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use guess_bactid for GLIMS codes

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dr. M.S. (Matthijs) Berends 2018-03-19 21:23:21 +01:00
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5 changed files with 19 additions and 12 deletions
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4
R/data.R
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@ -85,14 +85,14 @@
#' Translation table for UMCG with ~1100 microorganisms
#'
#' A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{bactlist}$bactid}, using \code{\link{left_join_bactlist}}.
#' A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{bactlist}$bactid} (using \code{\link{left_join_bactlist}}). GLIMS codes can also be translated to valid \code{bactid}'s with \code{\link{guess_bactid}}.
#' @format A data.frame with 1090 observations and 2 variables:
#' \describe{
#' \item{\code{mocode}}{Code of microorganism according to UMCG MMB}
#' \item{\code{bactid}}{Code of microorganism in \code{\link{bactlist}}}
#' }
#' @source MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl}
#' @seealso \code{\link{bactlist}}
#' @seealso \code{\link{guess_bactid}} \code{\link{bactlist}}
"bactlist.umcg"
#' Dataset with 2000 blood culture isolates of septic patients

14
R/first_isolates.R
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@ -41,10 +41,10 @@
#' 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}{[1]}. 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}.
#'
#' \strong{DETERMINING WEIGHTED ISOLATES} \cr
#' \strong{1. Using \code{type = "keyantibiotics"} and parameter \code{ignore_I}} \cr
#' To determine weighted isolates, the difference between key antibiotics will be checked. 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 and fast method. \cr
#' \strong{2. Using \code{type = "points"} and parameter \code{points_threshold}} \cr
#' To determine weighted isolates, difference between antimicrobial interpretations will be measured with points. 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}, an isolate will be (re)selected as a first weighted isolate. This method is being used by the Infection Prevention department (Dr M. Lokate) of the University Medical Center Groningen (UMCG).
#' \strong{1. Using} \code{type = "keyantibiotics"} \strong{and parameter} \code{ignore_I} \cr
#' To determine weighted isolates, the difference between key antibiotics will be checked. 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. \cr
#' \strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr
#' To determine weighted isolates, difference between antimicrobial interpretations will be measured with points. 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}, an isolate will be (re)selected as a first weighted isolate. This method is being used by the Infection Prevention department (Dr M. Lokate) of the University Medical Center Groningen (UMCG).
#' @keywords isolate isolates first
#' @export
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange
@ -676,6 +676,12 @@ guess_bactid <- function(x) {
# try only genus, with 'species' attached
found <- AMR::bactlist %>% filter(fullname %like% x_species[i])
}
if (nrow(found) == 0) {
# search for GLIMS code
if (toupper(x.bak[i]) %in% toupper(AMR::bactlist.umcg$mocode)) {
found <- AMR::bactlist.umcg %>% filter(toupper(mocode) == toupper(x.bak[i]))
}
}
if (nrow(found) == 0) {
# try splitting of characters and then find ID
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus

1
R/globals.R
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@ -30,6 +30,7 @@ globalVariables(c('.',
'key_ab_lag',
'key_ab_other',
'mic',
'mocode',
'n',
'other_pat_or_mo',
'patient_id',

4
man/bactlist.umcg.Rd
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@ -16,9 +16,9 @@ MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) -
bactlist.umcg
}
\description{
A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{bactlist}$bactid}, using \code{\link{left_join_bactlist}}.
A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{bactlist}$bactid} (using \code{\link{left_join_bactlist}}). GLIMS codes can also be translated to valid \code{bactid}'s with \code{\link{guess_bactid}}.
}
\seealso{
\code{\link{bactlist}}
\code{\link{guess_bactid}} \code{\link{bactlist}}
}
\keyword{datasets}

8
man/first_isolate.Rd
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@ -59,10 +59,10 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
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}{[1]}. 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}.
\strong{DETERMINING WEIGHTED ISOLATES} \cr
\strong{1. Using \code{type = "keyantibiotics"} and parameter \code{ignore_I}} \cr
To determine weighted isolates, the difference between key antibiotics will be checked. 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 and fast method. \cr
\strong{2. Using \code{type = "points"} and parameter \code{points_threshold}} \cr
To determine weighted isolates, difference between antimicrobial interpretations will be measured with points. 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}, an isolate will be (re)selected as a first weighted isolate. This method is being used by the Infection Prevention department (Dr M. Lokate) of the University Medical Center Groningen (UMCG).
\strong{1. Using} \code{type = "keyantibiotics"} \strong{and parameter} \code{ignore_I} \cr
To determine weighted isolates, the difference between key antibiotics will be checked. 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. \cr
\strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr
To determine weighted isolates, difference between antimicrobial interpretations will be measured with points. 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}, an isolate will be (re)selected as a first weighted isolate. This method is being used by the Infection Prevention department (Dr M. Lokate) of the University Medical Center Groningen (UMCG).
}
\examples{
# septic_patients is a dataset available in the AMR package