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(v0.7.1.9032) eucast_rules() improvements

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dr. M.S. (Matthijs) Berends 2019-08-09 14:28:46 +02:00
parent 1ce4b72dd2
commit 6a349bf757
33 changed files with 275 additions and 192 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9031
Date: 2019-08-08
Version: 0.7.1.9032
Date: 2019-08-09
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

12
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9031
# AMR 0.7.1.9032
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -36,8 +36,12 @@
Since this is a major change, usage of the old `also_single_tested` will throw an informative error that it has been replaced by `only_all_tested`.
### Changed
* Added more informative errors and warnings to `eucast_rules()`
* Fixed a bug in `eucast_rules()` for *Yersinia pseudotuberculosis*
* Function: `eucast_rules()`
* Fixed a bug for *Yersinia pseudotuberculosis*
* Added more informative errors and warnings
* Printed info now distinguishes between added and changes values
* Using Verbose mode (i.e. `eucast_rules(..., verbose = TRUE)`) returns more informative and readable output
* Using factors as input now adds missing factors levels when the function changes antibiotic results
* Added tibble printing support for classes `rsi`, `mic`, `ab` and `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red:
```r
(run this on your own console, as this page does not support colour printing)
@ -61,9 +65,7 @@
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* The `name` of `RIF` is now Rifampicin instead of Rifampin
* The `antibiotics` data set is now sorted by name
* Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output
* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
* Using factors as input for `eucast_rules()` now adds missing factors levels when the function changes antibiotic results
#### Other
* Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors

116
R/eucast_rules.R
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@ -29,7 +29,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' @param x data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
#' @param info print progress
#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
#' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a \code{data.frame} with extensive info about which rows and columns would be effected and in which way.
#' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.
#' @param ... column name of an antibiotic, see section Antibiotics
#' @inheritParams first_isolate
#' @details
@ -41,7 +41,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' @section Antibiotics:
#' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
#'
#' The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
#' The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
#'
#' \strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
#' \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
@ -175,9 +175,11 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' # 5 Pseudomonas aeruginosa R R - - R R R
#'
#'
#' \donttest{
#' # do not apply EUCAST rules, but rather get a data.frame
#' # with 18 rows, containing all details about the transformations:
#' c <- eucast_rules(a, verbose = TRUE)
#' }
eucast_rules <- function(x,
col_mo = NULL,
info = TRUE,
@ -186,7 +188,7 @@ eucast_rules <- function(x,
...) {
if (verbose == TRUE & interactive()) {
txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form: with extensive info about which rows and columns would be effected and in which way.",
txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
"\n\nThis may overwrite your existing data if you use e.g.:",
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
if ("rstudioapi" %in% rownames(installed.packages())) {
@ -230,16 +232,35 @@ eucast_rules <- function(x,
txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n\n") }
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING "))) }; warned <<- TRUE }
txt_ok <- function(no_of_changes) {
