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EUCAST update, as.mo bugfix for empty vlaues

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dr. M.S. (Matthijs) Berends 2019-01-08 16:23:45 +01:00
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commit 193a2d2863
54 changed files with 1504 additions and 972 deletions
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.gitignore vendored
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Meta Meta
doc doc
.Renviron
.Rproj.user .Rproj.user
.Rhistory .Rhistory
.RData .RData

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DESCRIPTION
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Package: AMR Package: AMR
Version: 0.5.0.9009 Version: 0.5.0.9009
Date: 2019-01-06 Date: 2019-01-08
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

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NEWS.md
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@ -28,9 +28,13 @@
* New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the *G*-test and more. These are also available (and even easier readable) on our website: https://msberends.gitlab.io/AMR. * New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the *G*-test and more. These are also available (and even easier readable) on our website: https://msberends.gitlab.io/AMR.
#### Changed #### Changed
* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be remover in future versions * Function `eucast_rules()`:
* Fixed a critical bug in `eucast_rules()` where some rules that depend on previous applied rules would not be applied adequately * Updated EUCAST Clinical breakpoints to [version 9.0 of 1 January 2019](http://www.eucast.org/clinical_breakpoints/)
* Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately
* Emphasised in manual that penicillin is meant as benzylpenicillin (ATC [J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01))
* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be removed in future versions
* Improvements for `as.mo()`: * Improvements for `as.mo()`:
* Fix for vector containing only empty values
* Finds better results when input is in other languages * Finds better results when input is in other languages
* Better handling for subspecies * Better handling for subspecies
* Better handling for *Salmonellae* * Better handling for *Salmonellae*

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R/data.R
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@ -127,7 +127,7 @@
#' Data set with taxonomic data from ITIS #' Data set with taxonomic data from ITIS
#' #'
#' A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using \code{\link{as.mo}}. #' A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection itis ITIS #' @inheritSection ITIS ITIS
#' @format A \code{\link{data.frame}} with 18,833 observations and 15 variables: #' @format A \code{\link{data.frame}} with 18,833 observations and 15 variables:
#' \describe{ #' \describe{
#' \item{\code{mo}}{ID of microorganism} #' \item{\code{mo}}{ID of microorganism}

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R/eucast_rules.R
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@ -34,68 +34,68 @@
#' #'
#' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code}) #' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
#' #'
#' \strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}), #' \strong{amcl}: amoxicillin+clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
#' \strong{amik}: amikacin (\emph{J01GB06}), #' \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
#' \strong{amox}: amoxicillin (\emph{J01CA04}), #' \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
#' \strong{ampi}: ampicillin (\emph{J01CA01}), #' \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
#' \strong{azit}: azithromycin (\emph{J01FA10}), #' \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
#' \strong{azlo}: azlocillin (\emph{J01CA09}), #' \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
#' \strong{aztr}: aztreonam (\emph{J01DF01}), #' \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
#' \strong{cefa}: cefaloridine (\emph{J01DB02}), #' \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
#' \strong{cfep}: cefepime (\emph{J01DE01}), #' \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
#' \strong{cfot}: cefotaxime (\emph{J01DD01}), #' \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
#' \strong{cfox}: cefoxitin (\emph{J01DC01}), #' \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
#' \strong{cfra}: cefradine (\emph{J01DB09}), #' \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
#' \strong{cfta}: ceftazidime (\emph{J01DD02}), #' \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
#' \strong{cftr}: ceftriaxone (\emph{J01DD04}), #' \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
#' \strong{cfur}: cefuroxime (\emph{J01DC02}), #' \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
#' \strong{chlo}: chloramphenicol (\emph{J01BA01}), #' \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
#' \strong{cipr}: ciprofloxacin (\emph{J01MA02}), #' \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
#' \strong{clar}: clarithromycin (\emph{J01FA09}), #' \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
#' \strong{clin}: clindamycin (\emph{J01FF01}), #' \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
#' \strong{clox}: flucloxacillin (\emph{J01CF05}), #' \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
#' \strong{coli}: colistin (\emph{J01XB01}), #' \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
#' \strong{czol}: cefazolin (\emph{J01DB04}), #' \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
#' \strong{dapt}: daptomycin (\emph{J01XX09}), #' \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
#' \strong{doxy}: doxycycline (\emph{J01AA02}), #' \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
#' \strong{erta}: ertapenem (\emph{J01DH03}), #' \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
#' \strong{eryt}: erythromycin (\emph{J01FA01}), #' \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
#' \strong{fosf}: fosfomycin (\emph{J01XX01}), #' \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
#' \strong{fusi}: fusidic acid (\emph{J01XC01}), #' \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
#' \strong{gent}: gentamicin (\emph{J01GB03}), #' \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
#' \strong{imip}: imipenem (\emph{J01DH51}), #' \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
#' \strong{kana}: kanamycin (\emph{J01GB04}), #' \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
#' \strong{levo}: levofloxacin (\emph{J01MA12}), #' \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
#' \strong{linc}: lincomycin (\emph{J01FF02}), #' \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
#' \strong{line}: linezolid (\emph{J01XX08}), #' \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
#' \strong{mero}: meropenem (\emph{J01DH02}), #' \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
#' \strong{mezl}: mezlocillin (\emph{J01CA10}), #' \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
#' \strong{mino}: minocycline (\emph{J01AA08}), #' \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
#' \strong{moxi}: moxifloxacin (\emph{J01MA14}), #' \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
#' \strong{nali}: nalidixic acid (\emph{J01MB02}), #' \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
#' \strong{neom}: neomycin (\emph{J01GB05}), #' \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
#' \strong{neti}: netilmicin (\emph{J01GB07}), #' \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
#' \strong{nitr}: nitrofurantoin (\emph{J01XE01}), #' \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
#' \strong{norf}: norfloxacin (\emph{J01MA06}), #' \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
#' \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}), #' \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
#' \strong{oflo}: ofloxacin (\emph{J01MA01}), #' \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
#' \strong{peni}: penicillin (\emph{J01RA01}), #' \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
#' \strong{pipe}: piperacillin (\emph{J01CA12}), #' \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
#' \strong{pita}: piperacillin+tazobactam (\emph{J01CR05}), #' \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
#' \strong{poly}: polymyxin B (\emph{J01XB02}), #' \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
#' \strong{pris}: pristinamycin (\emph{J01FG01}), #' \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
#' \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}), #' \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
#' \strong{rifa}: rifampicin (\emph{J04AB02}), #' \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
#' \strong{roxi}: roxithromycin (\emph{J01FA06}), #' \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
#' \strong{siso}: sisomicin (\emph{J01GB08}), #' \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
#' \strong{teic}: teicoplanin (\emph{J01XA02}), #' \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
#' \strong{tetr}: tetracycline (\emph{J01AA07}), #' \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
#' \strong{tica}: ticarcillin (\emph{J01CA13}), #' \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
#' \strong{tige}: tigecycline (\emph{J01AA12}), #' \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
#' \strong{tobr}: tobramycin (\emph{J01GB01}), #' \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
#' \strong{trim}: trimethoprim (\emph{J01EA01}), #' \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
#' \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}), #' \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
#' \strong{vanc}: vancomycin (\emph{J01XA01}). #' \strong{vanc}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
#' @keywords interpretive eucast reading resistance #' @keywords interpretive eucast reading resistance
#' @rdname eucast_rules #' @rdname eucast_rules
#' @export #' @export
@ -114,8 +114,8 @@
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf} #' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
#' } #' }
#' \item{ #' \item{
#' EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. \cr #' EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx} #' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
#' } #' }
#' } #' }
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!

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R/itis.R
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@ -30,8 +30,8 @@
#' #'
#' ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. #' ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @name itis #' @name ITIS
#' @rdname itis #' @rdname ITIS
#' @examples #' @examples
#' # Get a note when a species was renamed #' # Get a note when a species was renamed
#' mo_shortname("Chlamydia psittaci") #' mo_shortname("Chlamydia psittaci")

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R/mo.R
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@ -76,7 +76,7 @@
#' \item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.} #' \item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
#' } #' }
#' #'
#' @inheritSection itis ITIS #' @inheritSection ITIS ITIS
# (source as a section, so it can be inherited by other man pages) # (source as a section, so it can be inherited by other man pages)
#' @section Source: #' @section Source:
#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13} #' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
@ -211,8 +211,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
reference_df[] <- lapply(reference_df, as.character) reference_df[] <- lapply(reference_df, as.character)
) )
} }
if (all(identical(trimws(x_input), "") | is.na(x_input))) {
if (all(x %in% microorganismsDT[["mo"]])) { # all empty
if (property == "mo") {
return(structure(rep(NA_character_, length(x_input)), class = "mo"))
} else if (property == "tsn") {
return(rep(NA_integer_, length(x_input)))
} else {
return(rep(NA_character_, length(x_input)))
}
} else if (all(x %in% microorganismsDT[["mo"]])) {
# existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL") # existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL")
x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]] x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
} else if (!is.null(reference_df) } else if (!is.null(reference_df)
@ -665,6 +673,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
} }
} }
# (4) not yet implemented taxonomic changes in ITIS
found <- suppressMessages(suppressWarnings(exec_as.mo(temp_changes(b.x_trimmed), clear_options = FALSE, allow_uncertain = FALSE)))
if (!is.na(found)) {
found <- microorganismsDT[mo == found, ..property][[1]]
warning(red(paste0('UNCERTAIN - "',
a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
call. = FALSE, immediate. = FALSE)
return(found[1L])
}
# didn't found in uncertain results too # didn't found in uncertain results too
return(NA_character_) return(NA_character_)
} }
@ -780,6 +798,10 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
x x
} }
temp_changes <- function(x) {
x[x %like% 'Cutibacterium'] <- gsub('Cutibacterium', 'Propionibacterium', x[x %like% 'Cutibacterium'])
}
#' @importFrom crayon blue italic #' @importFrom crayon blue italic
renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "") { renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "") {
if (!is.na(ref_old)) { if (!is.na(ref_old)) {

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R/mo_property.R
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@ -33,7 +33,7 @@
#' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)} #' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
#' } #' }
#' @inheritSection get_locale Supported languages #' @inheritSection get_locale Supported languages
#' @inheritSection itis ITIS #' @inheritSection ITIS ITIS
#' @inheritSection as.mo Source #' @inheritSection as.mo Source
#' @rdname mo_property #' @rdname mo_property
#' @name mo_property #' @name mo_property
@ -480,6 +480,12 @@ mo_validate <- function(x, property, ...) {
| Lancefield %in% c(TRUE, "all")) { | Lancefield %in% c(TRUE, "all")) {
exec_as.mo(x, property = property, ...) exec_as.mo(x, property = property, ...)
} else { } else {
x if (property == "mo") {
return(structure(x, class = "mo"))
} else if (property == "tsn") {
return(as.integer(x))
} else {
return(x)
}
} }
} }

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_pkgdown.yml
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@ -71,13 +71,13 @@ navbar:
href: 'LICENSE-text.html' href: 'LICENSE-text.html'
reference: reference:
- title: Backround information - title: 'Background information'
desc: > desc: >
Some pages about our package and its external sources. Some pages about our package and its external sources.
contents: contents:
- '`AMR`' - '`AMR`'
- '`itis`' - '`ITIS`'
- title: Cleaning your data - title: 'Cleaning your data'
desc: > desc: >
Functions for cleaning and optimising your data, to be able Functions for cleaning and optimising your data, to be able
to add variables later on (like taxonomic properties) or to to add variables later on (like taxonomic properties) or to
@ -87,7 +87,7 @@ reference:
- '`eucast_rules`' - '`eucast_rules`'
- '`guess_ab`' - '`guess_ab`'
- '`read.4D`' - '`read.4D`'
- title: Adding variables to your data - title: 'Adding variables to your data'
desc: > desc: >
Functions to add new data to existing data, like the determination Functions to add new data to existing data, like the determination
of first isolates, of first isolates,
@ -103,7 +103,7 @@ reference:
- '`age_groups`' - '`age_groups`'
- '`p.symbol`' - '`p.symbol`'
- '`join`' - '`join`'
- title: Analysing your data - title: 'Analysing your data'
desc: > desc: >
Functions for conducting AMR analysis Functions for conducting AMR analysis
contents: contents:
@ -116,7 +116,7 @@ reference:
- '`resistance_predict`' - '`resistance_predict`'
- '`rsi`' - '`rsi`'
- '`skewness`' - '`skewness`'
- title: Included data sets - title: 'Included data sets'
desc: > desc: >
References for microorganisms and antibiotics, and even a References for microorganisms and antibiotics, and even a
genuine data set with isolates from septic patients. genuine data set with isolates from septic patients.

