AMR/man/first_isolate.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/first_isolate.R
\name{first_isolate}
\alias{first_isolate}
\alias{filter_first_isolate}
\alias{filter_first_weighted_isolate}
\title{Determine first (weighted) isolates}
\source{
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(
  x,
  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,
  specimen_group = NULL,
  type = "keyantibiotics",
  ignore_I = TRUE,
  points_threshold = 2,
  info = TRUE,
  include_unknown = FALSE,
  ...
)

filter_first_isolate(
  x,
  col_date = NULL,
  col_patient_id = NULL,
  col_mo = NULL,
  ...
)

filter_first_weighted_isolate(
  x,
  col_date = NULL,
  col_patient_id = NULL,
  col_mo = NULL,
  col_keyantibiotics = NULL,
  ...
)
}
\arguments{
\item{x}{a \code{\link{data.frame}} containing isolates.}

\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class}

\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_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.}

\item{col_specimen}{column name of the specimen type or group}

\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)}

\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link[=key_antibiotics]{key_antibiotics()}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use \code{col_keyantibiotics = FALSE} to prevent this.}

\item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see Source.}

\item{testcodes_exclude}{character vector with test codes that should be excluded (case-insensitive)}

\item{icu_exclude}{logical whether ICU isolates should be excluded (rows with value \code{TRUE} in column \code{col_icu})}

\item{specimen_group}{value in column \code{col_specimen} to filter on}

\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details}

\item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details}

\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details}

\item{info}{print progress}

\item{include_unknown}{logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}

\item{...}{parameters passed on to the \code{\link[=first_isolate]{first_isolate()}} function}
}
\value{
A \code{\link{logical}} vector
}
\description{
Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
}
\details{
\strong{WHY THIS IS SO IMPORTANT} \cr
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode \href{https://www.ncbi.nlm.nih.gov/pubmed/17304462}{(ref)}. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.

All isolates with a microbial ID of \code{NA} will be excluded as first isolate.

The functions \code{\link[=filter_first_isolate]{filter_first_isolate()}} and \code{\link[=filter_first_weighted_isolate]{filter_first_weighted_isolate()}} are helper functions to quickly filter on first isolates. The function \code{\link[=filter_first_isolate]{filter_first_isolate()}} is essentially equal to:\preformatted{ x \%>\%
   mutate(only_firsts = first_isolate(x, ...)) \%>\%
   filter(only_firsts == TRUE) \%>\%
   select(-only_firsts)
}

The function \code{\link[=filter_first_weighted_isolate]{filter_first_weighted_isolate()}} is essentially equal to:\preformatted{ x \%>\%
   mutate(keyab = key_antibiotics(.)) \%>\%
   mutate(only_weighted_firsts = first_isolate(x,
                                               col_keyantibiotics = "keyab", ...)) \%>\%
   filter(only_weighted_firsts == TRUE) \%>\%
   select(-only_weighted_firsts)
}
}
\section{Key antibiotics}{

There are two ways to determine whether isolates can be included as first \emph{weighted} isolates which will give generally the same results:
\enumerate{
\item Using \code{type = "keyantibiotics"} and parameter \code{ignore_I}

Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function.
\item Using \code{type = "points"} and parameter \code{points_threshold}

A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate.
}
}

\section{Read more on our website!}{

On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}

\examples{
# `example_isolates` is a dataset available in the AMR package.
# See ?example_isolates.

library(dplyr)
# Filter on first isolates:
example_isolates \%>\%
  mutate(first_isolate = first_isolate(.,
                                       col_date = "date",
                                       col_patient_id = "patient_id",
                                       col_mo = "mo")) \%>\%
  filter(first_isolate == TRUE)

# Which can be shortened to:
example_isolates \%>\%
  filter_first_isolate()
# or for first weighted isolates:
example_isolates \%>\%
  filter_first_weighted_isolate()

# Now let's see if first isolates matter:
A <- example_isolates \%>\%
  group_by(hospital_id) \%>\%
  summarise(count = n_rsi(GEN),            # gentamicin availability
            resistance = resistance(GEN))  # gentamicin resistance

B <- example_isolates \%>\%
  filter_first_weighted_isolate() \%>\%      # the 1st isolate filter
  group_by(hospital_id) \%>\%
  summarise(count = n_rsi(GEN),            # gentamicin availability
            resistance = resistance(GEN))  # gentamicin resistance

# Have a look at A and B.
# B is more reliable because every isolate is only counted once.
# Gentamicin resitance in hospital D appears to be 3.1\% higher than
# when you (erroneously) would have used all isolates for analysis.


## OTHER EXAMPLES:

\dontrun{

# set key antibiotics to a new variable
x$keyab <- key_antibiotics(x)

x$first_isolate <- first_isolate(x)

x$first_isolate_weighed <- first_isolate(x, col_keyantibiotics = 'keyab')

x$first_blood_isolate <- first_isolate(x, specimen_group = "Blood")
}
}
\seealso{
\code{\link[=key_antibiotics]{key_antibiotics()}}
}