txt_ok <- function(no_added, no_changed) {
if (warned == FALSE) {
if (no_of_changes > 0) {
if (no_of_changes == 1) {
cat(blue(" (1 value changed)\n"))
if (no_added + no_changed == 0) {
cat(green(" (no changes)\n"))
} else {
cat(blue(paste0(" (", formatnr(no_of_changes), " values changed)\n")))
# opening
cat(blue(" ("))
# additions
if (no_added > 0) {
if (no_added == 1) {
cat(blue("1 value added"))
} else {
cat(blue(formatnr(no_added), "values added"))
}
}
# separator
if (no_added > 0 & no_changed > 0) {
cat(blue(", "))
}
# changes
if (no_changed > 0) {
if (no_changed == 1) {
cat(blue("1 value changed"))
} else {
cat(green(" (no values changed)\n"))
cat(blue(formatnr(no_changed), "values changed"))
}
}
# closing
cat(blue(")\n"))
}
warned <<- FALSE
}
@ -384,8 +405,8 @@ eucast_rules <- function(x,
verbose_info <- data.frame(row = integer(0),
col = character(0),
mo_fullname = character(0),
old = character(0),
new = character(0),
old = as.rsi(character(0)),
new = as.rsi(character(0)),
rule = character(0),
rule_group = character(0),
rule_name = character(0),
@ -420,7 +441,7 @@ eucast_rules <- function(x,
ifelse(length(rows) > 10, "...", ""),
' while writing value "', to,
'" to column(s) `', paste(cols, collapse = "`, `"),
"` (data class: ", paste(class(x_original), collapse = "/"), "):\n", e$message),
"`:\n", e$message),
call. = FALSE)
}
)
@ -428,22 +449,23 @@ eucast_rules <- function(x,
tryCatch(
x[rows, cols] <<- x_original[rows, cols],
error = function(e) {
stop(paste0("Error in row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
'... while writing value "', to,
'" to column(s) `', paste(cols, collapse = "`, `"),
"` (data class:", paste(class(x), collapse = "/"), "):\n", e$message), call. = FALSE)
"`:\n", e$message), call. = FALSE)
}
)
# before_df might not be a data.frame, but a tibble or data.table instead
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,]
no_of_changes_this_run <- 0
track_changes <- list(added = 0,
changed = 0)
for (i in 1:length(cols)) {
verbose_new <- data.frame(row = rows,
col = cols[i],
mo_fullname = x[rows, "fullname"],
old = as.character(old[, cols[i]]),
new = as.character(x[rows, cols[i]]),
old = as.rsi(as.character(old[, cols[i]]), warn = FALSE),
new = as.rsi(as.character(x[rows, cols[i]])),
rule = strip_style(rule[1]),
rule_group = strip_style(rule[2]),
rule_name = strip_style(rule[3]),
@ -452,13 +474,16 @@ eucast_rules <- function(x,
verbose_new <- verbose_new %>% filter(old != new | is.na(old))
# save changes to data set 'verbose_info'
verbose_info <<- rbind(verbose_info, verbose_new)
no_of_changes_this_run <- no_of_changes_this_run + nrow(verbose_new)
# count adds and changes
track_changes$added <- track_changes$added + verbose_new %>% filter(is.na(old)) %>% nrow()
track_changes$changed <- track_changes$changed + verbose_new %>% filter(!is.na(old)) %>% nrow()
}
# after the applied changes: return number of (new) changes
return(no_of_changes_this_run)
# after the applied changes: return list with counts of added and changed
return(track_changes)
}
# no changes were applied: return number of (new) changes: none.
return(0)
return(list(added = 0,
changed = 0))
}
# save original table
@ -538,9 +563,38 @@ eucast_rules <- function(x,
sort() %>%
paste(collapse = ", ")
}
format_antibiotic_names <- function(ab_names, ab_results) {
ab_names <- trimws(unlist(strsplit(ab_names, ",")))
ab_results <- trimws(unlist(strsplit(ab_results, ",")))
if (length(ab_results) == 1) {
if (length(ab_names) == 1) {
# like FOX S
x <- paste(ab_names, "is")
} else if (length(ab_names) == 2) {
# like PEN,FOX S
x <- paste(paste0(ab_names, collapse = " and "), "are both")
} else {
# like PEN,FOX,GEN S (although dependency on > 2 ABx does not exist at the moment)
x <- paste(paste0(ab_names, collapse = " and "), "are all")
}
return(paste0(x, " '", ab_results, "'"))
} else {
if (length(ab_names) == 2) {
# like PEN,FOX S,R
paste0(ab_names[1], " is '", ab_results[1], "' and ",
ab_names[2], " is '", ab_results[2], "'")
} else {