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<h1>How to apply EUCAST rules</h1> <h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 January 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div> <div class="hidden name"><code>EUCAST.Rmd</code></div>
@ -186,7 +187,7 @@
<blockquote> <blockquote>
<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p> <p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
</blockquote> </blockquote>
<p>In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p> <p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 9.0, 2019). Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p><em>(more will be available soon)</em></p> <p><em>(more will be available soon)</em></p>
<div id="benefit-for-empiric-therapy-success-estimation" class="section level3"> <div id="benefit-for-empiric-therapy-success-estimation" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

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<h1>How to use the <em>G</em>-test</h1> <h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 January 2019</h4>
<div class="hidden name"><code>G_test.Rmd</code></div> <div class="hidden name"><code>G_test.Rmd</code></div>
@ -179,7 +180,7 @@
<p><em>(will be available soon - in the meanwhile, please read about <a href="./reference/g.test.html">this <em>G</em>-test in the manual</a>)</em></p> <p><em>(will be available soon - in the meanwhile, please read about <a href="./../reference/g.test.html">this <em>G</em>-test in the manual</a>)</em></p>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

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<h1>How to predict antimicrobial resistance</h1> <h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 January 2019</h4>
<div class="hidden name"><code>Predict.Rmd</code></div> <div class="hidden name"><code>Predict.Rmd</code></div>

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<h1>How to get properties of an antibiotic</h1> <h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 January 2019</h4>
<div class="hidden name"><code>ab_property.Rmd</code></div> <div class="hidden name"><code>ab_property.Rmd</code></div>

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<h1>How to create frequency tables</h1> <h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 January 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div> <div class="hidden name"><code>freq.Rmd</code></div>
@ -188,7 +189,7 @@
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#frequencies-of-one-variable" class="anchor"></a>Frequencies of one variable</h2> <a href="#frequencies-of-one-variable" class="anchor"></a>Frequencies of one variable</h2>
<p>To only show and quickly review the content of one variable, you can just select this variable in various ways. Let’s say we want to get the frequencies of the <code>gender</code> variable of the <code>septic_patients</code> dataset:</p> <p>To only show and quickly review the content of one variable, you can just select this variable in various ways. Let’s say we want to get the frequencies of the <code>gender</code> variable of the <code>septic_patients</code> dataset:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</code></pre></div> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
<p><strong>Frequency table of <code>gender</code></strong></p> <p><strong>Frequency table of <code>gender</code></strong></p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
@ -225,21 +226,21 @@
<a href="#frequencies-of-more-than-one-variable" class="anchor"></a>Frequencies of more than one variable</h2> <a href="#frequencies-of-more-than-one-variable" class="anchor"></a>Frequencies of more than one variable</h2>
<p>Multiple variables will be pasted into one variable to review individual cases, keeping a univariate frequency table.</p> <p>Multiple variables will be pasted into one variable to review individual cases, keeping a univariate frequency table.</p>
<p>For illustration, we could add some more variables to the <code>septic_patients</code> dataset to learn about bacterial properties:</p> <p>For illustration, we could add some more variables to the <code>septic_patients</code> dataset to learn about bacterial properties:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">my_patients &lt;-<span class="st"> </span>septic_patients %&gt;%<span class="st"> </span><span class="kw"><a href="../reference/join.html">left_join_microorganisms</a></span>() <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">my_patients &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/join.html">left_join_microorganisms</a></span>()</a>
<span class="co"># Joining, by = "mo"</span></code></pre></div> <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="co"># Joining, by = "mo"</span></a></code></pre></div>
<p>Now all variables of the <code>microorganisms</code> dataset have been joined to the <code>septic_patients</code> dataset. The <code>microorganisms</code> dataset consists of the following variables:</p> <p>Now all variables of the <code>microorganisms</code> dataset have been joined to the <code>septic_patients</code> dataset. The <code>microorganisms</code> dataset consists of the following variables:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(microorganisms) <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(microorganisms)</a>
<span class="co"># [1] "mo" "tsn" "genus" "species" "subspecies"</span> <a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># [1] "mo" "tsn" "genus" "species" "subspecies"</span></a>
<span class="co"># [6] "fullname" "family" "order" "class" "phylum" </span> <a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># [6] "fullname" "family" "order" "class" "phylum" </span></a>
<span class="co"># [11] "subkingdom" "kingdom" "gramstain" "prevalence" "ref"</span></code></pre></div> <a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># [11] "subkingdom" "kingdom" "gramstain" "prevalence" "ref"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:</p> <p>If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(septic_patients) <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(septic_patients)</a>
<span class="co"># [1] 2000 49</span> <a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># [1] 2000 49</span></a>
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_patients) <a class="sourceLine" id="cb4-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_patients)</a>
<span class="co"># [1] 2000 63</span></code></pre></div> <a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># [1] 2000 63</span></a></code></pre></div>
<p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p> <p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">my_patients %&gt;% <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">my_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</code></pre></div> <a class="sourceLine" id="cb5-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code></strong></p> <p><strong>Frequency table of <code>genus</code> and <code>species</code></strong></p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
@ -380,10 +381,10 @@
<a href="#frequencies-of-numeric-values" class="anchor"></a>Frequencies of numeric values</h2> <a href="#frequencies-of-numeric-values" class="anchor"></a>Frequencies of numeric values</h2>
<p>Frequency tables can be created of any input.</p> <p>Frequency tables can be created of any input.</p>
<p>In case of numeric values (like integers, doubles, etc.) additional descriptive statistics will be calculated and shown into the header:</p> <p>In case of numeric values (like integers, doubles, etc.) additional descriptive statistics will be calculated and shown into the header:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># # get age distribution of unique patients</span> <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># # get age distribution of unique patients</span></a>
septic_patients %&gt;%<span class="st"> </span> <a class="sourceLine" id="cb6-2" data-line-number="2">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<span class="st"> </span><span class="kw">distinct</span>(patient_id, <span class="dt">.keep_all =</span> <span class="ot">TRUE</span>) %&gt;%<span class="st"> </span> <a class="sourceLine" id="cb6-3" data-line-number="3"><span class="st"> </span><span class="kw">distinct</span>(patient_id, <span class="dt">.keep_all =</span> <span class="ot">TRUE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</code></pre></div> <a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>age</code></strong><br> <p><strong>Frequency table of <code>age</code></strong><br>
Class: numeric<br> Class: numeric<br>
Length: 981 (of which NA: 0 = 0.00%)<br> Length: 981 (of which NA: 0 = 0.00%)<br>
@ -461,8 +462,8 @@ Outliers: 15 (unique count: 12)</p>
<a href="#frequencies-of-factors" class="anchor"></a>Frequencies of factors</h2> <a href="#frequencies-of-factors" class="anchor"></a>Frequencies of factors</h2>
<p>To sort frequencies of factors on factor level instead of item count, use the <code>sort.count</code> parameter.</p> <p>To sort frequencies of factors on factor level instead of item count, use the <code>sort.count</code> parameter.</p>
<p><code>sort.count</code> is <code>TRUE</code> by default. Compare this default behaviour…</p> <p><code>sort.count</code> is <code>TRUE</code> by default. Compare this default behaviour…</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;% <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id)</code></pre></div> <a class="sourceLine" id="cb7-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id)</a></code></pre></div>
<p><strong>Frequency table of <code>hospital_id</code></strong></p> <p><strong>Frequency table of <code>hospital_id</code></strong></p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
@ -509,8 +510,8 @@ Outliers: 15 (unique count: 12)</p>
</tbody> </tbody>
</table> </table>
<p>… with this, where items are now sorted on count:</p> <p>… with this, where items are now sorted on count:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;% <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">sort.count =</span> <span class="ot">FALSE</span>)</code></pre></div> <a class="sourceLine" id="cb8-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">sort.count =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>hospital_id</code></strong></p> <p><strong>Frequency table of <code>hospital_id</code></strong></p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
@ -557,8 +558,8 @@ Outliers: 15 (unique count: 12)</p>
</tbody> </tbody>
</table> </table>
<p>All classes will be printed into the header (default is <code>FALSE</code> when using markdown like this document). Variables with the new <code>rsi</code> class of this AMR package are actually ordered factors and have three classes (look at <code>Class</code> in the header):</p> <p>All classes will be printed into the header (default is <code>FALSE</code> when using markdown like this document). Variables with the new <code>rsi</code> class of this AMR package are actually ordered factors and have three classes (look at <code>Class</code> in the header):</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;% <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">header =</span> <span class="ot">TRUE</span>)</code></pre></div> <a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>amox</code></strong><br> <p><strong>Frequency table of <code>amox</code></strong><br>
Class: factor &gt; ordered &gt; rsi (numeric)<br> Class: factor &gt; ordered &gt; rsi (numeric)<br>
Levels: S &lt; I &lt; R<br> Levels: S &lt; I &lt; R<br>
@ -606,8 +607,8 @@ Unique: 3</p>
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#frequencies-of-dates" class="anchor"></a>Frequencies of dates</h2> <a href="#frequencies-of-dates" class="anchor"></a>Frequencies of dates</h2>
<p>Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:</p> <p>Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;% <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(date, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</code></pre></div> <a class="sourceLine" id="cb10-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(date, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>date</code></strong><br> <p><strong>Frequency table of <code>date</code></strong><br>
Class: Date (numeric)<br> Class: Date (numeric)<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br> Length: 2,000 (of which NA: 0 = 0.00%)<br>
@ -673,11 +674,11 @@ Median: 31 July 2009 (47.39%)</p>
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#assigning-a-frequency-table-to-an-object" class="anchor"></a>Assigning a frequency table to an object</h2> <a href="#assigning-a-frequency-table-to-an-object" class="anchor"></a>Assigning a frequency table to an object</h2>
<p>A frequency table is actaually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p> <p>A frequency table is actaually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">my_df &lt;-<span class="st"> </span>septic_patients %&gt;%<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">my_df &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(my_df)</code></pre></div> <a class="sourceLine" id="cb11-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(my_df)</a></code></pre></div>
<p>[1] “frequency_tbl” “data.frame”</p> <p>[1] “frequency_tbl” “data.frame”</p>
<p>Because of this additional class, a frequency table prints like the examples above. But the object itself contains the complete table without a row limitation:</p> <p>Because of this additional class, a frequency table prints like the examples above. But the object itself contains the complete table without a row limitation:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_df)</code></pre></div> <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_df)</a></code></pre></div>
<p>[1] 74 5</p> <p>[1] 74 5</p>
</div> </div>
<div id="additional-parameters" class="section level2"> <div id="additional-parameters" class="section level2">
@ -688,8 +689,8 @@ Median: 31 July 2009 (47.39%)</p>
<a href="#parameter-na-rm" class="anchor"></a>Parameter <code>na.rm</code> <a href="#parameter-na-rm" class="anchor"></a>Parameter <code>na.rm</code>
</h3> </h3>
<p>With the <code>na.rm</code> parameter (defaults to <code>TRUE</code>, but they will always be shown into the header), you can include <code>NA</code> values in the frequency table:</p> <p>With the <code>na.rm</code> parameter (defaults to <code>TRUE</code>, but they will always be shown into the header), you can include <code>NA</code> values in the frequency table:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;% <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</code></pre></div> <a class="sourceLine" id="cb13-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>amox</code></strong></p> <p><strong>Frequency table of <code>amox</code></strong></p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
@ -741,8 +742,8 @@ Median: 31 July 2009 (47.39%)</p>
<a href="#parameter-row-names" class="anchor"></a>Parameter <code>row.names</code> <a href="#parameter-row-names" class="anchor"></a>Parameter <code>row.names</code>
</h3> </h3>
<p>The default frequency tables shows row indices. To remove them, use <code>row.names = FALSE</code>:</p> <p>The default frequency tables shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;% <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</code></pre></div> <a class="sourceLine" id="cb14-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>hospital_id</code></strong></p> <p><strong>Frequency table of <code>hospital_id</code></strong></p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
@ -789,8 +790,8 @@ Median: 31 July 2009 (47.39%)</p>
<a href="#parameter-markdown" class="anchor"></a>Parameter <code>markdown</code> <a href="#parameter-markdown" class="anchor"></a>Parameter <code>markdown</code>
</h3> </h3>
<p>The <code>markdown</code> parameter is <code>TRUE</code> at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless <code>nmax</code> is set.</p> <p>The <code>markdown</code> parameter is <code>TRUE</code> at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless <code>nmax</code> is set.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;% <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">markdown =</span> <span class="ot">TRUE</span>)</code></pre></div> <a class="sourceLine" id="cb15-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">markdown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>hospital_id</code></strong></p> <p><strong>Frequency table of <code>hospital_id</code></strong></p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">

