mirror of https://github.com/msberends/AMR.git
MDRO update
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.4.0.9010
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Date: 2018-11-09
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Version: 0.4.0.9011
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Date: 2018-11-16
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -35,11 +35,7 @@ S3method(skewness,matrix)
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S3method(summary,mic)
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S3method(summary,rsi)
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export("%like%")
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export(BRMO)
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export(EUCAST_exceptional_phenotypes)
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export(EUCAST_rules)
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export(MDRO)
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export(MRGN)
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export(ab_atc)
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export(ab_certe)
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export(ab_name)
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@ -58,6 +54,7 @@ export(as.rsi)
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export(atc_ddd)
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export(atc_groups)
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export(atc_property)
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export(brmo)
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export(count_I)
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export(count_IR)
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export(count_R)
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@ -65,6 +62,8 @@ export(count_S)
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export(count_SI)
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export(count_all)
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export(count_df)
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export(eucast_exceptional_phenotypes)
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export(eucast_rules)
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export(facet_rsi)
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export(first_isolate)
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export(freq)
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@ -91,6 +90,7 @@ export(kurtosis)
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export(labels_rsi_count)
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export(left_join_microorganisms)
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export(like)
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export(mdro)
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export(mo_TSN)
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export(mo_authors)
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export(mo_class)
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@ -110,6 +110,7 @@ export(mo_subspecies)
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export(mo_taxonomy)
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export(mo_type)
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export(mo_year)
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export(mrgn)
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export(n_rsi)
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export(p.symbol)
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export(portion_I)
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10
NEWS.md
10
NEWS.md
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@ -9,14 +9,16 @@
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* Functions `mo_authors` and `mo_year` to get specific values about the scientific reference of a taxonomic entry
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#### Changed
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* Big changes to the `EUCAST_rules` function:
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* Functions `MDRO`, `BRMO`, `MRGN` and `EUCAST_exceptional_phenotypes` were renamed to `mdro`, `brmo`, `mrgn` and `eucast_exceptional_phenotypes`
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* `EUCAST_rules` was renamed to `eucast_rules`, the old function still exists as a deprecated function
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* Big changes to the `eucast_rules` function:
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* Now also applies rules from the EUCAST 'Breakpoint tables for bacteria', version 8.1, 2018, http://www.eucast.org/clinical_breakpoints/ (see Source of the function)
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* New parameter `rules` to specify which rules should be applied (expert rules, breakpoints, others or all)
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* New parameter `verbose` which can be set to `TRUE` to get very specific messages about which columns and rows were affected
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* Better error handling when rules cannot be applied (i.e. new values could not be inserted)
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* The number of affected values will now only be measured once per row/column combination
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* Data set `septic_patients` now reflects these changes
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* Added parameter `pipe` for piperacillin (J01CA12), also to the `MDRO` function
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* Added parameter `pipe` for piperacillin (J01CA12), also to the `mdro` function
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* Small fixes to EUCAST clinical breakpoint rules
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* Added column `kingdom` to the microorganisms data set, and function `mo_kingdom` to look up values
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* Tremendous speed improvement for `as.mo` (and subsequently all `mo_*` functions), as empty values wil be ignored *a priori*
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@ -41,11 +43,11 @@
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* New parameter `header` to turn it off (default when `markdown = TRUE`)
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* New parameter `title` to replace the automatically set title
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* `first_isolate` now tries to find columns to use as input when parameters are left blank
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* Improvement for MDRO algorithm
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* Improvement for MDRO algorithm (function `mdro`)
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* Data set `septic_patients` is now a `data.frame`, not a tibble anymore
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* Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters
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* Fix for `mo_property` not working properly
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* Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
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* Fix for `eucast_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
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* Support for named vectors of class `mo`, useful for `top_freq()`
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* `ggplot_rsi` and `scale_y_percent` have `breaks` parameter
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* AI improvements for `as.mo`:
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@ -25,7 +25,7 @@
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#' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected
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#' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Details
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#' @param col_bactid deprecated, use \code{col_mo} instead.
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#' @param ... parameters that are passed on to \code{EUCAST_rules}
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#' @param ... parameters that are passed on to \code{eucast_rules}
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#' @inheritParams first_isolate
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#' @details To define antibiotics column names, input a text or use \code{NA} to skip a column (e.g. \code{tica = NA}). Non-existing columns will anyway be skipped with a warning. See the Antibiotics section for an explanation of the abbreviations.