# like PEN,FOX,GEN S,R,R (although dependency on > 2 ABx does not exist at the moment)
paste0(ab_names[1], " is '", ab_results[1], "' and ",
ab_names[2], " is '", ab_results[2], "' and ",
ab_names[3], " is '", ab_results[3], "'")
}
}
}
eucast_rules_df <- eucast_rules_file # internal data file
no_of_changes <- 0
no_added <- 0
no_changed <- 0
for (i in 1:nrow(eucast_rules_df)) {
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule"]
@ -553,7 +607,8 @@ eucast_rules <- function(x,
rule_text <- paste0("always report as '", eucast_rules_df[i, 7], "': ", get_antibiotic_names(eucast_rules_df[i, 6]))
} else {
rule_text <- paste0("report as '", eucast_rules_df[i, 7], "' when ",
get_antibiotic_names(eucast_rules_df[i, 4]), " is '", eucast_rules_df[i, 5], "': ",
format_antibiotic_names(ab_names = get_antibiotic_names(eucast_rules_df[i, 4]),
ab_results = eucast_rules_df[i, 5]), ": ",
get_antibiotic_names(eucast_rules_df[i, 6]))
}
if (i == 1) {
@ -687,16 +742,20 @@ eucast_rules <- function(x,
# Apply rule on data ------------------------------------------------------
# this will return the unique number of changes
no_of_changes <- no_of_changes + edit_rsi(to = target_value,
run_changes <- edit_rsi(to = target_value,
rule = c(rule_text, rule_group_current, rule_current),
rows = rows,
cols = cols)
no_added <- no_added + run_changes$added
no_changed <- no_changed + run_changes$changed
# Print number of new changes ---------------------------------------------
if (info == TRUE & rule_next != rule_current) {
# print only on last one of rules in this group
txt_ok(no_of_changes = no_of_changes)
no_of_changes <- 0
txt_ok(no_added = no_added, no_changed = no_changed)
# and reset counters
no_added <- 0
no_changed <- 0
}
}
@ -734,8 +793,6 @@ eucast_rules <- function(x,
if (n_added > 0) {
verbose_info %>%
filter(is.na(old)) %>%
# sort it well: S < I < R
mutate(new = as.rsi(new)) %>%
group_by(new) %>%
summarise(n = n()) %>%
mutate(plural = ifelse(n > 1, "s", ""),
@ -762,9 +819,6 @@ eucast_rules <- function(x,
if (n_changed > 0) {
verbose_info %>%
filter(!is.na(old)) %>%
# sort it well: S < I < R
mutate(old = as.rsi(old),
new = as.rsi(new)) %>%
group_by(old, new) %>%
summarise(n = n()) %>%
mutate(plural = ifelse(n > 1, "s", ""),

6
R/globals.R
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@ -57,6 +57,12 @@ globalVariables(c(".",
"more_than_episode_ago",
"name",
"new",
"newvar_date",
"newvar_genus_species",
"newvar_mo",
"newvar_patient_id",
"newvar_row_index",
"newvar_row_index_sorted",
"observations",
"observed",
"old",

4
R/guess_ab_col.R
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@ -23,9 +23,9 @@
#'
#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations.
#' @param x a \code{data.frame}
#' @param search_string a text to search \code{x} for
#' @param search_string a text to search \code{x} for, will be checked with \code{\link{as.ab}} if this value is not a column in \code{x}
#' @param verbose a logical to indicate whether additional info should be printed
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \code{\link{antibiotics}} data set for any column containing a name or ATC code of that antibiotic. \strong{Longer columns names take precendence over shorter column names.}
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \code{\link{antibiotics}} data set for any column containing a name or code of that antibiotic. \strong{Longer columns names take precendence over shorter column names.}
#' @importFrom dplyr %>% select filter_all any_vars
#' @importFrom crayon blue
#' @return A column name of \code{x}, or \code{NULL} when no result is found.

4
R/mo.R
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@ -1581,7 +1581,7 @@ mo_uncertainties <- function() {
}
#' @exportMethod print.mo_uncertainties
#' @importFrom crayon green yellow red white bgGreen bgYellow bgRed
#' @importFrom crayon green yellow red white black bgGreen bgYellow bgRed
#' @export
#' @noRd
print.mo_uncertainties <- function(x, ...) {
@ -1600,7 +1600,7 @@ print.mo_uncertainties <- function(x, ...) {
colour2 <- function(...) bgGreen(white(...))
