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first isolate missing dates fix
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@ -9,22 +9,22 @@
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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/}.
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}
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\usage{
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first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
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first_isolate(x, col_date = NULL, col_patient_id = NULL,
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col_mo = NULL, col_testcode = NULL, col_specimen = NULL,
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col_icu = NULL, col_keyantibiotics = NULL, episode_days = 365,
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testcodes_exclude = NULL, icu_exclude = FALSE,
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specimen_group = NULL, type = "keyantibiotics", ignore_I = TRUE,
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points_threshold = 2, info = TRUE, ...)
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filter_first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
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filter_first_isolate(x, col_date = NULL, col_patient_id = NULL,
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col_mo = NULL, ...)
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filter_first_weighted_isolate(tbl, col_date = NULL,
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filter_first_weighted_isolate(x, col_date = NULL,
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col_patient_id = NULL, col_mo = NULL, col_keyantibiotics = NULL,
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...)
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}
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\arguments{
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\item{tbl}{a \code{data.frame} containing isolates.}
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\item{x}{a \code{data.frame} containing isolates.}
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\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}
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@ -70,16 +70,16 @@ To conduct an analysis of antimicrobial resistance, you should only include the
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The functions \code{filter_first_isolate} and \code{filter_first_weighted_isolate} are helper functions to quickly filter on first isolates. The function \code{filter_first_isolate} is essentially equal to:
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\preformatted{
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tbl \%>\%
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mutate(only_firsts = first_isolate(tbl, ...)) \%>\%
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x \%>\%
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mutate(only_firsts = first_isolate(x, ...)) \%>\%
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filter(only_firsts == TRUE) \%>\%
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select(-only_firsts)
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}
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The function \code{filter_first_weighted_isolate} is essentially equal to:
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\preformatted{
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tbl \%>\%
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x \%>\%
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mutate(keyab = key_antibiotics(.)) \%>\%
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mutate(only_weighted_firsts = first_isolate(tbl,
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mutate(only_weighted_firsts = first_isolate(x,
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col_keyantibiotics = "keyab", ...)) \%>\%
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filter(only_weighted_firsts == TRUE) \%>\%
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select(-only_weighted_firsts)
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@ -144,39 +144,39 @@ B <- septic_patients \%>\%
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\dontrun{
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# set key antibiotics to a new variable
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tbl$keyab <- key_antibiotics(tbl)
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x$keyab <- key_antibiotics(x)
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tbl$first_isolate <-
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first_isolate(tbl)
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x$first_isolate <-
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first_isolate(x)
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tbl$first_isolate_weighed <-
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first_isolate(tbl,
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x$first_isolate_weighed <-
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first_isolate(x,
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col_keyantibiotics = 'keyab')
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tbl$first_blood_isolate <-
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first_isolate(tbl,
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x$first_blood_isolate <-
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first_isolate(x,
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specimen_group = 'Blood')
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tbl$first_blood_isolate_weighed <-
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first_isolate(tbl,
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x$first_blood_isolate_weighed <-
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first_isolate(x,
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specimen_group = 'Blood',
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col_keyantibiotics = 'keyab')
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tbl$first_urine_isolate <-
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first_isolate(tbl,
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x$first_urine_isolate <-
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first_isolate(x,
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specimen_group = 'Urine')
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tbl$first_urine_isolate_weighed <-
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first_isolate(tbl,
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x$first_urine_isolate_weighed <-
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first_isolate(x,
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specimen_group = 'Urine',
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col_keyantibiotics = 'keyab')
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tbl$first_resp_isolate <-
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first_isolate(tbl,
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x$first_resp_isolate <-
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first_isolate(x,
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specimen_group = 'Respiratory')
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tbl$first_resp_isolate_weighed <-
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first_isolate(tbl,
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x$first_resp_isolate_weighed <-
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first_isolate(x,
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specimen_group = 'Respiratory',
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col_keyantibiotics = 'keyab')
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}
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@ -4,7 +4,7 @@
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\name{microorganisms}
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\alias{microorganisms}
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\title{Data set with ~65,000 microorganisms}
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\format{A \code{\link{data.frame}} with 65,629 observations and 16 variables:
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\format{A \code{\link{data.frame}} with 67,903 observations and 16 variables:
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\describe{
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\item{\code{mo}}{ID of microorganism as used by this package}
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\item{\code{col_id}}{Catalogue of Life ID}
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@ -24,8 +24,6 @@ ggplot_rsi_predict(x, main = paste("Resistance prediction of",
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attributes(x)$ab), ribbon = TRUE, ...)
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}
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\arguments{
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\item{tbl}{a \code{data.frame} containing isolates.}
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\item{col_ab}{column name of \code{tbl} with antimicrobial interpretations (\code{R}, \code{I} and \code{S})}
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\item{col_date}{column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class}
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@ -46,9 +44,7 @@ ggplot_rsi_predict(x, main = paste("Resistance prediction of",
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\item{info}{a logical to indicate whether textual analysis should be printed with the name and \code{\link{summary}} of the statistical model.}
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\item{x}{the coordinates of points in the plot. Alternatively, a
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single plotting structure, function or \emph{any \R object with a
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\code{plot} method} can be provided.}
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\item{x}{a \code{data.frame} containing isolates.}
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\item{main}{title of the plot}
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