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#' @section Antibiotics:
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@ -94,7 +94,7 @@
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#' \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
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#' \strong{vanc}: vancomycin (\emph{J01XA01}).
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#' @keywords interpretive eucast reading resistance
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#' @rdname EUCAST
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#' @rdname eucast_rules
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#' @export
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#' @importFrom dplyr %>% select pull mutate_at vars
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#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style
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@ -116,7 +116,7 @@
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#' }
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#' }
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#' @examples
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#' a <- EUCAST_rules(septic_patients)
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#' a <- eucast_rules(septic_patients)
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#'
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#' a <- data.frame(mo = c("Staphylococcus aureus",
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#' "Enterococcus faecalis",
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@ -140,7 +140,7 @@
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#' # 4 Klebsiella pneumoniae - - - - - S S
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#' # 5 Pseudomonas aeruginosa - - - - - S S
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#'
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#' b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
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#' b <- eucast_rules(a, "mo") # 18 results are forced as R or S
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#'
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#' b
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#' # mo vanc amox coli cfta cfur peni cfox
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@ -149,7 +149,7 @@
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#' # 3 Escherichia coli R - - - - R S
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#' # 4 Klebsiella pneumoniae R R - - - R S
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#' # 5 Pseudomonas aeruginosa R R - - R R R
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EUCAST_rules <- function(tbl,
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eucast_rules <- function(tbl,
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col_mo = NULL,
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info = TRUE,
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rules = c("breakpoints", "expert", "other", "all"),
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@ -1745,8 +1745,16 @@ EUCAST_rules <- function(tbl,
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tbl_original
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}
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#' @rdname EUCAST
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#' @rdname eucast_rules
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#' @export
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EUCAST_rules <- function(...) {
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.Deprecated("eucast_rules")
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eucast_rules(...)
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}
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#' @rdname eucast_rules
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#' @export
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interpretive_reading <- function(...) {
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EUCAST_rules(...)
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.Deprecated("eucast_rules")
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eucast_rules(...)
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}
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253
R/mdro.R
253
R/mdro.R
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@ -22,13 +22,13 @@
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#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @param country country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).
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#' @param info print progress
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#' @inheritParams EUCAST_rules
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#' @inheritParams eucast_rules
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#' @param metr column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.
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#' @param ... parameters that are passed on to methods
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#' @inheritSection EUCAST_rules Antibiotics
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#' @inheritSection eucast_rules Antibiotics
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#' @details When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
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#' @return Ordered factor with levels \code{Unknown < Negative < Unconfirmed < Positive}.
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#' @rdname MDRO
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#' @return Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
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#' @rdname mdro
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#' @importFrom dplyr %>%
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#' @importFrom crayon red blue
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#' @export
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@ -36,9 +36,9 @@
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#' library(dplyr)
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#'
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#' septic_patients %>%
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#' mutate(EUCAST = MDRO(.),
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#' BRMO = BRMO(.))
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MDRO <- function(tbl,
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#' mutate(EUCAST = mdro(.),
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#' BRMO = brmo(.))
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mdro <- function(tbl,
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country = NULL,
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col_mo = NULL,
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info = TRUE,
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@ -129,8 +129,8 @@ MDRO <- function(tbl,
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country <- 'EUCAST'
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}
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country <- trimws(country)
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if (country != 'EUCAST' & !country %like% '^[a-z]{2}$') {
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stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?MDRO.', call. = FALSE)
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if (tolower(country) != 'eucast' & !country %like% '^[a-z]{2}$') {
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stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?mdro.', call. = FALSE)
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}
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# create list and make country code case-independent
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@ -152,9 +152,9 @@ MDRO <- function(tbl,
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guideline$name <- 'WIP-Richtlijn BRMO'
