name \%like\% "trim"}}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".}
}

2
man/as.sir.Rd
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@ -94,7 +94,7 @@ sir_interpretation_history(clean = FALSE)
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to \code{TRUE}. Can also be set with the option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{clean}{a \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results}
}

2
man/bug_drug_combinations.Rd
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@ -23,7 +23,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
\arguments{
\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{FUN}{the function to call on the \code{mo} column to transform the microorganism codes, defaults to \code{\link[=mo_shortname]{mo_shortname()}}}

2
man/eucast_rules.Rd
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@ -38,7 +38,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
\arguments{
\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{info}{a \link{logical} to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}

8
man/first_isolate.Rd
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@ -52,7 +52,7 @@ filter_first_isolate(
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (such as test codes for screening). In that case \code{testcodes_exclude} will be ignored.}
@ -168,7 +168,7 @@ The default method is phenotype-based (using \code{type = "points"}) and episode
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
example_isolates[first_isolate(), ]
example_isolates[first_isolate(info = TRUE), ]
\donttest{
# get all first Gram-negatives
example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
@ -176,7 +176,7 @@ example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
if (require("dplyr")) {
# filter on first isolates using dplyr:
example_isolates \%>\%
filter(first_isolate())
filter(first_isolate(info = TRUE))
}
if (require("dplyr")) {
# short-hand version:
@ -187,7 +187,7 @@ if (require("dplyr")) {
# flag the first isolates per group:
example_isolates \%>\%
group_by(ward) \%>\%
mutate(first = first_isolate()) \%>\%
mutate(first = first_isolate(info = TRUE)) \%>\%
select(ward, date, patient, mo, first)
}
}

5
man/get_episode.Rd
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@ -23,7 +23,7 @@ is_new_episode(x, episode_days, ...)
}
}
\description{
These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument \code{episode_days}. This can be used to determine clinical episodes for any epidemiological analysis. The \code{\link[=get_episode]{get_episode()}} function returns the index number of the episode per group, while the \code{\link[=is_new_episode]{is_new_episode()}} function returns values \code{TRUE}/\code{FALSE} for where \code{\link[=get_episode]{get_episode()}} returns 1, and is thus equal to \code{get_episode(...) == 1}.
These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument \code{episode_days}. This can be used to determine clinical episodes for any epidemiological analysis. The \code{\link[=get_episode]{get_episode()}} function returns the index number of the episode per group, while the \code{\link[=is_new_episode]{is_new_episode()}} function returns \code{TRUE} for every new \code{\link[=get_episode]{get_episode()}} index, and is thus equal to \code{!duplicated(get_episode(...))}.
}
\details{
Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least \code{episode_days} days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least \code{episode_days} days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
@ -70,7 +70,8 @@ if (require("dplyr")) {
patient,
new_index = get_episode(date, 60),
new_logical = is_new_episode(date, 60)
)
) \%>\%
arrange(patient, ward, date)
}
if (require("dplyr")) {

2
man/key_antimicrobials.Rd
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@ -35,7 +35,7 @@ antimicrobials_equal(
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{universal}{names of \strong{broad-spectrum} antimicrobial drugs, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antimicrobial drugs}

2
man/mdro.Rd
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@ -48,7 +48,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE, ...)
\item{guideline}{a specific guideline to follow, see sections \emph{Supported international / national guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{info}{a \link{logical} to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}