} else if (x[i, "uncertainty"] == 2) {
colour1 <- yellow
colour2 <- bgYellow
colour2 <- function(...) bgYellow(black(...))
} else {
colour1 <- red
colour2 <- function(...) bgRed(white(...))

31
R/mo_property.R
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@ -21,7 +21,7 @@
#' Property of a microorganism
#'
#' Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with \code{\link{as.mo}}, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
#' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
#' @param property one of the column names of the \code{\link{microorganisms}} data set or \code{"shortname"}
#' @param language language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.
@ -53,7 +53,7 @@
#' @seealso \code{\link{microorganisms}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' ## taxonomic tree
#' # taxonomic tree -----------------------------------------------------------
#' mo_kingdom("E. coli") # "Bacteria"
#' mo_phylum("E. coli") # "Proteobacteria"
#' mo_class("E. coli") # "Gammaproteobacteria"
@ -63,35 +63,33 @@
#' mo_species("E. coli") # "coli"
#' mo_subspecies("E. coli") # ""
#'
#' ## colloquial properties
#' # colloquial properties ----------------------------------------------------
#' mo_name("E. coli") # "Escherichia coli"
#' mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
#' mo_shortname("E. coli") # "E. coli"
#'
#' ## other properties
#' # other properties ---------------------------------------------------------
#' mo_gramstain("E. coli") # "Gram-negative"
#' mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
#' mo_rank("E. coli") # "species"
#' mo_url("E. coli") # get the direct url to the online database entry
#' mo_synonyms("E. coli") # get previously accepted taxonomic names
#'
#' ## scientific reference
#' # scientific reference -----------------------------------------------------
#' mo_ref("E. coli") # "Castellani et al., 1919"
#' mo_authors("E. coli") # "Castellani et al."
#' mo_year("E. coli") # 1919
#'
#'
#' # Abbreviations known in the field
#' # abbreviations known in the field -----------------------------------------
#' mo_genus("MRSA") # "Staphylococcus"
#' mo_species("MRSA") # "aureus"
#' mo_shortname("MRSA") # "S. aureus"
#' mo_gramstain("MRSA") # "Gram-positive"
#' mo_shortname("VISA") # "S. aureus"
#' mo_gramstain("VISA") # "Gram-positive"
#'
#' mo_genus("VISA") # "Staphylococcus"
#' mo_species("VISA") # "aureus"
#' mo_genus("EHEC") # "Escherichia"
#' mo_species("EHEC") # "coli"
#'
#'
#' # Known subspecies
#' # known subspecies ---------------------------------------------------------
#' mo_name("doylei") # "Campylobacter jejuni doylei"
#' mo_genus("doylei") # "Campylobacter"
#' mo_species("doylei") # "jejuni"
@ -100,14 +98,14 @@
#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
#' mo_shortname("K. pneu rh") # "K. pneumoniae"
#'
#'
#' # Becker classification, see ?as.mo
#' \donttest{
#' # Becker classification, see ?as.mo ----------------------------------------
#' mo_fullname("S. epi") # "Staphylococcus epidermidis"
#' mo_fullname("S. epi", Becker = TRUE) # "Coagulase-negative Staphylococcus (CoNS)"
#' mo_shortname("S. epi") # "S. epidermidis"
#' mo_shortname("S. epi", Becker = TRUE) # "CoNS"
#'
#' # Lancefield classification, see ?as.mo
#' # Lancefield classification, see ?as.mo ------------------------------------
#' mo_fullname("S. pyo") # "Streptococcus pyogenes"
#' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
#' mo_shortname("S. pyo") # "S. pyogenes"
@ -136,6 +134,7 @@
#' mo_taxonomy("E. coli")
#' # get a list with the taxonomy, the authors and the URL to the online database
#' mo_info("E. coli")
#' }
mo_name <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "fullname", ...), language = language, only_unknown = FALSE)
}

2
R/rsi.R
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@ -130,6 +130,7 @@ as.rsi.default <- function(x, ...) {
x[!x %in% c('S', 'I', 'R')] <- NA
na_after <- x[is.na(x) | x == ''] %>% length()
if (!isFALSE(list(...)$warn)) { # so as.rsi(..., warn = FALSE) will never throw a warning
if (na_before != na_after) {
list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ''] %>%
unique() %>%
@ -140,6 +141,7 @@ as.rsi.default <- function(x, ...) {
'%) that were invalid antimicrobial interpretations: ',
list_missing, call. = FALSE)
}
}
structure(.Data = factor(x, levels = c("S", "I", "R"), ordered = TRUE),
class = c('rsi', 'ordered', 'factor'))

4
R/whocc.R
View File

@ -24,11 +24,13 @@
#' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
#' @section WHOCC:
#' \if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
#' This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
#' This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
#'
#' These have become the gold standard for international drug utilisation monitoring and research.