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guideline$version <- 'Revision of December 2017'
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guideline$source <- 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'
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# add here more countries like this:
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# } else if (country$code == 'xx') {
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# country$name <- 'country name'
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# add here more countries like this:
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# } else if (country$code == 'xx') {
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# country$name <- 'country name'
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} else {
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stop('This country code is currently unsupported: ', guideline$country$code, call. = FALSE)
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}
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@ -243,10 +243,17 @@ MDRO <- function(tbl,
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fluoroquinolones <- c(oflo, cipr, levo, moxi)
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# helper function for editing the table
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trans_tbl <- function(to, rows, cols) {
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trans_tbl <- function(to, rows, cols, any_all) {
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 & length(cols) > 0) {
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col_filter <- which(tbl[, cols] == 'R')
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if (any_all == "any") {
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col_filter <- which(tbl[, cols] == 'R')
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} else if (any_all == "all") {
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col_filter <- tbl %>%
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mutate(index = 1:nrow(.)) %>%
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filter_at(vars(cols), all_vars(. == "R")) %>%
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pull((index))
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}
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rows <- rows[rows %in% col_filter]
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tbl[rows, 'MDRO'] <<- to
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}
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@ -265,52 +272,66 @@ MDRO <- function(tbl,
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if (guideline$country$code == 'eucast') {
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# EUCAST ------------------------------------------------------------------
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# Table 5
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trans_tbl(4,
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trans_tbl(3,
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which(tbl$family == 'Enterobacteriaceae'
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| tbl$fullname %like% '^Pseudomonas aeruginosa'
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| tbl$genus == 'Acinetobacter'),
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coli)
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trans_tbl(4,
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coli,
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"all")
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trans_tbl(3,
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which(tbl$fullname %like% '^Salmonella Typhi'),
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c(carbapenems, fluoroquinolones))
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trans_tbl(4,
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c(carbapenems, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl$fullname %like% '^Haemophilus influenzae'),
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c(cephalosporins_3rd, carbapenems, fluoroquinolones))
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trans_tbl(4,
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c(cephalosporins_3rd, carbapenems, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl$fullname %like% '^Moraxella catarrhalis'),
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c(cephalosporins_3rd, fluoroquinolones))
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trans_tbl(4,
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl$fullname %like% '^Neisseria meningitidis'),
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c(cephalosporins_3rd, fluoroquinolones))
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trans_tbl(4,
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(tbl$fullname %like% '^Neisseria gonorrhoeae'),
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azit)
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azit,
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"any")
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# Table 6
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trans_tbl(4,
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trans_tbl(3,
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which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
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c(vanc, teic, dapt, line, qida, tige))
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trans_tbl(4,
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c(vanc, teic, dapt, line, qida, tige),
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"any")
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trans_tbl(3,
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which(tbl$genus == 'Corynebacterium'),
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c(vanc, teic, dapt, line, qida, tige))
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trans_tbl(4,
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c(vanc, teic, dapt, line, qida, tige),
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"any")
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trans_tbl(3,
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which(tbl$fullname %like% '^Streptococcus pneumoniae'),
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c(carbapenems, vanc, teic, dapt, line, qida, tige, rifa))
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trans_tbl(4, # Sr. groups A/B/C/G
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c(carbapenems, vanc, teic, dapt, line, qida, tige, rifa),
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"any")
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trans_tbl(3, # Sr. groups A/B/C/G
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which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)'),
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c(peni, cephalosporins, vanc, teic, dapt, line, qida, tige))
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trans_tbl(4,
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c(peni, cephalosporins, vanc, teic, dapt, line, qida, tige),
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"any")
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trans_tbl(3,
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which(tbl$genus == 'Enterococcus'),
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c(dapt, line, tige, teic))
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trans_tbl(4,
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c(dapt, line, tige, teic),
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"any")
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trans_tbl(3,
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which(tbl$fullname %like% '^Enterococcus faecalis'),
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c(ampi, amox))
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c(ampi, amox),
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"any")
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# Table 7