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@ -171,6 +171,7 @@
<h1>How to get properties of a microorganism</h1> <h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 January 2019</h4>
<div class="hidden name"><code>mo_property.Rmd</code></div> <div class="hidden name"><code>mo_property.Rmd</code></div>

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@ -59,7 +59,7 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
/* syntax font */ /* syntax font */
pre, code { pre, code {
font-family: 'Courier New'; font-family: 'Courier New', monospace;
font-size: 100% !important; font-size: 100% !important;
font-weight: bold; font-weight: bold;
background-color: transparent; background-color: transparent;
@ -102,6 +102,15 @@ help {
display: none; display: none;
} }
/* Date of vignettes */
.template-article .date:before {
content: 'Last updated: ';
}
.template-article .date {
font-size: 14px;
padding-top: 40px;
}
/* more space between icon and text in top menu */ /* more space between icon and text in top menu */
#navbar .fa, #navbar .fa,
#navbar .fab, #navbar .fab,

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@ -38,3 +38,5 @@ $( document ).ready(function() {
// Edit title of manual // Edit title of manual
$('.template-reference-index h1').text('Manual'); $('.template-reference-index h1').text('Manual');
}); });
$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR','*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");

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@ -215,7 +215,7 @@
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#get-this-package" class="anchor"></a>Get this package</h3> <a href="#get-this-package" class="anchor"></a>Get this package</h3>
<p>This package is available on the official R network (CRAN). Install this package in R with:</p> <p>This package is available on the official R network (CRAN). Install this package in R with:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</code></pre></div> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
<p>It will be downloaded and installed automatically.</p> <p>It will be downloaded and installed automatically.</p>
</div> </div>
<div id="get-started" class="section level3"> <div id="get-started" class="section level3">
@ -231,17 +231,17 @@
<p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists.</p> <p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists.</p>
<p>The <code>AMR</code> package basically does four important things:</p> <p>The <code>AMR</code> package basically does four important things:</p>
<ol> <ol>
<li>It <strong>cleanses existing data</strong>, by transforming it to reproducible and profound <em>classes</em>, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:</li> <li>
</ol> <p>It <strong>cleanses existing data</strong>, by transforming it to reproducible and profound <em>classes</em>, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:</p>
<ul> <ul>
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” and “esccol”. Even <code><a href="reference/as.mo.html">as.mo("MRSA")</a></code> will return the ID of <em>S. aureus</em>. Moreover, it can group all coagulase negative and positive <em>Staphylococci</em>, and can transform <em>Streptococci</em> into Lancefield groups. To find bacteria based on your input, it uses Artificial Intelligence to look up values in the included ITIS data, consisting of more than 18,000 microorganisms.</li> <li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” and “esccol”. Even <code><a href="reference/as.mo.html">as.mo("MRSA")</a></code> will return the ID of <em>S. aureus</em>. Moreover, it can group all coagulase negative and positive <em>Staphylococci</em>, and can transform <em>Streptococci</em> into Lancefield groups. To find bacteria based on your input, it uses Artificial Intelligence to look up values in the included ITIS data, consisting of more than 18,000 microorganisms.</li>
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li> <li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li> <li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
<li>Use <code><a href="reference/as.atc.html">as.atc()</a></code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.</li> <li>Use <code><a href="reference/as.atc.html">as.atc()</a></code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.</li>
</ul> </ul>
<ol> </li>
<li>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</li> <li>
</ol> <p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
<ul> <ul>
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a>.</li> <li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a>.</li>
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute). <li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
@ -253,9 +253,9 @@
<li>The data set <code>microorganisms</code> contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. As they use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use artificial intelligence. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li> <li>The data set <code>microorganisms</code> contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. As they use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use artificial intelligence. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
<li>The data set <code>antibiotics</code> contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.atc.html">as.atc()</a></code> internally so they support AI to guess your expected result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li> <li>The data set <code>antibiotics</code> contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.atc.html">as.atc()</a></code> internally so they support AI to guess your expected result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
</ul> </ul>
<ol> </li>
<li>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</li> <li>
</ol> <p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul> <ul>
<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code><a href="reference/portion.html">portion_R()</a></code>, <code><a href="reference/portion.html">portion_IR()</a></code>, <code><a href="reference/portion.html">portion_I()</a></code>, <code><a href="reference/portion.html">portion_SI()</a></code> and <code><a href="reference/portion.html">portion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_R()</a></code>, <code><a href="reference/count.html">count_IR()</a></code>, <code><a href="reference/count.html">count_I()</a></code>, <code><a href="reference/count.html">count_SI()</a></code> and <code><a href="reference/count.html">count_S()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise()</code>)</li> <li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code><a href="reference/portion.html">portion_R()</a></code>, <code><a href="reference/portion.html">portion_IR()</a></code>, <code><a href="reference/portion.html">portion_I()</a></code>, <code><a href="reference/portion.html">portion_SI()</a></code> and <code><a href="reference/portion.html">portion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_R()</a></code>, <code><a href="reference/count.html">count_IR()</a></code>, <code><a href="reference/count.html">count_I()</a></code>, <code><a href="reference/count.html">count_SI()</a></code> and <code><a href="reference/count.html">count_S()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise()</code>)</li>
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li> <li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
@ -263,9 +263,9 @@
<li>Conduct descriptive statistics to enhance base R: calculate <code><a href="reference/kurtosis.html">kurtosis()</a></code>, <code><a href="reference/skewness.html">skewness()</a></code> and create frequency tables with <code><a href="reference/freq.html">freq()</a></code> <li>Conduct descriptive statistics to enhance base R: calculate <code><a href="reference/kurtosis.html">kurtosis()</a></code>, <code><a href="reference/skewness.html">skewness()</a></code> and create frequency tables with <code><a href="reference/freq.html">freq()</a></code>
</li> </li>
</ul> </ul>
<ol> </li>
<li>It <strong>teaches the user</strong> how to use all the above actions.</li> <li>
</ol> <p>It <strong>teaches the user</strong> how to use all the above actions.</p>
<ul> <ul>
<li>The package contains extensive help pages with many examples.</li> <li>The package contains extensive help pages with many examples.</li>
<li>It also contains an example data set called <code>septic_patients</code>. This data set contains: <li>It also contains an example data set called <code>septic_patients</code>. This data set contains:
@ -276,6 +276,8 @@
</ul> </ul>
</li> </li>
</ul> </ul>
</li>
</ol>
<hr> <hr>
<p><a href="https://www.rug.nl"><img src="./logo_rug.png" height="60px"></a> <a href="https://www.umcg.nl"><img src="./logo_umcg.png" height="60px"></a> <a href="https://www.certe.nl"><img src="./logo_certe.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" height="60px"></a></p> <p><a href="https://www.rug.nl"><img src="./logo_rug.png" height="60px"></a> <a href="https://www.umcg.nl"><img src="./logo_umcg.png" height="60px"></a> <a href="https://www.certe.nl"><img src="./logo_certe.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" height="60px"></a></p>
</div> </div>