#'
#' The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
#'
#' \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
#' @inheritSection AMR Read more on our website!
#' @name WHOCC
#' @rdname WHOCC

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>

6
docs/authors.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -249,6 +249,10 @@
<p><strong>Erwin E. A. Hassing</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Annick Lenglet</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Bart C. Meijer</strong>. Contributor.
</p>

4
docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -315,7 +315,7 @@
<li>
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
<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> (not the translation from MIC to RSI values).</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> (not the translation from MIC to RSI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</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).
<ul>
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>

26
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -225,16 +225,16 @@
</div>
<div id="amr-0-7-1-9031" class="section level1">
<div id="amr-0-7-1-9032" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9031" class="anchor"></a>AMR 0.7.1.9031<small> Unreleased </small>
<a href="#amr-0-7-1-9032" class="anchor"></a>AMR 0.7.1.9032<small> Unreleased </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
<ul>
<li>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the <code>freq()</code> function. The <a href="https://github.com/msberends/clean"><code>clean</code></a> package is available on CRAN and will be installed automatically when updating the <code>AMR</code> package, that now imports it. In a later stage, the <code><a href="../reference/skewness.html">skewness()</a></code> and <code><a href="../reference/kurtosis.html">kurtosis()</a></code> functions will be moved to the <code>clean</code> package too.</li>
<li>Selection of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial codes <code>NA</code> and <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>: <code>first_isolates(..., include_unknown = TRUE)</code>. For WHONET users, this means that all records with microbial codes <code>"xxx"</code> (<em>no growth</em>) and <code>"con"</code> (<em>contamination</em>) will be excluded at default.</li>
<li>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>: <code>first_isolates(..., include_unknown = TRUE)</code>. For WHONET users, this means that all records with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>.</li>
</ul>
</div>
<div id="new" class="section level3">
@ -274,9 +274,15 @@
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Added more informative errors and warnings to <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
<li>Function: <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
<ul>
<li>Fixed a bug for <em>Yersinia pseudotuberculosis</em>
</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> for <em>Yersinia pseudotuberculosis</em>
<li>Added more informative errors and warnings</li>
<li>Printed info now distinguishes between added and changes values</li>
<li>Using Verbose mode (i.e. <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code>) returns more informative and readable output</li>
<li>Using factors as input now adds missing factors levels when the function changes antibiotic results</li>
</ul>
</li>
<li>
<p>Added tibble printing support for classes <code>rsi</code>, <code>mic</code>, <code>ab</code> and <code>mo</code>. When using tibbles containing antibiotic columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red:</p>
@ -306,15 +312,13 @@
<li>Deprecated the <code>country</code> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead of Rifampin</li>
<li>The <code>antibiotics</code> data set is now sorted by name</li>
<li>Using verbose mode with <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> returns more informative and readable output</li>
<li>Speed improvement for <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30 times faster for antibiotic abbreviations</li>
<li><p>Using factors as input for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now adds missing factors levels when the function changes antibiotic results</p></li>
<li><p>Speed improvement for <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30 times faster for antibiotic abbreviations</p></li>
</ul>
<div id="other" class="section level4">
<h4 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h4>
<ul>
<li>Added Dr Bart Meijer and Dr Dennis Souverein as contributors</li>
<li>Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors</li>
</ul>
</div>
</div>
@ -1228,7 +1232,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9031">0.7.1.9031</a></li>
<li><a href="#amr-0-7-1-9032">0.7.1.9032</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

5
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -239,9 +239,10 @@
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>). <strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></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>

5
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -269,9 +269,10 @@
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>). <strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></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>

5
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -267,9 +267,10 @@
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>). <strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href='https://www.whocc.no/copyright_disclaimer/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></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>

2
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>

7
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -258,7 +258,7 @@