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trans_tbl(4,
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trans_tbl(3,
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which(tbl$genus == 'Bacteroides'),
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metr)
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trans_tbl(4,
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metr,
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"any")
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trans_tbl(3,
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which(tbl$fullname %like% '^Clostridium difficile'),
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c(metr, vanc))
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c(metr, vanc),
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"any")
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}
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if (guideline$country$code == 'de') {
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@ -325,112 +346,88 @@ MDRO <- function(tbl,
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carbapenems <- carbapenems[!is.na(carbapenems)]
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# Table 1
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tbl[which(
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tbl$family == 'Enterobacteriaceae'
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& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
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& rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
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), 'MDRO'] <- 4
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tbl[which(
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tbl$family == 'Enterobacteriaceae'
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& rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
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), 'MDRO'] <- 3
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# rest is negative
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tbl[which(
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tbl$family == 'Enterobacteriaceae'
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& tbl$MDRO == 1
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), 'MDRO'] <- 2
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trans_tbl(3,
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which(tbl$family == 'Enterobacteriaceae'),
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c(aminoglycosides, fluoroquinolones),
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"all")
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trans_tbl(2,
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which(tbl$family == 'Enterobacteriaceae'),
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c(carbapenems),
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"any")
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# Table 2
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tbl[which(
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tbl$genus == 'Acinetobacter'
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& rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
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), 'MDRO'] <- 3
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tbl[which(
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tbl$genus == 'Acinetobacter'
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& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
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& rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
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), 'MDRO'] <- 4
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# rest of Acinetobacter is negative
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tbl[which(
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tbl$genus == 'Acinetobacter'
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& tbl$MDRO == 1
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), 'MDRO'] <- 2
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trans_tbl(2,
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which(tbl$genus == 'Acinetobacter'),
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c(carbapenems),
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"any")
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trans_tbl(3,
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which(tbl$genus == 'Acinetobacter'),
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c(aminoglycosides, fluoroquinolones),
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"all")
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tbl[which(
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tbl$fullname %like% 'Stenotrophomonas maltophilia'
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& tbl[, trsu] == 'R'
|
||||
), 'MDRO'] <- 4
|
||||
# rest of Stenotrophomonas is negative
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Stenotrophomonas maltophilia'
|
||||
& tbl$MDRO == 1
|
||||
), 'MDRO'] <- 2
|
||||
trans_tbl(3,
|
||||
which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
|
||||
trsu,
|
||||
"all")
|
||||
|
||||
tbl <- tbl %>% mutate(
|
||||
psae = 0,
|
||||
psae = ifelse(mero == "R" | imip == "R", psae + 1, psae),
|
||||
psae = ifelse(gent == "R" & tobr == "R", psae + 1, psae),
|
||||
psae = ifelse(cipr == "R", psae + 1, psae),
|
||||
psae = ifelse(cfta == "R", psae + 1, psae),
|
||||
psae = ifelse(pita == "R", psae + 1, psae),
|
||||
psae = ifelse(is.na(psae), 0, psae)
|
||||
)
|
||||
if (!is.na(mero) & !is.na(imip)
|
||||
& !is.na(gent) & !is.na(tobr)
|
||||
& !is.na(cipr)
|
||||
& !is.na(cfta)
|
||||
& !is.na(pita) ) {
|
||||
tbl <- tbl %>% mutate(
|
||||
psae = 0,
|
||||
psae = ifelse(mero == "R" | imip == "R", psae + 1, psae),
|
||||
psae = ifelse(gent == "R" & tobr == "R", psae + 1, psae),
|
||||
psae = ifelse(cipr == "R", psae + 1, psae),
|
||||
psae = ifelse(cfta == "R", psae + 1, psae),
|
||||
psae = ifelse(pita == "R", psae + 1, psae),
|
||||
psae = ifelse(is.na(psae), 0, psae)
|
||||
)
|
||||
} else {
|
||||
tbl$psae <- 0
|
||||
}
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Pseudomonas aeruginosa'
|
||||
& tbl$psae >= 3
|
||||
), 'MDRO'] <- 4
|
||||
# rest of Pseudomonas is negative
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Pseudomonas aeruginosa'
|
||||
& tbl$MDRO == 1
|
||||
), 'MDRO'] <- 2
|
||||
), 'MDRO'] <- 3
|
||||
|
||||
# Table 3
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Streptococcus pneumoniae'
|
||||
& tbl[, peni] == 'R'
|
||||
), 'MDRO'] <- 4
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Streptococcus pneumoniae'
|
||||
& tbl[, vanc] == 'R'
|
||||
), 'MDRO'] <- 4
|
||||
# rest of Streptococcus pneumoniae is negative
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Streptococcus pneumoniae'
|
||||
& tbl$MDRO == 1
|
||||
), 'MDRO'] <- 2
|
||||
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Enterococcus faecium'
|
||||
& rowSums(tbl[, c(peni, vanc)] == 'R', na.rm = TRUE) >= 1
|
||||
), 'MDRO'] <- 4
|
||||
# rest of Enterococcus faecium is negative
|
||||
tbl[which(
|
||||
tbl$fullname %like% 'Enterococcus faecium'
|
||||
& tbl$MDRO == 1
|
||||
), 'MDRO'] <- 2
|
||||
trans_tbl(3,
|
||||
which(tbl$fullname %like% 'Streptococcus pneumoniae'),
|
||||
peni,
|
||||
"all")
|
||||
trans_tbl(3,
|
||||
which(tbl$fullname %like% 'Streptococcus pneumoniae'),
|
||||
vanc,
|
||||
"all")
|
||||
trans_tbl(3,
|
||||
which(tbl$fullname %like% 'Enterococcus faecium'),
|
||||
c(peni, vanc),
|
||||
"all")
|
||||
}
|
||||
|
||||
factor(x = tbl$MDRO,
|
||||
levels = c(1:4),
|
||||
labels = c('Not evaluated', 'Negative', 'Unconfirmed', 'Positive'),
|
||||
levels = 1:3,
|
||||
labels = c('Negative', 'Positive, unconfirmed', 'Positive'),
|
||||
ordered = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname MDRO
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
BRMO <- function(tbl, country = "nl", ...) {
|
||||
MDRO(tbl = tbl, country = "nl", ...)