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@ -222,27 +222,48 @@
<ul> <ul>
<li> <li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li> <strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
<li>New website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</li> <li>New website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li> <li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li> <li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li>
</ul>
</li>
<li>Support for <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li> <li>Support for <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>Function <code>guess_ab</code> to find an antibiotic column in a table</li> <li>Function <code>guess_ab</code> to find an antibiotic column in a table</li>
<li>Function <code><a href="../reference/mo_failures.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 25 uncoerced values.</li> <li>Function <code><a href="../reference/mo_failures.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 25 uncoerced values.</li>
<li>Function <code><a href="../reference/mo_renamed.html">mo_renamed()</a></code> to get a list of all returned values from <code><a href="../reference/as.mo.html">as.mo()</a></code> that have had taxonomic renaming</li> <li>Function <code><a href="../reference/mo_renamed.html">mo_renamed()</a></code> to get a list of all returned values from <code><a href="../reference/as.mo.html">as.mo()</a></code> that have had taxonomic renaming</li>
<li>Function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age in years</li> <li>Function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age in years</li>
<li>Function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li> <li>Function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.: <code>r septic_patients %&gt;% filter_first_isolate() # or filter_first_isolate(septic_patients)</code> is equal to: <code>r septic_patients %&gt;% mutate(only_firsts = first_isolate(septic_patients, ...)) %&gt;% filter(only_firsts == TRUE) %&gt;% select(-only_firsts)</code> <li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>()</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients)</a></code></pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
</li> </li>
<li>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</li> <li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul> </ul>
</div> </div>
<div id="changed" class="section level4"> <div id="changed" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h4> <a href="#changed" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be remover in future versions</li> <li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<li>Fixed a critical bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where some rules that depend on previous applied rules would not be applied adequately</li> <ul>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</li> <li>Updated EUCAST Clinical breakpoints to <a href="http://www.eucast.org/clinical_breakpoints/">version 9.0 of 1 January 2019</a>
</li>
<li>Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately</li>
<li>Emphasised in manual that penicillin is meant as benzylpenicillin (ATC <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01">J01CE01</a>)</li>
</ul>
</li>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li> <li>Finds better results when input is in other languages</li>
<li>Better handling for subspecies</li> <li>Better handling for subspecies</li>
<li>Better handling for <em>Salmonellae</em> <li>Better handling for <em>Salmonellae</em>
@ -251,12 +272,17 @@
<li>Manual now contains more info about the algorithms</li> <li>Manual now contains more info about the algorithms</li>
<li>Progress bar will be shown when it takes more than 3 seconds to get results</li> <li>Progress bar will be shown when it takes more than 3 seconds to get results</li>
<li>Support for formatted console text</li> <li>Support for formatted console text</li>
<li>Function <code><a href="../reference/first_isolate.html">first_isolate()</a></code>:</li> </ul>
</li>
<li>Function <code><a href="../reference/first_isolate.html">first_isolate()</a></code>:
<ul>
<li>Fixed a bug where distances between dates would not be calculated right - in the <code>septic_patients</code> data set this yielded a difference of 0.15% more isolates</li> <li>Fixed a bug where distances between dates would not be calculated right - in the <code>septic_patients</code> data set this yielded a difference of 0.15% more isolates</li>
<li>Will now use a column named like “patid” for the patient ID (parameter <code>col_patientid</code>), when this parameter was left blank</li> <li>Will now use a column named like “patid” for the patient ID (parameter <code>col_patientid</code>), when this parameter was left blank</li>
<li>Will now use a column named like “key(…)ab” or “key(…)antibiotics” for the key antibiotics (parameter <code>col_keyantibiotics()</code>), when this parameter was left blank</li> <li>Will now use a column named like “key(…)ab” or “key(…)antibiotics” for the key antibiotics (parameter <code>col_keyantibiotics()</code>), when this parameter was left blank</li>
<li>Removed parameter <code>output_logical</code>, the function will now always return a logical value</li> <li>Removed parameter <code>output_logical</code>, the function will now always return a logical value</li>
<li>Renamed parameter <code>filter_specimen</code> to <code>specimen_group</code>, although using <code>filter_specimen</code> will still work</li> <li>Renamed parameter <code>filter_specimen</code> to <code>specimen_group</code>, although using <code>filter_specimen</code> will still work</li>
</ul>
</li>
<li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li> <li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li>
<li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li> <li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li>
<li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> <li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code>
@ -265,7 +291,8 @@
</li> </li>
<li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code> <li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code>
</li> </li>
<li>Frequency tables (<code><a href="../reference/freq.html">freq()</a></code> function):</li> <li>Frequency tables (<code><a href="../reference/freq.html">freq()</a></code> function):
<ul>
<li>Header info is now available as a list, with the <code>header</code> function</li> <li>Header info is now available as a list, with the <code>header</code> function</li>
<li>Added header info for class <code>mo</code> to show unique count of families, genera and species</li> <li>Added header info for class <code>mo</code> to show unique count of families, genera and species</li>
<li>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code><a href="https://www.rdocumentation.org/packages/base/topics/options">getOption("OutDec")</a></code> <li>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code><a href="https://www.rdocumentation.org/packages/base/topics/options">getOption("OutDec")</a></code>
@ -275,6 +302,8 @@
</li> </li>
<li>New parameter <code>droplevels</code> to exclude empty factor levels when input is a factor</li> <li>New parameter <code>droplevels</code> to exclude empty factor levels when input is a factor</li>
<li>Factor levels will be in header when present in input data</li> <li>Factor levels will be in header when present in input data</li>
</ul>
</li>
<li>Function <code><a href="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the <code>limits</code> parameter</li> <li>Function <code><a href="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the <code>limits</code> parameter</li>
<li>Automatic parameter filling for <code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> <li>Automatic parameter filling for <code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li> </li>
@ -316,7 +345,8 @@
</li> </li>
<li> <li>
<code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</li> <code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</li>
<li>Big changes to the <code>eucast_rules</code> function:</li> <li>Big changes to the <code>eucast_rules</code> function:
<ul>
<li>Now also applies rules from the EUCAST ‘Breakpoint tables for bacteria’, version 8.1, 2018, <a href="http://www.eucast.org/clinical_breakpoints/" class="uri">http://www.eucast.org/clinical_breakpoints/</a> (see Source of the function)</li> <li>Now also applies rules from the EUCAST ‘Breakpoint tables for bacteria’, version 8.1, 2018, <a href="http://www.eucast.org/clinical_breakpoints/" class="uri">http://www.eucast.org/clinical_breakpoints/</a> (see Source of the function)</li>
<li>New parameter <code>rules</code> to specify which rules should be applied (expert rules, breakpoints, others or all)</li> <li>New parameter <code>rules</code> to specify which rules should be applied (expert rules, breakpoints, others or all)</li>
<li>New parameter <code>verbose</code> which can be set to <code>TRUE</code> to get very specific messages about which columns and rows were affected</li> <li>New parameter <code>verbose</code> which can be set to <code>TRUE</code> to get very specific messages about which columns and rows were affected</li>
@ -325,11 +355,18 @@
<li>Data set <code>septic_patients</code> now reflects these changes</li> <li>Data set <code>septic_patients</code> now reflects these changes</li>
<li>Added parameter <code>pipe</code> for piperacillin (J01CA12), also to the <code>mdro</code> function</li> <li>Added parameter <code>pipe</code> for piperacillin (J01CA12), also to the <code>mdro</code> function</li>
<li>Small fixes to EUCAST clinical breakpoint rules</li> <li>Small fixes to EUCAST clinical breakpoint rules</li>
</ul>
</li>
<li>Added column <code>kingdom</code> to the microorganisms data set, and function <code>mo_kingdom</code> to look up values</li> <li>Added column <code>kingdom</code> to the microorganisms data set, and function <code>mo_kingdom</code> to look up values</li>
<li>Tremendous speed improvement for <code>as.mo</code> (and subsequently all <code>mo_*</code> functions), as empty values wil be ignored <em>a priori</em> <li>Tremendous speed improvement for <code>as.mo</code> (and subsequently all <code>mo_*</code> functions), as empty values wil be ignored <em>a priori</em>
</li> </li>
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li> <li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached <code>r as.mo("E. species") # B_ESCHR mo_fullname("E. spp.") # "Escherichia species" as.mo("S. spp") # B_STPHY mo_fullname("S. species") # "Staphylococcus species"</code> <li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li> <li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li> <li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@ -338,18 +375,19 @@
<li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code> <li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code>
</li> </li>
<li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li> <li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li>
<li>Frequency tables - <code><a href="../reference/freq.html">freq()</a></code>:</li> <li>Frequency tables - <code><a href="../reference/freq.html">freq()</a></code>:
<ul>
<li> <li>
<p>Support for grouping variables, test with:</p> <p>Support for grouping variables, test with:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%<span class="st"> </span> <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<span class="st"> </span><span class="kw">group_by</span>(hospital_id) %&gt;%<span class="st"> </span> <a class="sourceLine" id="cb4-2" data-line-number="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</code></pre></div> <a class="sourceLine" id="cb4-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li> </li>
<li> <li>
<p>Support for (un)selecting columns:</p> <p>Support for (un)selecting columns:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%<span class="st"> </span> <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) %&gt;%<span class="st"> </span> <a class="sourceLine" id="cb5-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<span class="st"> </span><span class="kw">select</span>(-count, -cum_count) <span class="co"># only get item, percent, cum_percent</span></code></pre></div> <a class="sourceLine" id="cb5-3" data-line-number="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li> </li>
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code> <li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
</li> </li>
@ -360,6 +398,8 @@
<li>New parameter <code>na</code>, to choose which character to print for empty values</li> <li>New parameter <code>na</code>, to choose which character to print for empty values</li>
<li>New parameter <code>header</code> to turn the header info off (default when <code>markdown = TRUE</code>)</li> <li>New parameter <code>header</code> to turn the header info off (default when <code>markdown = TRUE</code>)</li>
<li>New parameter <code>title</code> to manually setbthe title of the frequency table</li> <li>New parameter <code>title</code> to manually setbthe title of the frequency table</li>
</ul>
</li>
<li> <li>
<code>first_isolate</code> now tries to find columns to use as input when parameters are left blank</li> <code>first_isolate</code> now tries to find columns to use as input when parameters are left blank</li>
<li>Improvements for MDRO algorithm (function <code>mdro</code>)</li> <li>Improvements for MDRO algorithm (function <code>mdro</code>)</li>
@ -371,7 +411,8 @@
</li> </li>
<li> <li>
<code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</li> <code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</li>
<li>AI improvements for <code>as.mo</code>:</li> <li>AI improvements for <code>as.mo</code>:
<ul>
<li> <li>
<code>"CRS"</code> -&gt; <em>Stenotrophomonas maltophilia</em> <code>"CRS"</code> -&gt; <em>Stenotrophomonas maltophilia</em>
</li> </li>
@ -384,6 +425,8 @@
<li> <li>
<code>"MSSE"</code> -&gt; <em>Staphylococcus epidermidis</em> <code>"MSSE"</code> -&gt; <em>Staphylococcus epidermidis</em>
</li> </li>
</ul>
</li>
<li>Fix for <code>join</code> functions</li> <li>Fix for <code>join</code> functions</li>
<li>Speed improvement for <code>is.rsi.eligible</code>, now 15-20 times faster</li> <li>Speed improvement for <code>is.rsi.eligible</code>, now 15-20 times faster</li>
<li>In <code>g.test</code>, when <code><a href="https://www.rdocumentation.org/packages/base/topics/sum">sum(x)</a></code> is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested</li> <li>In <code>g.test</code>, when <code><a href="https://www.rdocumentation.org/packages/base/topics/sum">sum(x)</a></code> is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested</li>
@ -412,7 +455,8 @@
<a href="#new-2" class="anchor"></a>New</h4> <a href="#new-2" class="anchor"></a>New</h4>
<ul> <ul>
<li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li> <li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
<li>New functions based on the existing function <code>mo_property</code>:</li> <li>New functions based on the existing function <code>mo_property</code>:
<ul>
<li>Taxonomic names: <code>mo_phylum</code>, <code>mo_class</code>, <code>mo_order</code>, <code>mo_family</code>, <code>mo_genus</code>, <code>mo_species</code>, <code>mo_subspecies</code> <li>Taxonomic names: <code>mo_phylum</code>, <code>mo_class</code>, <code>mo_order</code>, <code>mo_family</code>, <code>mo_genus</code>, <code>mo_species</code>, <code>mo_subspecies</code>
</li> </li>
<li>Semantic names: <code>mo_fullname</code>, <code>mo_shortname</code> <li>Semantic names: <code>mo_fullname</code>, <code>mo_shortname</code>
@ -422,22 +466,52 @@
<li>Author and year: <code>mo_ref</code> <li>Author and year: <code>mo_ref</code>
</li> </li>
</ul> </ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese: <code>r mo_gramstain("E. coli") # [1] "Gram negative" mo_gramstain("E. coli", language = "de") # German # [1] "Gramnegativ" mo_gramstain("E. coli", language = "es") # Spanish # [1] "Gram negativo" mo_fullname("S. group A", language = "pt") # Portuguese # [1] "Streptococcus grupo A"</code></p> <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name: <code>r mo_gramstain("Esc blattae") # Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010) # [1] "Gram negative"</code></p> <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</li>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul> <ul>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates</li>
<li>Extra function <code>count_df</code> (which works like <code>portion_df</code>) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables</li> <li>Extra function <code>count_df</code> (which works like <code>portion_df</code>) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables</li>
</ul>
</li>
<li>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code> <li>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code>
</li> </li>
<li>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI): <code>r as.mo("E. coli") # [1] B_ESCHR_COL as.mo("MRSA") # [1] B_STPHY_AUR as.mo("S group A") # [1] B_STRPTC_GRA</code> And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items: <code>r thousands_of_E_colis &lt;- rep("E. coli", 25000) microbenchmark::microbenchmark(as.mo(thousands_of_E_colis), unit = "s") # Unit: seconds # min median max neval # 0.01817717 0.01843957 0.03878077 100</code> <li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI):</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb8-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb9-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li> <li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:</li> <li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
<ul>
<li>Column names inputs of <code>EUCAST_rules</code>, <code>first_isolate</code> and <code>key_antibiotics</code> <li>Column names inputs of <code>EUCAST_rules</code>, <code>first_isolate</code> and <code>key_antibiotics</code>
</li> </li>
<li>Column names of datasets <code>microorganisms</code> and <code>septic_patients</code> <li>Column names of datasets <code>microorganisms</code> and <code>septic_patients</code>
</li> </li>
<li>All old syntaxes will still work with this version, but will throw warnings</li> <li>All old syntaxes will still work with this version, but will throw warnings</li>
</ul>
</li>
<li>Function <code>labels_rsi_count</code> to print datalabels on a RSI <code>ggplot2</code> model</li> <li>Function <code>labels_rsi_count</code> to print datalabels on a RSI <code>ggplot2</code> model</li>
<li><p>Functions <code>as.atc</code> and <code>is.atc</code> to transform/look up antibiotic ATC codes as defined by the WHO. The existing function <code>guess_atc</code> is now an alias of <code>as.atc</code>.</p></li> <li><p>Functions <code>as.atc</code> and <code>is.atc</code> to transform/look up antibiotic ATC codes as defined by the WHO. The existing function <code>guess_atc</code> is now an alias of <code>as.atc</code>.</p></li>
<li>Function <code>ab_property</code> and its aliases: <code>ab_name</code>, <code>ab_tradenames</code>, <code>ab_certe</code>, <code>ab_umcg</code> and <code>ab_trivial_nl</code> <li>Function <code>ab_property</code> and its aliases: <code>ab_name</code>, <code>ab_tradenames</code>, <code>ab_certe</code>, <code>ab_umcg</code> and <code>ab_trivial_nl</code>
@ -452,7 +526,14 @@
<a href="#changed-2" class="anchor"></a>Changed</h4> <a href="#changed-2" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li> <li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.: <code>r ab_official("Bactroban") # [1] "Mupirocin" ab_name(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) # [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin" ab_atc(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) # [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</code> <li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="../reference/ab_property.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb10-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb10-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</li> </li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li> <li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li> <li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@ -461,9 +542,36 @@
<li>Added <code>prevalence</code> column to the <code>microorganisms</code> data set</li> <li>Added <code>prevalence</code> column to the <code>microorganisms</code> data set</li>
<li>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code> <li>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code>
</li> </li>
<li>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns. ```r septic_patients %&gt;% select(amox, cipr) %&gt;% count_IR() # which is the same as: septic_patients %&gt;% count_IR(amox, cipr)</li> <li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb11-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb11-4" data-line-number="4"></a>
<a class="sourceLine" id="cb11-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb11-6" data-line-number="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb11-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
</li>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
<li>Added datalabels function <code>labels_rsi_count</code> to <code>ggplot_rsi</code>
</li>
<li>Added possibility to set any parameter to <code>geom_rsi</code> (and <code>ggplot_rsi</code>) so you can set your own preferences</li>
<li>Fix for joins, where predefined suffices would not be honoured</li>
<li>Added parameter <code>quote</code> to the <code>freq</code> function</li>
<li>Added generic function <code>diff</code> for frequency tables</li>
<li>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code>
</li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb13-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb13-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
</ul> </ul>
<p>septic_patients %&gt;% portion_S(amcl) septic_patients %&gt;% portion_S(amcl, gent) septic_patients %&gt;% portion_S(amcl, gent, pita) <code>* Edited `ggplot_rsi` and `geom_rsi` so they can cope with `count_df`. The new `fun` parameter has value `portion_df` at default, but can be set to `count_df`. * Fix for `ggplot_rsi` when the `ggplot2` package was not loaded * Added datalabels function `labels_rsi_count` to `ggplot_rsi` * Added possibility to set any parameter to `geom_rsi` (and `ggplot_rsi`) so you can set your own preferences * Fix for joins, where predefined suffices would not be honoured * Added parameter `quote` to the `freq` function * Added generic function `diff` for frequency tables * Added longest en shortest character length in the frequency table (`freq`) header of class `character` * Support for types (classes) list and matrix for `freq`</code>r my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2)) freq(my_matrix) <code>For lists, subsetting is possible:</code>r my_list = list(age = septic_patients$age, gender = septic_patients$gender) my_list %&gt;% freq(age) my_list %&gt;% freq(gender) ```</p>
</div> </div>
<div id="other-2" class="section level4"> <div id="other-2" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
@ -482,15 +590,21 @@
<a href="#new-3" class="anchor"></a>New</h4> <a href="#new-3" class="anchor"></a>New</h4>
<ul> <ul>
<li> <li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.</li> <strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
<ul>
<li>New function <code>portion_df</code> to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables</li> <li>New function <code>portion_df</code> to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables</li>
</ul>
</li>
<li> <li>
<strong>BREAKING</strong>: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call <em>key antibiotics</em>) to include more first isolates (afterwards called first <em>weighted</em> isolates) are now as follows:</li> <strong>BREAKING</strong>: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call <em>key antibiotics</em>) to include more first isolates (afterwards called first <em>weighted</em> isolates) are now as follows:
<ul>
<li>Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole</li> <li>Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole</li>
<li>Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin</li> <li>Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin</li>
<li>Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem</li> <li>Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem</li>
<li>Support for <code>ggplot2</code> </ul>
</li> </li>
<li>Support for <code>ggplot2</code>
<ul>
<li>New functions <code>geom_rsi</code>, <code>facet_rsi</code>, <code>scale_y_percent</code>, <code>scale_rsi_colours</code> and <code>theme_rsi</code> <li>New functions <code>geom_rsi</code>, <code>facet_rsi</code>, <code>scale_y_percent</code>, <code>scale_rsi_colours</code> and <code>theme_rsi</code>
</li> </li>
<li>New wrapper function <code>ggplot_rsi</code> to apply all above functions on a data set: <li>New wrapper function <code>ggplot_rsi</code> to apply all above functions on a data set:
@ -501,22 +615,32 @@
</li> </li>
</ul> </ul>
</li> </li>
<li>Determining bacterial ID:</li> </ul>
</li>
<li>Determining bacterial ID:
<ul>
<li>New functions <code>as.bactid</code> and <code>is.bactid</code> to transform/ look up microbial ID’s.</li> <li>New functions <code>as.bactid</code> and <code>is.bactid</code> to transform/ look up microbial ID’s.</li>
<li>The existing function <code>guess_bactid</code> is now an alias of <code>as.bactid</code> <li>The existing function <code>guess_bactid</code> is now an alias of <code>as.bactid</code>
</li> </li>
<li>New Becker classification for <em>Staphylococcus</em> to categorise them into Coagulase Negative <em>Staphylococci</em> (CoNS) and Coagulase Positve <em>Staphylococci</em> (CoPS)</li> <li>New Becker classification for <em>Staphylococcus</em> to categorise them into Coagulase Negative <em>Staphylococci</em> (CoNS) and Coagulase Positve <em>Staphylococci</em> (CoPS)</li>
<li>New Lancefield classification for <em>Streptococcus</em> to categorise them into Lancefield groups</li> <li>New Lancefield classification for <em>Streptococcus</em> to categorise them into Lancefield groups</li>
</ul>
</li>
<li>For convience, new descriptive statistical functions <code>kurtosis</code> and <code>skewness</code> that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices</li> <li>For convience, new descriptive statistical functions <code>kurtosis</code> and <code>skewness</code> that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices</li>
<li>Function <code>g.test</code> to perform the Χ<sup>2</sup> distributed <a href="https://en.wikipedia.org/wiki/G-test"><em>G</em>-test</a>, which use is the same as <code>chisq.test</code> <li>Function <code>g.test</code> to perform the Χ<sup>2</sup> distributed <a href="https://en.wikipedia.org/wiki/G-test"><em>G</em>-test</a>, which use is the same as <code>chisq.test</code>
</li> </li>
<li><del>Function <code>ratio</code> to transform a vector of values to a preset ratio</del></li> <li>
<del>Function <code>ratio</code> to transform a vector of values to a preset ratio</del>
<ul>
<li><del>For example: <code><a href="../reference/AMR-deprecated.html">ratio(c(10, 500, 10), ratio = "1:2:1")</a></code> would return <code>130, 260, 130</code></del></li> <li><del>For example: <code><a href="../reference/AMR-deprecated.html">ratio(c(10, 500, 10), ratio = "1:2:1")</a></code> would return <code>130, 260, 130</code></del></li>
</ul>
</li>
<li>Support for Addins menu in RStudio to quickly insert <code>%in%</code> or <code>%like%</code> (and give them keyboard shortcuts), or to view the datasets that come with this package</li> <li>Support for Addins menu in RStudio to quickly insert <code>%in%</code> or <code>%like%</code> (and give them keyboard shortcuts), or to view the datasets that come with this package</li>
<li>Function <code>p.symbol</code> to transform p values to their related symbols: <code>0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code> <li>Function <code>p.symbol</code> to transform p values to their related symbols: <code>0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code>
</li> </li>
<li>Functions <code>clipboard_import</code> and <code>clipboard_export</code> as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the <code>clipr</code> package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)</li> <li>Functions <code>clipboard_import</code> and <code>clipboard_export</code> as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the <code>clipr</code> package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)</li>
<li>New for frequency tables (function <code>freq</code>):</li> <li>New for frequency tables (function <code>freq</code>):
<ul>
<li>A vignette to explain its usage</li> <li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li> <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code><a href="../reference/freq.html">freq(table(x, y))</a></code> <li>Support for <code>table</code> to use as input: <code><a href="../reference/freq.html">freq(table(x, y))</a></code>
@ -531,6 +655,8 @@
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li> <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
<li>Possibility to globally set the default for the amount of items to print, with <code><a href="https://www.rdocumentation.org/packages/base/topics/options">options(max.print.freq = n)</a></code> where <em>n</em> is your preset value</li> <li>Possibility to globally set the default for the amount of items to print, with <code><a href="https://www.rdocumentation.org/packages/base/topics/options">options(max.print.freq = n)</a></code> where <em>n</em> is your preset value</li>
</ul> </ul>
</li>
</ul>
</div> </div>
<div id="changed-3" class="section level4"> <div id="changed-3" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
@ -552,21 +678,27 @@
</li> </li>
<li>Small improvements to the <code>microorganisms</code> dataset (especially for <em>Salmonella</em>) and the column <code>bactid</code> now has the new class <code>"bactid"</code> <li>Small improvements to the <code>microorganisms</code> dataset (especially for <em>Salmonella</em>) and the column <code>bactid</code> now has the new class <code>"bactid"</code>
</li> </li>
<li>Combined MIC/RSI values will now be coerced by the <code>rsi</code> and <code>mic</code> functions:</li> <li>Combined MIC/RSI values will now be coerced by the <code>rsi</code> and <code>mic</code> functions:
<ul>
<li> <li>
<code><a href="../reference/as.rsi.html">as.rsi("&lt;=0.002; S")</a></code> will return <code>S</code> <code><a href="../reference/as.rsi.html">as.rsi("&lt;=0.002; S")</a></code> will return <code>S</code>
</li> </li>
<li> <li>
<code><a href="../reference/as.mic.html">as.mic("&lt;=0.002; S")</a></code> will return <code>&lt;=0.002</code> <code><a href="../reference/as.mic.html">as.mic("&lt;=0.002; S")</a></code> will return <code>&lt;=0.002</code>
</li> </li>
</ul>
</li>
<li>Now possible to coerce MIC values with a space between operator and value, i.e. <code><a href="../reference/as.mic.html">as.mic("&lt;= 0.002")</a></code> now works</li> <li>Now possible to coerce MIC values with a space between operator and value, i.e. <code><a href="../reference/as.mic.html">as.mic("&lt;= 0.002")</a></code> now works</li>
<li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li> <li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li>
<li>Added <code>"groups"</code> option for <code><a href="../reference/atc_property.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <a href="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li> <li>Added <code>"groups"</code> option for <code><a href="../reference/atc_property.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <a href="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
<li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li> <li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li>
<li>Improved <code>first_isolate</code> algorithm to exclude isolates where bacteria ID or genus is unavailable</li> <li>Improved <code>first_isolate</code> algorithm to exclude isolates where bacteria ID or genus is unavailable</li>
<li>Fix for warning <em>hybrid evaluation forced for row_number</em> (<a href="https://github.com/tidyverse/dplyr/commit/924b62"><code>924b62</code></a>) from the <code>dplyr</code> package v0.7.5 and above</li> <li>Fix for warning <em>hybrid evaluation forced for row_number</em> (<a href="https://github.com/tidyverse/dplyr/commit/924b62"><code>924b62</code></a>) from the <code>dplyr</code> package v0.7.5 and above</li>
<li>Support for empty values and for 1 or 2 columns as input for <code>guess_bactid</code> (now called <code>as.bactid</code>)</li> <li>Support for empty values and for 1 or 2 columns as input for <code>guess_bactid</code> (now called <code>as.bactid</code>)
<ul>
<li>So <code>yourdata %&gt;% select(genus, species) %&gt;% as.bactid()</code> now also works</li> <li>So <code>yourdata %&gt;% select(genus, species) %&gt;% as.bactid()</code> now also works</li>
</ul>
</li>
<li>Other small fixes</li> <li>Other small fixes</li>
</ul> </ul>
</div> </div>
@ -574,11 +706,14 @@
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#other-3" class="anchor"></a>Other</h4> <a href="#other-3" class="anchor"></a>Other</h4>
<ul> <ul>
<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher</li> <li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
<ul>
<li>Linux and macOS: <a href="https://travis-ci.org/msberends/AMR" class="uri">https://travis-ci.org/msberends/AMR</a> <li>Linux and macOS: <a href="https://travis-ci.org/msberends/AMR" class="uri">https://travis-ci.org/msberends/AMR</a>
</li> </li>
<li>Windows: <a href="https://ci.appveyor.com/project/msberends/amr" class="uri">https://ci.appveyor.com/project/msberends/amr</a> <li>Windows: <a href="https://ci.appveyor.com/project/msberends/amr" class="uri">https://ci.appveyor.com/project/msberends/amr</a>
</li> </li>
</ul>
</li>
<li>Added thesis advisors to DESCRIPTION file</li> <li>Added thesis advisors to DESCRIPTION file</li>
</ul> </ul>
</div> </div>
@ -597,10 +732,13 @@
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li> <li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li> <li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li> <li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
<li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant Organisms (MDRO)</strong> with support for country-specific guidelines.</li> <li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant Organisms (MDRO)</strong> with support for country-specific guidelines.
<ul>
<li> <li>
<a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance">Exceptional resistances defined by EUCAST</a> are also supported instead of countries alone</li> <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance">Exceptional resistances defined by EUCAST</a> are also supported instead of countries alone</li>
<li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for Dutch and German guidelines, respectively</li> <li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for Dutch and German guidelines, respectively</li>
</ul>
</li>
<li>New algorithm to determine weighted isolates, can now be <code>"points"</code> or <code>"keyantibiotics"</code>, see <code><a href="../reference/first_isolate.html">?first_isolate</a></code> <li>New algorithm to determine weighted isolates, can now be <code>"points"</code> or <code>"keyantibiotics"</code>, see <code><a href="../reference/first_isolate.html">?first_isolate</a></code>
</li> </li>
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li> <li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>