</tr>
<tr>
<th>verbose</th>
<td><p>a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a <code>data.frame</code> with extensive info about which rows and columns would be effected and in which way.</p></td>
<td><p>a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.</p></td>
</tr>
<tr>
<th>...</th>
@ -292,7 +292,7 @@
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code>eucast_rules</code> and <code><a href='mdro.html'>mdro</a></code>. These are shown in the format '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)', sorted by name:</p>
<p>The following antibiotics are used for the functions <code>eucast_rules</code> and <code><a href='mdro.html'>mdro</a></code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)', sorted by name:</p>
<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
@ -409,6 +409,7 @@
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
<span class='co'># with 18 rows, containing all details about the transformations:</span>
<span class='no'>c</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)

5
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -317,7 +317,7 @@
</tr>
<tr>
<th>include_unknown</th>
<td><p>logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code <code>"UNKNOWN"</code>, which defaults to <code>FALSE</code>. For WHONET users, this means that all records with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default.</p></td>
<td><p>logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code <code>"UNKNOWN"</code>, which defaults to <code>FALSE</code>. For WHONET users, this means that all records with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default. Isolates with a microbial ID of <code>NA</code> will always be excluded as first isolate.</p></td>
</tr>
<tr>
<th>...</th>
@ -337,6 +337,7 @@
<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode <a href='https://www.ncbi.nlm.nih.gov/pubmed/17304462'>[1]</a>. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all <em>S. aureus</em> isolates would be overestimated, because you included this MRSA more than once. It would be <a href='https://en.wikipedia.org/wiki/Selection_bias'>selection bias</a>.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p>
<p>The functions <code>filter_first_isolate</code> and <code>filter_first_weighted_isolate</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate</code> is essentially equal to:</p><pre>
x %&gt;%
mutate(only_firsts = first_isolate(x, ...)) %&gt;%

6
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -245,7 +245,7 @@
</tr>
<tr>
<th>search_string</th>
<td><p>a text to search <code>x</code> for</p></td>
<td><p>a text to search <code>x</code> for, will be checked with <code><a href='as.ab.html'>as.ab</a></code> if this value is not a column in <code>x</code></p></td>
</tr>
<tr>
<th>verbose</th>
@ -259,7 +259,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <code><a href='antibiotics.html'>antibiotics</a></code> data set for any column containing a name or ATC code of that antibiotic. <strong>Longer columns names take precendence over shorter column names.</strong></p>
<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <code><a href='antibiotics.html'>antibiotics</a></code> data set for any column containing a name or code of that antibiotic. <strong>Longer columns names take precendence over shorter column names.</strong></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>

2
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>

4
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -299,7 +299,7 @@
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules</a></code> and <code>mdro</code>. These are shown in the format '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)', sorted by name:</p>
<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules</a></code> and <code>mdro</code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)', sorted by name:</p>
<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),

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docs/reference/mo_property.html
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@ -47,7 +47,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Property of a microorganism — mo_property" />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism from the microorganisms data set. All input values will be evaluated internally with as.mo." />
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9032</span>
</span>
</div>
@ -230,7 +230,7 @@
<div class="ref-description">
<p>Use these functions to return a specific property of a microorganism from the <code><a href='microorganisms.html'>microorganisms</a></code> data set. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo</a></code>.</p>
<p>Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo</a></code>, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.</p>
</div>
@ -352,7 +352,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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'>## taxonomic tree</span>
<span class='co'># taxonomic tree -----------------------------------------------------------</span>
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span>
<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span>
@ -362,35 +362,33 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>
<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># ""</span>
<span class='co'>## colloquial properties</span>
<span class='co'># colloquial properties ----------------------------------------------------</span>
<span class='fu'>mo_name</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli", same as mo_name()</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
<span class='co'>## other properties</span>
<span class='co'># other properties ---------------------------------------------------------</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram-negative"</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