|
||||
brmo <- function(..., country = "nl") {
|
||||
mdro(..., country = "nl")
|
||||
}
|
||||
|
||||
#' @rdname MDRO
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
MRGN <- function(tbl, country = "de", ...) {
|
||||
MDRO(tbl = tbl, country = "de", ...)
|
||||
mrgn <- function(tbl, country = "de", ...) {
|
||||
mdro(tbl = tbl, country = "de", ...)
|
||||
}
|
||||
|
||||
#' @rdname MDRO
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
EUCAST_exceptional_phenotypes <- function(tbl, country = "EUCAST", ...) {
|
||||
MDRO(tbl = tbl, country = "EUCAST", ...)
|
||||
eucast_exceptional_phenotypes <- function(tbl, country = "EUCAST", ...) {
|
||||
mdro(tbl = tbl, country = "EUCAST", ...)
|
||||
}
|
||||
|
|
|
|||
13
R/read.4d.R
13
R/read.4d.R
|
|
@ -110,7 +110,7 @@ read.4D <- function(file,
|
|||
|
||||
# backup original column names
|
||||
colnames.bak <- toupper(colnames(data_4D))
|
||||
colnames.bak[colnames.bak == "AGE"] <- NULL
|
||||
colnames.bak[colnames.bak == "AGE"] <- NA_character_
|
||||
|
||||
# rename of columns
|
||||
colnames(data_4D) <- gsub("patientnr", "patient_id", colnames(data_4D), fixed = TRUE)
|
||||
|
|
@ -162,9 +162,18 @@ read.4D <- function(file,
|
|||
message("OK\nSetting original column names as label... ", appendLF = FALSE)
|
||||
}
|
||||
for (i in 1:ncol(data_4D)) {
|
||||
attr(data_4D[, i], "label") <- colnames.bak[i]
|
||||
if (!is.na(colnames.bak[i])) {
|
||||
attr(data_4D[, i], "label") <- colnames.bak[i]
|
||||
}
|
||||
}
|
||||
|
||||
if (info == TRUE) {
|
||||
message("OK\nSetting query as label to data.frame... ", appendLF = FALSE)
|
||||
}
|
||||
qry <- readLines(con <- file(file, open="r"))[1]
|
||||
close(con)
|
||||
attr(data_4D, "label") <- qry
|
||||
|
||||
if (info == TRUE) {
|
||||
message("OK")
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/eucast.R
|
||||
\name{EUCAST_rules}
|
||||
% Please edit documentation in R/eucast_rules.R
|
||||
\name{eucast_rules}
|
||||
\alias{eucast_rules}
|
||||
\alias{EUCAST_rules}
|
||||
\alias{interpretive_reading}
|
||||
\title{EUCAST rules}
|
||||
|
|
@ -22,7 +23,7 @@
|
|||
}
|
||||
}
|
||||
\usage{
|
||||
EUCAST_rules(tbl, col_mo = NULL, info = TRUE,
|
||||
eucast_rules(tbl, col_mo = NULL, info = TRUE,
|
||||
rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
|
||||
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
|
||||
azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa",
|
||||
|
|
@ -41,6 +42,8 @@ EUCAST_rules(tbl, col_mo = NULL, info = TRUE,
|
|||
tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
|
||||
trim = "trim", trsu = "trsu", vanc = "vanc", col_bactid = NULL)
|
||||
|
||||
EUCAST_rules(...)
|
||||
|
||||
interpretive_reading(...)
|
||||
}
|
||||
\arguments{
|
||||
|
|
@ -58,7 +61,7 @@ interpretive_reading(...)