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pkgdown: 1.3.0 pkgdown: 1.3.0
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<h1>ITIS: Integrated Taxonomic Information System</h1>
<div class="hidden name"><code>ITIS.Rd</code></div>
</div>
<div class="ref-description">
<p>All taxonomic names of all microorganisms are included in this package, using the authoritative Integrated Taxonomic Information System (ITIS).</p>
</div>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<p><img src='figures/itis_logo.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># Get a note when a species was renamed</span>
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='st'>"Chlamydia psittaci"</span>)
<span class='co'># Note: 'Chlamydia psittaci' (Page, 1968) was renamed</span>
<span class='co'># 'Chlamydophila psittaci' (Everett et al., 1999)</span>
<span class='co'># [1] "C. psittaci"</span>
<span class='co'># Get any property from the entire taxonomic tree for all included species</span>
<span class='fu'><a href='mo_property.html'>mo_class</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Gammaproteobacteria"</span>
<span class='fu'><a href='mo_property.html'>mo_family</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Enterobacteriaceae"</span>
<span class='fu'><a href='mo_property.html'>mo_subkingdom</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Negibacteria"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># based on subkingdom</span>
<span class='co'># [1] "Gram negative"</span>
<span class='fu'><a href='mo_property.html'>mo_ref</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Castellani and Chalmers, 1919"</span>
<span class='co'># Do not get mistaken - the package only includes microorganisms</span>
<span class='fu'><a href='mo_property.html'>mo_phylum</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Cyanobacteria" # Bacteria?!</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span>
<span class='co'># }</span></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#itis">ITIS</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
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@ -289,11 +289,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># resistance of ciprofloxacine per age group</span> <span class='co'># resistance of ciprofloxacine per age group</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span> <span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>) <span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>