<span class='fu'>mo_synonyms</span>(<span class='st'>"E. coli"</span>) <span class='co'># get previously accepted taxonomic names</span>
<span class='co'>## scientific reference</span>
<span class='co'># scientific reference -----------------------------------------------------</span>
<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al., 1919"</span>
<span class='fu'>mo_authors</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al."</span>
<span class='fu'>mo_year</span>(<span class='st'>"E. coli"</span>) <span class='co'># 1919</span>
<span class='co'># Abbreviations known in the field</span>
<span class='co'># abbreviations known in the field -----------------------------------------</span>
<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>) <span class='co'># "aureus"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"MRSA"</span>) <span class='co'># "S. aureus"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Gram-positive"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"VISA"</span>) <span class='co'># "S. aureus"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"VISA"</span>) <span class='co'># "Gram-positive"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"VISA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"VISA"</span>) <span class='co'># "aureus"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"EHEC"</span>) <span class='co'># "Escherichia"</span>
<span class='fu'>mo_species</span>(<span class='st'>"EHEC"</span>) <span class='co'># "coli"</span>
<span class='co'># Known subspecies</span>
<span class='co'># known subspecies ---------------------------------------------------------</span>
<span class='fu'>mo_name</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter jejuni doylei"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter"</span>
<span class='fu'>mo_species</span>(<span class='st'>"doylei"</span>) <span class='co'># "jejuni"</span>
@ -399,14 +397,14 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_fullname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "K. pneumoniae"</span>
<span class='co'># Becker classification, see ?as.mo</span>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># Becker classification, see ?as.mo ----------------------------------------</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "Staphylococcus epidermidis"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "S. epidermidis"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "CoNS"</span>
<span class='co'># Lancefield classification, see ?as.mo</span>
<span class='co'># Lancefield classification, see ?as.mo ------------------------------------</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "Streptococcus pyogenes"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "Streptococcus group A"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "S. pyogenes"</span>

2
index.md
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@ -141,7 +141,7 @@ The `AMR` package basically does four important things:
2. It **enhances existing data** and **adds new data** from data sets included in this package.
* Use `eucast_rules()` to apply [EUCAST expert rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) (not the translation from MIC to RSI values).
* Use `eucast_rules()` to apply [EUCAST expert rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) (not the translation from MIC to RSI values, use `as.rsi()` for that).
* Use `first_isolate()` to identify the first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute).
* You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.
* Use `mdro()` (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.

4
man/WHOCC.Rd
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@ -9,11 +9,13 @@ All antimicrobial drugs and their official names, ATC codes, ATC groups and defi
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
}
\section{Read more on our website!}{

4
man/antibiotics.Rd
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@ -41,11 +41,13 @@ Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and co
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
}
\section{Read more on our website!}{

4
man/as.ab.Rd
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@ -35,11 +35,13 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
\section{WHOCC}{
\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
}
\section{Read more on our website!}{

6
man/eucast_rules.Rd
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@ -33,7 +33,7 @@ eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a \code{data.frame} with extensive info about which rows and columns would be effected and in which way.}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.}
\item{...}{column name of an antibiotic, see section Antibiotics}
}
@ -53,7 +53,7 @@ The file containing all EUCAST rules is located here: \url{https://gitlab.com/ms
To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
@ -170,10 +170,12 @@ b
# 5 Pseudomonas aeruginosa R R - - R R R
\donttest{
# do not apply EUCAST rules, but rather get a data.frame
# with 18 rows, containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE)
}
}
\keyword{eucast}
\keyword{interpretive}
\keyword{reading}

4
man/guess_ab_col.Rd
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@ -9,7 +9,7 @@ guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE)
\arguments{
\item{x}{a \code{data.frame}}
\item{search_string}{a text to search \code{x} for}
\item{search_string}{a text to search \code{x} for, will be checked with \code{\link{as.ab}} if this value is not a column in \code{x}}
\item{verbose}{a logical to indicate whether additional info should be printed}
}
@ -20,7 +20,7 @@ A column name of \code{x}, or \code{NULL} when no result is found.