|
|||
|
||||
\item{col_bactid}{deprecated, use \code{col_mo} instead.}
|
||||
|
||||
\item{...}{parameters that are passed on to \code{EUCAST_rules}}
|
||||
\item{...}{parameters that are passed on to \code{eucast_rules}}
|
||||
}
|
||||
\value{
|
||||
The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
|
||||
|
|
@ -138,7 +141,7 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
|
|||
}
|
||||
|
||||
\examples{
|
||||
a <- EUCAST_rules(septic_patients)
|
||||
a <- eucast_rules(septic_patients)
|
||||
|
||||
a <- data.frame(mo = c("Staphylococcus aureus",
|
||||
"Enterococcus faecalis",
|
||||
|
|
@ -162,7 +165,7 @@ a
|
|||
# 4 Klebsiella pneumoniae - - - - - S S
|
||||
# 5 Pseudomonas aeruginosa - - - - - S S
|
||||
|
||||
b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
|
||||
b <- eucast_rules(a, "mo") # 18 results are forced as R or S
|
||||
|
||||
b
|
||||
# mo vanc amox coli cfta cfur peni cfox
|
||||
|
|
@ -1,13 +1,13 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/mdro.R
|
||||
\name{MDRO}
|
||||
\alias{MDRO}
|
||||
\alias{BRMO}
|
||||
\alias{MRGN}
|
||||
\alias{EUCAST_exceptional_phenotypes}
|
||||
\name{mdro}
|
||||
\alias{mdro}
|
||||
\alias{brmo}
|
||||
\alias{mrgn}
|
||||
\alias{eucast_exceptional_phenotypes}
|
||||
\title{Determine multidrug-resistant organisms (MDRO)}
|
||||
\usage{
|
||||
MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
|
||||
mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
|
||||
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
|
||||
azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
|
||||
cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
|
||||
|
|
@ -25,11 +25,11 @@ MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
|
|||
tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc",
|
||||
col_bactid = NULL)
|
||||
|
||||
BRMO(tbl, country = "nl", ...)
|
||||
brmo(..., country = "nl")
|
||||
|
||||
MRGN(tbl, country = "de", ...)
|
||||
mrgn(tbl, country = "de", ...)
|
||||
|
||||
EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
|
||||
eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
|
||||
|
|
@ -165,7 +165,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
|
|||
\item{...}{parameters that are passed on to methods}
|
||||
}
|
||||
\value{
|
||||
Ordered factor with levels \code{Unknown < Negative < Unconfirmed < Positive}.
|
||||
Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
|
||||
}
|
||||
\description{
|
||||
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
|
||||
|
|
@ -245,6 +245,6 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
|
|||
library(dplyr)
|
||||
|
||||
septic_patients \%>\%
|
||||
mutate(EUCAST = MDRO(.),
|
||||
BRMO = BRMO(.))
|
||||
mutate(EUCAST = mdro(.),
|
||||
BRMO = brmo(.))
|
||||
}
|
||||
|
|
@ -1,11 +1,11 @@
|
|||
context("eucast.R")
|
||||
context("eucast_rules.R")
|
||||
|
||||
test_that("EUCAST rules work", {
|
||||
|
||||
expect_error(suppressWarnings(EUCAST_rules(septic_patients, col_mo = "Non-existing")))
|
||||
expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
|
||||
|
||||
expect_identical(colnames(septic_patients),
|
||||
colnames(suppressWarnings(EUCAST_rules(septic_patients))))
|
||||
colnames(suppressWarnings(eucast_rules(septic_patients))))
|
||||
|
||||
a <- data.frame(mo = c("KLEPNE", # Klebsiella pneumoniae
|
||||
"PSEAER", # Pseudomonas aeruginosa
|
||||
|
|
@ -17,7 +17,8 @@ test_that("EUCAST rules work", {
|
|||
"ENTAER"), # Enterobacter aerogenes
|
||||
amox = "R", # Amoxicillin
|
||||
stringsAsFactors = FALSE)
|
||||
expect_identical(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
|
||||
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
|
||||
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
|
||||
expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
|
||||
|
||||
a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
|
||||
|
|
@ -28,7 +29,7 @@ test_that("EUCAST rules work", {