4
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@ -270,11 +270,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># using dplyr's mutate</span> <span class='co'># using dplyr's mutate</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='http://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>) <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span> <span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
<span class='no'>as.rsi</span>) <span class='no'>as.rsi</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>
</div> </div>

16
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@ -217,7 +217,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<div class="ref-description"> <div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p> <p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>count_R</code> and <code>count_IR</code> can be used to count resistant isolates, <code>count_S</code> and <code>count_SI</code> can be used to count susceptible isolates.<br /></p> <p><code>count_R</code> and <code>count_IR</code> can be used to count resistant isolates, <code>count_S</code> and <code>count_SI</code> can be used to count susceptible isolates.<br /></p>
</div> </div>
@ -275,7 +275,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p> <p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='http://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p> <p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p> <p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -314,13 +314,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>), <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>), <span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>), <span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span> <span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span> <span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span> <span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span> <span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span> <span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
@ -338,13 +338,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># Get portions S/I/R immediately of all rsi columns</span> <span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span> <span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>

128
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@ -289,8 +289,8 @@
<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li> <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <br /> <li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li> <a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. <br /> <li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx</a></p></li> <a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
</ul> </ul>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@ -302,68 +302,68 @@
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab.html'>guess_ab</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p> <p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab.html'>guess_ab</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p> <p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>), <p><strong>amcl</strong>: amoxicillin+clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>), <strong>amik</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>amox</strong>: amoxicillin (<em>J01CA04</em>), <strong>amox</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>ampi</strong>: ampicillin (<em>J01CA01</em>), <strong>ampi</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>azit</strong>: azithromycin (<em>J01FA10</em>), <strong>azit</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>azlo</strong>: azlocillin (<em>J01CA09</em>), <strong>azlo</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>aztr</strong>: aztreonam (<em>J01DF01</em>), <strong>aztr</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>cefa</strong>: cefaloridine (<em>J01DB02</em>), <strong>cefa</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>cfep</strong>: cefepime (<em>J01DE01</em>), <strong>cfep</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>cfot</strong>: cefotaxime (<em>J01DD01</em>), <strong>cfot</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>cfox</strong>: cefoxitin (<em>J01DC01</em>), <strong>cfox</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
<strong>cfra</strong>: cefradine (<em>J01DB09</em>), <strong>cfra</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
<strong>cfta</strong>: ceftazidime (<em>J01DD02</em>), <strong>cfta</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
<strong>cftr</strong>: ceftriaxone (<em>J01DD04</em>), <strong>cftr</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
<strong>cfur</strong>: cefuroxime (<em>J01DC02</em>), <strong>cfur</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
<strong>chlo</strong>: chloramphenicol (<em>J01BA01</em>), <strong>chlo</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
<strong>cipr</strong>: ciprofloxacin (<em>J01MA02</em>), <strong>cipr</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>clar</strong>: clarithromycin (<em>J01FA09</em>), <strong>clar</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>clin</strong>: clindamycin (<em>J01FF01</em>), <strong>clin</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>clox</strong>: flucloxacillin (<em>J01CF05</em>), <strong>clox</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>coli</strong>: colistin (<em>J01XB01</em>), <strong>coli</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>czol</strong>: cefazolin (<em>J01DB04</em>), <strong>czol</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>dapt</strong>: daptomycin (<em>J01XX09</em>), <strong>dapt</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>doxy</strong>: doxycycline (<em>J01AA02</em>), <strong>doxy</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>erta</strong>: ertapenem (<em>J01DH03</em>), <strong>erta</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>eryt</strong>: erythromycin (<em>J01FA01</em>), <strong>eryt</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>fosf</strong>: fosfomycin (<em>J01XX01</em>), <strong>fosf</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>fusi</strong>: fusidic acid (<em>J01XC01</em>), <strong>fusi</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>gent</strong>: gentamicin (<em>J01GB03</em>), <strong>gent</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>imip</strong>: imipenem (<em>J01DH51</em>), <strong>imip</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>kana</strong>: kanamycin (<em>J01GB04</em>), <strong>kana</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>levo</strong>: levofloxacin (<em>J01MA12</em>), <strong>levo</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>linc</strong>: lincomycin (<em>J01FF02</em>), <strong>linc</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>line</strong>: linezolid (<em>J01XX08</em>), <strong>line</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>mero</strong>: meropenem (<em>J01DH02</em>), <strong>mero</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>mezl</strong>: mezlocillin (<em>J01CA10</em>), <strong>mezl</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>mino</strong>: minocycline (<em>J01AA08</em>), <strong>mino</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>moxi</strong>: moxifloxacin (<em>J01MA14</em>), <strong>moxi</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>nali</strong>: nalidixic acid (<em>J01MB02</em>), <strong>nali</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>neom</strong>: neomycin (<em>J01GB05</em>), <strong>neom</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>neti</strong>: netilmicin (<em>J01GB07</em>), <strong>neti</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
<strong>nitr</strong>: nitrofurantoin (<em>J01XE01</em>), <strong>nitr</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
<strong>norf</strong>: norfloxacin (<em>J01MA06</em>), <strong>norf</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>novo</strong>: novobiocin (an ATCvet code: <em>QJ01XX95</em>), <strong>novo</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>oflo</strong>: ofloxacin (<em>J01MA01</em>), <strong>oflo</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>peni</strong>: penicillin (<em>J01RA01</em>), <strong>peni</strong>: (benzyl)penicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>pipe</strong>: piperacillin (<em>J01CA12</em>), <strong>pipe</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>pita</strong>: piperacillin+tazobactam (<em>J01CR05</em>), <strong>pita</strong>: piperacillin+tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>poly</strong>: polymyxin B (<em>J01XB02</em>), <strong>poly</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>pris</strong>: pristinamycin (<em>J01FG01</em>), <strong>pris</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>qida</strong>: quinupristin/dalfopristin (<em>J01FG02</em>), <strong>qida</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>rifa</strong>: rifampicin (<em>J04AB02</em>), <strong>rifa</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>roxi</strong>: roxithromycin (<em>J01FA06</em>), <strong>roxi</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>siso</strong>: sisomicin (<em>J01GB08</em>), <strong>siso</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>teic</strong>: teicoplanin (<em>J01XA02</em>), <strong>teic</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
<strong>tetr</strong>: tetracycline (<em>J01AA07</em>), <strong>tetr</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
<strong>tica</strong>: ticarcillin (<em>J01CA13</em>), <strong>tica</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
<strong>tige</strong>: tigecycline (<em>J01AA12</em>), <strong>tige</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
<strong>tobr</strong>: tobramycin (<em>J01GB01</em>), <strong>tobr</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
<strong>trim</strong>: trimethoprim (<em>J01EA01</em>), <strong>trim</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>), <strong>trsu</strong>: sulfamethoxazole and trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p> <strong>vanc</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

12
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@ -361,11 +361,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># Filter on first isolates:</span> <span class='co'># Filter on first isolates:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>, <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span> <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
<span class='co'># Which can be shortened to:</span> <span class='co'># Which can be shortened to:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
@ -376,14 +376,14 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># Now let's see if first isolates matter:</span> <span class='co'># Now let's see if first isolates matter:</span>
<span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span> <span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
<span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span> <span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span> <span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
<span class='co'># Have a look at A and B.</span> <span class='co'># Have a look at A and B.</span>

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@ -354,7 +354,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
<li><p>Median, using <code><a href='https://www.rdocumentation.org/packages/stats/topics/median'>median</a></code>, with percentage since oldest</p></li> <li><p>Median, using <code><a href='https://www.rdocumentation.org/packages/stats/topics/median'>median</a></code>, with percentage since oldest</p></li>
</ul> </ul>
<p>In factors, all factor levels that are not existing in the input data will be dropped.</p> <p>In factors, all factor levels that are not existing in the input data will be dropped.</p>
<p>The function <code>top_freq</code> uses <code><a href='http://dplyr.tidyverse.org/reference/top_n.html'>top_n</a></code> internally and will include more than <code>n</code> rows if there are ties.</p> <p>The function <code>top_freq</code> uses <code><a href='https://dplyr.tidyverse.org/reference/top_n.html'>top_n</a></code> internally and will include more than <code>n</code> rows if there are ties.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -378,34 +378,34 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># you could also use `select` or `pull` to get your variables</span> <span class='co'># you could also use `select` or `pull` to get your variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>() <span class='fu'>freq</span>()
<span class='co'># multiple selected variables will be pasted together</span> <span class='co'># multiple selected variables will be pasted together</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='no'>left_join_microorganisms</span> <span class='kw'>%&gt;%</span> <span class='no'>left_join_microorganisms</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='fu'>freq</span>(<span class='no'>genus</span>, <span class='no'>species</span>)
<span class='co'># group a variable and analyse another</span> <span class='co'># group a variable and analyse another</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>gender</span>) <span class='fu'>freq</span>(<span class='no'>gender</span>)
<span class='co'># get top 10 bugs of hospital A as a vector</span> <span class='co'># get top 10 bugs of hospital A as a vector</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>top_freq</span>(<span class='fl'>10</span>) <span class='fu'>top_freq</span>(<span class='fl'>10</span>)
<span class='co'># save frequency table to an object</span> <span class='co'># save frequency table to an object</span>
<span class='no'>years</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>years</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>year</span>) <span class='fu'>freq</span>(<span class='no'>year</span>)
@ -456,11 +456,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># only get selected columns</span> <span class='co'># only get selected columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>) <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>) <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
<span class='co'># check differences between frequency tables</span> <span class='co'># check differences between frequency tables</span>

36
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@ -327,7 +327,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>)
<span class='co'># get antimicrobial results for drugs against a UTI:</span> <span class='co'># get antimicrobial results for drugs against a UTI:</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
<span class='fu'>geom_rsi</span>() <span class='fu'>geom_rsi</span>()
<span class='co'># prettify the plot using some additional functions:</span> <span class='co'># prettify the plot using some additional functions:</span>
@ -341,17 +341,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span> <span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() <span class='fu'>ggplot_rsi</span>()
<span class='co'># get only portions and no counts:</span> <span class='co'># get only portions and no counts:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>portion_df</span>) <span class='fu'>ggplot_rsi</span>(<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>portion_df</span>)
<span class='co'># add other ggplot2 parameters as you like:</span> <span class='co'># add other ggplot2 parameters as you like:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>, <span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
<span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
@ -360,25 +360,25 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># resistance of ciprofloxacine per age group</span> <span class='co'># resistance of ciprofloxacine per age group</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span> <span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># `age_group` is also a function of this package:</span> <span class='co'># `age_group` is also a function of this package:</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>) <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span> <span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span> <span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>() <span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span> <span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>, <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) + <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
@ -388,22 +388,22 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># genuine analysis: check 2 most prevalent microorganisms</span> <span class='co'># genuine analysis: check 2 most prevalent microorganisms</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span> <span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on top three bacterial ID's</span> <span class='co'># filter on top three bacterial ID's</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># determine first isolates</span> <span class='co'># determine first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>, <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span> <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first isolates</span> <span class='co'># filter on first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
<span class='co'># get short MO names (like "E. coli")</span> <span class='co'># get short MO names (like "E. coli")</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># select this short name and some antiseptic drugs</span> <span class='co'># select this short name and some antiseptic drugs</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='co'># group by MO</span> <span class='co'># group by MO</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='co'># plot the thing, putting MOs on the facet</span> <span class='co'># plot the thing, putting MOs on the facet</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>, <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</span>,