This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations.
}
\details{
You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \code{\link{antibiotics}} data set for any column containing a name or ATC code of that antibiotic. \strong{Longer columns names take precendence over shorter column names.}
You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \code{\link{antibiotics}} data set for any column containing a name or code of that antibiotic. \strong{Longer columns names take precendence over shorter column names.}
}
\section{Read more on our website!}{

2
man/mdro.Rd
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@ -62,7 +62,7 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h
To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),

31
man/mo_property.Rd
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@ -89,7 +89,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
}
}
\description{
Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with \code{\link{as.mo}}, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
}
\details{
All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
@ -130,7 +130,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\examples{
## taxonomic tree
# taxonomic tree -----------------------------------------------------------
mo_kingdom("E. coli") # "Bacteria"
mo_phylum("E. coli") # "Proteobacteria"
mo_class("E. coli") # "Gammaproteobacteria"
@ -140,35 +140,33 @@ mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"
mo_subspecies("E. coli") # ""
## colloquial properties
# colloquial properties ----------------------------------------------------
mo_name("E. coli") # "Escherichia coli"
mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
mo_shortname("E. coli") # "E. coli"
## other properties
# other properties ---------------------------------------------------------
mo_gramstain("E. coli") # "Gram-negative"
mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
mo_rank("E. coli") # "species"
mo_url("E. coli") # get the direct url to the online database entry
mo_synonyms("E. coli") # get previously accepted taxonomic names
## scientific reference
# scientific reference -----------------------------------------------------
mo_ref("E. coli") # "Castellani et al., 1919"
mo_authors("E. coli") # "Castellani et al."
mo_year("E. coli") # 1919
# Abbreviations known in the field
# abbreviations known in the field -----------------------------------------
mo_genus("MRSA") # "Staphylococcus"
mo_species("MRSA") # "aureus"
mo_shortname("MRSA") # "S. aureus"
mo_gramstain("MRSA") # "Gram-positive"
mo_shortname("VISA") # "S. aureus"
mo_gramstain("VISA") # "Gram-positive"
mo_genus("VISA") # "Staphylococcus"
mo_species("VISA") # "aureus"
mo_genus("EHEC") # "Escherichia"
mo_species("EHEC") # "coli"
# Known subspecies
# known subspecies ---------------------------------------------------------
mo_name("doylei") # "Campylobacter jejuni doylei"
mo_genus("doylei") # "Campylobacter"
mo_species("doylei") # "jejuni"
@ -177,14 +175,14 @@ mo_subspecies("doylei") # "doylei"
mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
mo_shortname("K. pneu rh") # "K. pneumoniae"
# Becker classification, see ?as.mo
\donttest{
# Becker classification, see ?as.mo ----------------------------------------
mo_fullname("S. epi") # "Staphylococcus epidermidis"
mo_fullname("S. epi", Becker = TRUE) # "Coagulase-negative Staphylococcus (CoNS)"
mo_shortname("S. epi") # "S. epidermidis"
mo_shortname("S. epi", Becker = TRUE) # "CoNS"
# Lancefield classification, see ?as.mo
# Lancefield classification, see ?as.mo ------------------------------------
mo_fullname("S. pyo") # "Streptococcus pyogenes"
mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
mo_shortname("S. pyo") # "S. pyogenes"
@ -214,6 +212,7 @@ mo_taxonomy("E. coli")
# get a list with the taxonomy, the authors and the URL to the online database
mo_info("E. coli")
}
}
\seealso{
\code{\link{microorganisms}}
}