|
|||
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
|
||||
coli = "R", # Colistin
|
||||
stringsAsFactors = FALSE)
|
||||
expect_equal(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
|
||||
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
|
||||
|
||||
# piperacillin must be R in Enterobacteriaceae when tica is R
|
||||
library(dplyr)
|
||||
|
|
@ -36,7 +37,7 @@ test_that("EUCAST rules work", {
|
|||
septic_patients %>%
|
||||
mutate(tica = as.rsi("R"),
|
||||
pipe = as.rsi("S")) %>%
|
||||
EUCAST_rules(col_mo = "mo") %>%
|
||||
eucast_rules(col_mo = "mo") %>%
|
||||
left_join_microorganisms() %>%
|
||||
filter(family == "Enterobacteriaceae") %>%
|
||||
pull(pipe) %>%
|
||||
|
|
@ -51,12 +52,12 @@ test_that("EUCAST rules work", {
|
|||
eryt,
|
||||
azit = as.rsi("R"),
|
||||
clar = as.rsi("R")) %>%
|
||||
EUCAST_rules(col_mo = "mo") %>%
|
||||
eucast_rules(col_mo = "mo") %>%
|
||||
pull(clar))
|
||||
b <- suppressWarnings(
|
||||
septic_patients %>%
|
||||
select(mo, eryt) %>%
|
||||
EUCAST_rules(col_mo = "mo") %>%
|
||||
eucast_rules(col_mo = "mo") %>%
|
||||
pull(eryt))
|
||||
|
||||
expect_identical(a[!is.na(b)],
|
||||
|
|
@ -64,7 +65,7 @@ test_that("EUCAST rules work", {
|
|||
|
||||
# amox is inferred by benzylpenicillin in Kingella kingae
|
||||
expect_equal(
|
||||
as.list(EUCAST_rules(
|
||||
as.list(eucast_rules(
|
||||
data.frame(mo = as.mo("Kingella kingae"),
|
||||
peni = "S",
|
||||
amox = "-",
|
||||
|
|
@ -72,6 +73,6 @@ test_that("EUCAST rules work", {
|
|||
, info = FALSE))$amox,
|
||||
"S")
|
||||
|
||||
expect_output(suppressWarnings(EUCAST_rules(septic_patients, verbose = TRUE)))
|
||||
expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))
|
||||
|
||||
})
|
||||
|
|
@ -1,30 +1,30 @@
|
|||
context("mdro.R")
|
||||
|
||||
|
||||
test_that("MDRO works", {
|
||||
test_that("mdro works", {
|
||||
library(dplyr)
|
||||
|
||||
expect_error(suppressWarnings(MDRO(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
|
||||
expect_error(suppressWarnings(MDRO(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
|
||||
expect_error(suppressWarnings(MDRO(septic_patients, country = c("de", "nl"), info = TRUE)))
|
||||
expect_error(suppressWarnings(MDRO(septic_patients, col_mo = "invalid", info = TRUE)))
|
||||
expect_error(suppressWarnings(mdro(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
|
||||
expect_error(suppressWarnings(mdro(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
|
||||
expect_error(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
|
||||
expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
|
||||
|
||||
outcome <- suppressWarnings(MDRO(septic_patients))
|
||||
outcome <- suppressWarnings(EUCAST_exceptional_phenotypes(septic_patients, info = TRUE))
|
||||
outcome <- suppressWarnings(mdro(septic_patients))
|
||||
outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
|
||||
# check class
|
||||
expect_equal(outcome %>% class(), c('ordered', 'factor'))
|
||||
|
||||
outcome <- suppressWarnings(MDRO(septic_patients, "nl", info = TRUE))
|
||||
outcome <- suppressWarnings(mdro(septic_patients, "nl", info = TRUE))
|
||||
# check class
|
||||
expect_equal(outcome %>% class(), c('ordered', 'factor'))
|
||||
|
||||
# septic_patients should have these finding using Dutch guidelines
|
||||
expect_equal(outcome %>% freq() %>% pull(count),
|
||||
c(1167, 817, 14, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
|
||||
c(19989, 9, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
|
||||
|
||||
expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))
|
||||
expect_equal(brmo(septic_patients, info = FALSE), mdro(septic_patients, "nl", info = FALSE))
|
||||
|
||||
# still working on German guidelines
|
||||
expect_error(suppressWarnings(MRGN(septic_patients, info = TRUE)))
|
||||
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
|
||||
|
||||
})
|
||||
|
|
|
|||
Loading…
Reference in New Issue