6
docs/reference/index.html
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@ -221,7 +221,7 @@
<tbody> <tbody>
<tr> <tr>
<th colspan="2"> <th colspan="2">
<h2 id="section-backround-information" class="hasAnchor"><a href="#section-backround-information" class="anchor"></a>Backround information</h2> <h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
<p class="section-desc"><p>Some pages about our package and its external sources.</p></p> <p class="section-desc"><p>Some pages about our package and its external sources.</p></p>
</th> </th>
</tr> </tr>
@ -234,7 +234,7 @@
</tr><tr> </tr><tr>
<td> <td>
<p><code><a href="itis.html">itis</a></code> </p> <p><code><a href="ITIS.html">ITIS</a></code> </p>
</td> </td>
<td><p>ITIS: Integrated Taxonomic Information System</p></td> <td><p>ITIS: Integrated Taxonomic Information System</p></td>
</tr> </tr>
@ -513,7 +513,7 @@
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#section-backround-information">Backround information</a></li> <li><a href="#section-background-information">Background information</a></li>
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li> <li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li> <li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
<li><a href="#section-analysing-your-data">Analysing your data</a></li> <li><a href="#section-analysing-your-data">Analysing your data</a></li>

4
docs/reference/join.html
View File

@ -249,13 +249,13 @@
</tr> </tr>
<tr> <tr>
<th>...</th> <th>...</th>
<td><p>other parameters to pass on to <code>dplyr::<a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code>.</p></td> <td><p>other parameters to pass on to <code>dplyr::<a href='https://dplyr.tidyverse.org/reference/join.html'>join</a></code>.</p></td>
</tr> </tr>
</table> </table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Note:</strong> As opposed to the <code><a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code> functions of <code>dplyr</code>, characters vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code> for more information.</p> <p><strong>Note:</strong> As opposed to the <code><a href='https://dplyr.tidyverse.org/reference/join.html'>join</a></code> functions of <code>dplyr</code>, characters vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='https://dplyr.tidyverse.org/reference/join.html'>join</a></code> for more information.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

2
docs/reference/like.html
View File

@ -288,7 +288,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span> <span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>
</div> </div>

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<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab.html'>guess_ab</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p> <p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab.html'>guess_ab</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p> <p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>), <p><strong>amcl</strong>: amoxicillin+clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>), <strong>amik</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>amox</strong>: amoxicillin (<em>J01CA04</em>), <strong>amox</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>ampi</strong>: ampicillin (<em>J01CA01</em>), <strong>ampi</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>azit</strong>: azithromycin (<em>J01FA10</em>), <strong>azit</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>azlo</strong>: azlocillin (<em>J01CA09</em>), <strong>azlo</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>aztr</strong>: aztreonam (<em>J01DF01</em>), <strong>aztr</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>cefa</strong>: cefaloridine (<em>J01DB02</em>), <strong>cefa</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>cfep</strong>: cefepime (<em>J01DE01</em>), <strong>cfep</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>cfot</strong>: cefotaxime (<em>J01DD01</em>), <strong>cfot</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>cfox</strong>: cefoxitin (<em>J01DC01</em>), <strong>cfox</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
<strong>cfra</strong>: cefradine (<em>J01DB09</em>), <strong>cfra</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
<strong>cfta</strong>: ceftazidime (<em>J01DD02</em>), <strong>cfta</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
<strong>cftr</strong>: ceftriaxone (<em>J01DD04</em>), <strong>cftr</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
<strong>cfur</strong>: cefuroxime (<em>J01DC02</em>), <strong>cfur</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
<strong>chlo</strong>: chloramphenicol (<em>J01BA01</em>), <strong>chlo</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
<strong>cipr</strong>: ciprofloxacin (<em>J01MA02</em>), <strong>cipr</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>clar</strong>: clarithromycin (<em>J01FA09</em>), <strong>clar</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>clin</strong>: clindamycin (<em>J01FF01</em>), <strong>clin</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>clox</strong>: flucloxacillin (<em>J01CF05</em>), <strong>clox</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>coli</strong>: colistin (<em>J01XB01</em>), <strong>coli</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>czol</strong>: cefazolin (<em>J01DB04</em>), <strong>czol</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>dapt</strong>: daptomycin (<em>J01XX09</em>), <strong>dapt</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>doxy</strong>: doxycycline (<em>J01AA02</em>), <strong>doxy</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>erta</strong>: ertapenem (<em>J01DH03</em>), <strong>erta</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>eryt</strong>: erythromycin (<em>J01FA01</em>), <strong>eryt</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>fosf</strong>: fosfomycin (<em>J01XX01</em>), <strong>fosf</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>fusi</strong>: fusidic acid (<em>J01XC01</em>), <strong>fusi</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>gent</strong>: gentamicin (<em>J01GB03</em>), <strong>gent</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>imip</strong>: imipenem (<em>J01DH51</em>), <strong>imip</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>kana</strong>: kanamycin (<em>J01GB04</em>), <strong>kana</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>levo</strong>: levofloxacin (<em>J01MA12</em>), <strong>levo</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>linc</strong>: lincomycin (<em>J01FF02</em>), <strong>linc</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>line</strong>: linezolid (<em>J01XX08</em>), <strong>line</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>mero</strong>: meropenem (<em>J01DH02</em>), <strong>mero</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>mezl</strong>: mezlocillin (<em>J01CA10</em>), <strong>mezl</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>mino</strong>: minocycline (<em>J01AA08</em>), <strong>mino</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>moxi</strong>: moxifloxacin (<em>J01MA14</em>), <strong>moxi</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>nali</strong>: nalidixic acid (<em>J01MB02</em>), <strong>nali</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>neom</strong>: neomycin (<em>J01GB05</em>), <strong>neom</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>neti</strong>: netilmicin (<em>J01GB07</em>), <strong>neti</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
<strong>nitr</strong>: nitrofurantoin (<em>J01XE01</em>), <strong>nitr</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
<strong>norf</strong>: norfloxacin (<em>J01MA06</em>), <strong>norf</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>novo</strong>: novobiocin (an ATCvet code: <em>QJ01XX95</em>), <strong>novo</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>oflo</strong>: ofloxacin (<em>J01MA01</em>), <strong>oflo</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>peni</strong>: penicillin (<em>J01RA01</em>), <strong>peni</strong>: (benzyl)penicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>pipe</strong>: piperacillin (<em>J01CA12</em>), <strong>pipe</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>pita</strong>: piperacillin+tazobactam (<em>J01CR05</em>), <strong>pita</strong>: piperacillin+tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>poly</strong>: polymyxin B (<em>J01XB02</em>), <strong>poly</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>pris</strong>: pristinamycin (<em>J01FG01</em>), <strong>pris</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>qida</strong>: quinupristin/dalfopristin (<em>J01FG02</em>), <strong>qida</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>rifa</strong>: rifampicin (<em>J04AB02</em>), <strong>rifa</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>roxi</strong>: roxithromycin (<em>J01FA06</em>), <strong>roxi</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>siso</strong>: sisomicin (<em>J01GB08</em>), <strong>siso</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>teic</strong>: teicoplanin (<em>J01XA02</em>), <strong>teic</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
<strong>tetr</strong>: tetracycline (<em>J01AA07</em>), <strong>tetr</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
<strong>tica</strong>: ticarcillin (<em>J01CA13</em>), <strong>tica</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
<strong>tige</strong>: tigecycline (<em>J01AA12</em>), <strong>tige</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
<strong>tobr</strong>: tobramycin (<em>J01GB01</em>), <strong>tobr</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
<strong>trim</strong>: trimethoprim (<em>J01EA01</em>), <strong>trim</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>), <strong>trsu</strong>: sulfamethoxazole and trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p> <strong>vanc</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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@ -216,7 +216,7 @@
<div class="ref-description"> <div class="ref-description">
<p>A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='as.mo.html'>guess_mo</a></code>.</p> <p>A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='AMR-deprecated.html'>guess_mo</a></code>.</p>
</div> </div>

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@ -216,7 +216,7 @@
<div class="ref-description"> <div class="ref-description">
<p>A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='as.mo.html'>guess_mo</a></code>.</p> <p>A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='AMR-deprecated.html'>guess_mo</a></code>.</p>
</div> </div>

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@ -217,7 +217,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<div class="ref-description"> <div class="ref-description">
<p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p> <p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>portion_R</code> and <code>portion_IR</code> can be used to calculate resistance, <code>portion_S</code> and <code>portion_SI</code> can be used to calculate susceptibility.<br /></p> <p><code>portion_R</code> and <code>portion_IR</code> can be used to calculate resistance, <code>portion_S</code> and <code>portion_SI</code> can be used to calculate susceptibility.<br /></p>
</div> </div>
@ -333,17 +333,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>) <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>), <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span> <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</span> <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span> <span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span> <span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span> <span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
@ -358,8 +358,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>), <span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>),
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>), <span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>),
@ -368,22 +368,22 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># Get portions S/I/R immediately of all rsi columns</span> <span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span> <span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span> <span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span> <span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
<span class='no'>my_table</span> <span class='kw'>%&gt;%</span> <span class='no'>my_table</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%&gt;%</span> <span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</span>), <span class='co'># amoxicillin with metronidazole</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</span>), <span class='co'># amoxicillin with metronidazole</span>
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amox</span>, <span class='no'>metr</span>)) <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amox</span>, <span class='no'>metr</span>))
<span class='co'># }</span></pre> <span class='co'># }</span></pre>
</div> </div>

8
docs/reference/resistance_predict.html
View File

@ -311,7 +311,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># or use dplyr so you can actually read it:</span> <span class='co'># or use dplyr so you can actually read it:</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>tbl</span> <span class='kw'>%&gt;%</span> <span class='no'>tbl</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Haemophilus"</span>) <span class='kw'>%&gt;%</span> <span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Haemophilus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='no'>amcl</span>, <span class='no'>date</span>) <span class='fu'>resistance_predict</span>(<span class='no'>amcl</span>, <span class='no'>date</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span> <span class='co'># }</span><span class='co'># NOT RUN {</span>
@ -322,9 +322,9 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># get bacteria properties like genus and species</span> <span class='co'># get bacteria properties like genus and species</span>
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>(<span class='st'>"mo"</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='join.html'>left_join_microorganisms</a></span>(<span class='st'>"mo"</span>) <span class='kw'>%&gt;%</span>
<span class='co'># calculate first isolates</span> <span class='co'># calculate first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first E. coli isolates</span> <span class='co'># filter on first E. coli isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Escherichia"</span>, <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Escherichia"</span>,
<span class='no'>species</span> <span class='kw'>==</span> <span class='st'>"coli"</span>, <span class='no'>species</span> <span class='kw'>==</span> <span class='st'>"coli"</span>,
<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span> <span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
<span class='co'># predict resistance of cefotaxime for next years</span> <span class='co'># predict resistance of cefotaxime for next years</span>
@ -338,7 +338,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>require</a></span>(<span class='no'>ggplot2</span>)) { <span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>require</a></span>(<span class='no'>ggplot2</span>)) {
<span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,

6
docs/sitemap.xml
View File

@ -9,6 +9,9 @@
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/AMR.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/AMR.html</loc>
</url> </url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/ITIS.html</loc>
</url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/ab_property.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/ab_property.html</loc>
</url> </url>
@ -63,9 +66,6 @@
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/guess_ab.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/guess_ab.html</loc>
</url> </url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/itis.html</loc>
</url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/join.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/join.html</loc>
</url> </url>

4
man/itis.Rd → man/ITIS.Rd
View File

@ -1,7 +1,7 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/itis.R % Please edit documentation in R/itis.R
\name{itis} \name{ITIS}
\alias{itis} \alias{ITIS}
\title{ITIS: Integrated Taxonomic Information System} \title{ITIS: Integrated Taxonomic Information System}
\description{ \description{
All taxonomic names of all microorganisms are included in this package, using the authoritative Integrated Taxonomic Information System (ITIS). All taxonomic names of all microorganisms are included in this package, using the authoritative Integrated Taxonomic Information System (ITIS).

128
man/eucast_rules.Rd
View File

@ -17,8 +17,8 @@
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf} \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
} }
\item{ \item{
EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. \cr EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx} \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
} }
} }
} }
@ -78,68 +78,68 @@ To define antibiotics column names, leave as it is to determine it automatically
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code}) Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
\strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}), \strong{amcl}: amoxicillin+clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\strong{amik}: amikacin (\emph{J01GB06}), \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
\strong{amox}: amoxicillin (\emph{J01CA04}), \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
\strong{ampi}: ampicillin (\emph{J01CA01}), \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
\strong{azit}: azithromycin (\emph{J01FA10}), \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
\strong{azlo}: azlocillin (\emph{J01CA09}), \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
\strong{aztr}: aztreonam (\emph{J01DF01}), \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
\strong{cefa}: cefaloridine (\emph{J01DB02}), \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
\strong{cfep}: cefepime (\emph{J01DE01}), \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
\strong{cfot}: cefotaxime (\emph{J01DD01}), \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
\strong{cfox}: cefoxitin (\emph{J01DC01}), \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
\strong{cfra}: cefradine (\emph{J01DB09}), \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
\strong{cfta}: ceftazidime (\emph{J01DD02}), \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
\strong{cftr}: ceftriaxone (\emph{J01DD04}), \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
\strong{cfur}: cefuroxime (\emph{J01DC02}), \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
\strong{chlo}: chloramphenicol (\emph{J01BA01}), \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
\strong{cipr}: ciprofloxacin (\emph{J01MA02}), \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
\strong{clar}: clarithromycin (\emph{J01FA09}), \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
\strong{clin}: clindamycin (\emph{J01FF01}), \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
\strong{clox}: flucloxacillin (\emph{J01CF05}), \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{coli}: colistin (\emph{J01XB01}), \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
\strong{czol}: cefazolin (\emph{J01DB04}), \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{dapt}: daptomycin (\emph{J01XX09}), \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
\strong{doxy}: doxycycline (\emph{J01AA02}), \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
\strong{erta}: ertapenem (\emph{J01DH03}), \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
\strong{eryt}: erythromycin (\emph{J01FA01}), \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
\strong{fosf}: fosfomycin (\emph{J01XX01}), \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
\strong{fusi}: fusidic acid (\emph{J01XC01}), \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
\strong{gent}: gentamicin (\emph{J01GB03}), \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
\strong{imip}: imipenem (\emph{J01DH51}), \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
\strong{kana}: kanamycin (\emph{J01GB04}), \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
\strong{levo}: levofloxacin (\emph{J01MA12}), \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
\strong{linc}: lincomycin (\emph{J01FF02}), \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
\strong{line}: linezolid (\emph{J01XX08}), \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
\strong{mero}: meropenem (\emph{J01DH02}), \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
\strong{mezl}: mezlocillin (\emph{J01CA10}), \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
\strong{mino}: minocycline (\emph{J01AA08}), \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
\strong{moxi}: moxifloxacin (\emph{J01MA14}), \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
\strong{nali}: nalidixic acid (\emph{J01MB02}), \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
\strong{neom}: neomycin (\emph{J01GB05}), \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
\strong{neti}: netilmicin (\emph{J01GB07}), \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
\strong{nitr}: nitrofurantoin (\emph{J01XE01}), \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
\strong{norf}: norfloxacin (\emph{J01MA06}), \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}), \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
\strong{oflo}: ofloxacin (\emph{J01MA01}), \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
\strong{peni}: penicillin (\emph{J01RA01}), \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
\strong{pipe}: piperacillin (\emph{J01CA12}), \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}), \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
\strong{poly}: polymyxin B (\emph{J01XB02}), \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
\strong{pris}: pristinamycin (\emph{J01FG01}), \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
\strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}), \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
\strong{rifa}: rifampicin (\emph{J04AB02}), \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{roxi}: roxithromycin (\emph{J01FA06}), \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
\strong{siso}: sisomicin (\emph{J01GB08}), \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
\strong{teic}: teicoplanin (\emph{J01XA02}), \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
\strong{tetr}: tetracycline (\emph{J01AA07}), \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
\strong{tica}: ticarcillin (\emph{J01CA13}), \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
\strong{tige}: tigecycline (\emph{J01AA12}), \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
\strong{tobr}: tobramycin (\emph{J01GB01}), \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
\strong{trim}: trimethoprim (\emph{J01EA01}), \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
\strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}), \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
\strong{vanc}: vancomycin (\emph{J01XA01}). \strong{vanc}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
} }
\section{Read more on our website!}{ \section{Read more on our website!}{

124
man/mdro.Rd
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@ -181,68 +181,68 @@ To define antibiotics column names, leave as it is to determine it automatically
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code}) Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
\strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}), \strong{amcl}: amoxicillin+clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\strong{amik}: amikacin (\emph{J01GB06}), \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
\strong{amox}: amoxicillin (\emph{J01CA04}), \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
\strong{ampi}: ampicillin (\emph{J01CA01}), \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
\strong{azit}: azithromycin (\emph{J01FA10}), \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
\strong{azlo}: azlocillin (\emph{J01CA09}), \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
\strong{aztr}: aztreonam (\emph{J01DF01}), \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
\strong{cefa}: cefaloridine (\emph{J01DB02}), \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
\strong{cfep}: cefepime (\emph{J01DE01}), \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
\strong{cfot}: cefotaxime (\emph{J01DD01}), \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
\strong{cfox}: cefoxitin (\emph{J01DC01}), \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
\strong{cfra}: cefradine (\emph{J01DB09}), \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
\strong{cfta}: ceftazidime (\emph{J01DD02}), \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
\strong{cftr}: ceftriaxone (\emph{J01DD04}), \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
\strong{cfur}: cefuroxime (\emph{J01DC02}), \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
\strong{chlo}: chloramphenicol (\emph{J01BA01}), \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
\strong{cipr}: ciprofloxacin (\emph{J01MA02}), \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
\strong{clar}: clarithromycin (\emph{J01FA09}), \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
\strong{clin}: clindamycin (\emph{J01FF01}), \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
\strong{clox}: flucloxacillin (\emph{J01CF05}), \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{coli}: colistin (\emph{J01XB01}), \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
\strong{czol}: cefazolin (\emph{J01DB04}), \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{dapt}: daptomycin (\emph{J01XX09}), \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
\strong{doxy}: doxycycline (\emph{J01AA02}), \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
\strong{erta}: ertapenem (\emph{J01DH03}), \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
\strong{eryt}: erythromycin (\emph{J01FA01}), \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
\strong{fosf}: fosfomycin (\emph{J01XX01}), \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
\strong{fusi}: fusidic acid (\emph{J01XC01}), \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
\strong{gent}: gentamicin (\emph{J01GB03}), \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
\strong{imip}: imipenem (\emph{J01DH51}), \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
\strong{kana}: kanamycin (\emph{J01GB04}), \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
\strong{levo}: levofloxacin (\emph{J01MA12}), \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
\strong{linc}: lincomycin (\emph{J01FF02}), \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
\strong{line}: linezolid (\emph{J01XX08}), \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
\strong{mero}: meropenem (\emph{J01DH02}), \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
\strong{mezl}: mezlocillin (\emph{J01CA10}), \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
\strong{mino}: minocycline (\emph{J01AA08}), \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
\strong{moxi}: moxifloxacin (\emph{J01MA14}), \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
\strong{nali}: nalidixic acid (\emph{J01MB02}), \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
\strong{neom}: neomycin (\emph{J01GB05}), \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
\strong{neti}: netilmicin (\emph{J01GB07}), \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
\strong{nitr}: nitrofurantoin (\emph{J01XE01}), \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
\strong{norf}: norfloxacin (\emph{J01MA06}), \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}), \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
\strong{oflo}: ofloxacin (\emph{J01MA01}), \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
\strong{peni}: penicillin (\emph{J01RA01}), \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
\strong{pipe}: piperacillin (\emph{J01CA12}), \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}), \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
\strong{poly}: polymyxin B (\emph{J01XB02}), \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
\strong{pris}: pristinamycin (\emph{J01FG01}), \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
\strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}), \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
\strong{rifa}: rifampicin (\emph{J04AB02}), \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{roxi}: roxithromycin (\emph{J01FA06}), \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
\strong{siso}: sisomicin (\emph{J01GB08}), \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
\strong{teic}: teicoplanin (\emph{J01XA02}), \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
\strong{tetr}: tetracycline (\emph{J01AA07}), \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
\strong{tica}: ticarcillin (\emph{J01CA13}), \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
\strong{tige}: tigecycline (\emph{J01AA12}), \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
\strong{tobr}: tobramycin (\emph{J01GB01}), \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
\strong{trim}: trimethoprim (\emph{J01EA01}), \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
\strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}), \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
\strong{vanc}: vancomycin (\emph{J01XA01}). \strong{vanc}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
} }
\section{Read more on our website!}{ \section{Read more on our website!}{

11
pkgdown/extra.css
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@ -59,7 +59,7 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
/* syntax font */ /* syntax font */
pre, code { pre, code {
font-family: 'Courier New'; font-family: 'Courier New', monospace;
font-size: 100% !important; font-size: 100% !important;
font-weight: bold; font-weight: bold;
background-color: transparent; background-color: transparent;
@ -102,6 +102,15 @@ help {
display: none; display: none;
} }
/* Date of vignettes */
.template-article .date:before {
content: 'Last updated: ';
}
.template-article .date {
font-size: 14px;
padding-top: 40px;
}
/* more space between icon and text in top menu */ /* more space between icon and text in top menu */
#navbar .fa, #navbar .fa,
#navbar .fab, #navbar .fab,

2
pkgdown/extra.js
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@ -38,3 +38,5 @@ $( document ).ready(function() {
// Edit title of manual // Edit title of manual
$('.template-reference-index h1').text('Manual'); $('.template-reference-index h1').text('Manual');
}); });
$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR','*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");

1
vignettes/AMR.Rmd
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@ -1,6 +1,7 @@
--- ---
title: "How to conduct AMR analysis" title: "How to conduct AMR analysis"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true

3
vignettes/EUCAST.Rmd
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@ -1,6 +1,7 @@
--- ---
title: "How to apply EUCAST rules" title: "How to apply EUCAST rules"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true
@ -30,7 +31,7 @@ What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Te
> *EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.* > *EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.*
In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the `eucast_rules()` function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R. In Europe, a lot of medical microbiological laboratories already apply these rules ([Brown *et al.*, 2015](https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008)). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 9.0, 2019). Moreover, the `eucast_rules()` function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.
*(more will be available soon)* *(more will be available soon)*

3
vignettes/G_test.Rmd
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@ -1,6 +1,7 @@
--- ---
title: "How to use the *G*-test" title: "How to use the *G*-test"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true
@ -21,4 +22,4 @@ knitr::opts_chunk$set(
Sys.setlocale(locale = "C") Sys.setlocale(locale = "C")
``` ```
*(will be available soon - in the meanwhile, please read about [this *G*-test in the manual](./reference/g.test.html))* *(will be available soon - in the meanwhile, please read about [this *G*-test in the manual](./../reference/g.test.html))*

1
vignettes/Predict.Rmd
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@ -1,6 +1,7 @@
--- ---
title: "How to predict antimicrobial resistance" title: "How to predict antimicrobial resistance"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true

1
vignettes/ab_property.Rmd
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@ -1,6 +1,7 @@
--- ---
title: "How to get properties of an antibiotic" title: "How to get properties of an antibiotic"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true

1
vignettes/freq.Rmd
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@ -1,6 +1,7 @@
--- ---
title: "How to create frequency tables" title: "How to create frequency tables"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true

1
vignettes/mo_property.Rmd
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@ -1,6 +1,7 @@
--- ---
title: "How to get properties of a microorganism" title: "How to get properties of a microorganism"
author: "Matthijs S. Berends" author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true