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added boxplot for (grouped) freq()

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dr. M.S. (Matthijs) Berends 2019-05-29 19:56:17 +02:00
parent 62e6f41961
commit 8b5e2b030b
20 changed files with 464 additions and 297 deletions
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4
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR
Version: 0.6.1.9040
Date: 2019-05-28
Version: 0.6.1.9042
Date: 2019-05-29
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

37
NAMESPACE
View File

@ -2,7 +2,7 @@
S3method(as.data.frame,ab)
S3method(as.data.frame,atc)
S3method(as.data.frame,frequency_tbl)
S3method(as.data.frame,freq)
S3method(as.data.frame,mo)
S3method(as.double,mic)
S3method(as.integer,mic)
@ -11,19 +11,20 @@ S3method(as.rsi,data.frame)
S3method(as.rsi,default)
S3method(as.rsi,disk)
S3method(as.rsi,mic)
S3method(as.vector,frequency_tbl)
S3method(as_tibble,frequency_tbl)
S3method(as.vector,freq)
S3method(as_tibble,freq)
S3method(barplot,mic)
S3method(barplot,rsi)
S3method(diff,frequency_tbl)
S3method(boxplot,freq)
S3method(diff,freq)
S3method(droplevels,mic)
S3method(droplevels,rsi)
S3method(format,frequency_tbl)
S3method(hist,frequency_tbl)
S3method(format,freq)
S3method(hist,freq)
S3method(kurtosis,data.frame)
S3method(kurtosis,default)
S3method(kurtosis,matrix)
S3method(plot,frequency_tbl)
S3method(plot,freq)
S3method(plot,mic)
S3method(plot,resistance_predict)
S3method(plot,rsi)
@ -31,6 +32,7 @@ S3method(print,ab)
S3method(print,atc)
S3method(print,catalogue_of_life_version)
S3method(print,disk)
S3method(print,freq)
S3method(print,frequency_tbl)
S3method(print,mic)
S3method(print,mo)
@ -40,7 +42,7 @@ S3method(print,rsi)
S3method(pull,ab)
S3method(pull,atc)
S3method(pull,mo)
S3method(select,frequency_tbl)
S3method(select,freq)
S3method(skewness,data.frame)
S3method(skewness,default)
S3method(skewness,matrix)
@ -180,31 +182,33 @@ export(theme_rsi)
export(top_freq)
exportMethods(as.data.frame.ab)
exportMethods(as.data.frame.atc)
exportMethods(as.data.frame.frequency_tbl)
exportMethods(as.data.frame.freq)
exportMethods(as.data.frame.mo)
exportMethods(as.double.mic)
exportMethods(as.integer.mic)
exportMethods(as.numeric.mic)
exportMethods(as.vector.frequency_tbl)
exportMethods(as_tibble.frequency_tbl)
exportMethods(as.vector.freq)
exportMethods(as_tibble.freq)
exportMethods(barplot.mic)
exportMethods(barplot.rsi)
exportMethods(diff.frequency_tbl)
exportMethods(boxplot.freq)
exportMethods(diff.freq)
exportMethods(droplevels.mic)
exportMethods(droplevels.rsi)
exportMethods(format.frequency_tbl)
exportMethods(hist.frequency_tbl)
exportMethods(format.freq)
exportMethods(hist.freq)
exportMethods(kurtosis)
exportMethods(kurtosis.data.frame)
exportMethods(kurtosis.default)
exportMethods(kurtosis.matrix)
exportMethods(plot.frequency_tbl)
exportMethods(plot.freq)
exportMethods(plot.mic)
exportMethods(plot.rsi)
exportMethods(print.ab)
exportMethods(print.atc)
exportMethods(print.catalogue_of_life_version)
exportMethods(print.disk)
exportMethods(print.freq)
exportMethods(print.frequency_tbl)
exportMethods(print.mic)
exportMethods(print.mo)
@ -214,7 +218,7 @@ exportMethods(print.rsi)
exportMethods(pull.ab)
exportMethods(pull.atc)
exportMethods(pull.mo)
exportMethods(select.frequency_tbl)
exportMethods(select.freq)
exportMethods(skewness)
exportMethods(skewness.data.frame)
exportMethods(skewness.default)
@ -288,6 +292,7 @@ importFrom(grDevices,boxplot.stats)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,plot)
importFrom(graphics,points)

11
NEWS.md
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@ -28,6 +28,17 @@
* Frequency tables (`freq()`):
* speed improvement for microbial IDs
* fixed level names in markdown
* support for boxplots:
```r
septic_patients %>%
freq(age) %>%
boxplot()
# grouped boxplots:
septic_patients %>%
group_by(hospital_id) %>%
freq(age) %>%
boxplot()
```
* Removed all hardcoded EUCAST rules and replaced them with a new reference file: `./inst/eucast/eucast.tsv`
* Added ceftazidim intrinsic resistance to *Streptococci*
* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+

20
R/eucast_rules.R
View File

@ -45,16 +45,18 @@ 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.
#'
#' Available abbrevations of the column containing antibiotics in the form '\strong{antimicrobial ID}: name (\emph{ATC code})':
#' 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:
#'
#' \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
#' \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}),
#' \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
#' \strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
#' \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
#' \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
#' \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
#' \strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
#' \strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
#' \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
#' \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
#' \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
#' \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
@ -66,26 +68,28 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
#' \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
#' \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
#' \strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
#' \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
#' \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
#' \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
#' \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
#' \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
#' \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
#' \strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
#' \strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
#' \strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
#' \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
#' \strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
#' \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
#' \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
#' \strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
#' \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
#' \strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
#' \strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
#' \strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
#' \strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
#' \strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
#' \strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
#' \strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
#' \strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
#' \strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01XD01}),
#' \strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
#' \strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
#' \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
@ -93,14 +97,18 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
#' \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
#' \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
#' \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01CF04}),
#' \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
#' \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
#' \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
#' \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
#' \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
#' \strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
#' \strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
#' \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
#' \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
#' \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
#' \strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
#' \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
#' \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
#' \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
#' \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),

212
R/freq.R
View File

@ -75,7 +75,7 @@
#' @keywords summary summarise frequency freq
#' @rdname freq
#' @name freq
#' @return A \code{data.frame} (with an additional class \code{"frequency_tbl"}) with five columns: \code{item}, \code{count}, \code{percent}, \code{cum_count} and \code{cum_percent}.
#' @return A \code{data.frame} (with an additional class \code{"freq"}) with five columns: \code{item}, \code{count}, \code{percent}, \code{cum_count} and \code{cum_percent}.
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
@ -139,6 +139,16 @@
#' freq(age) %>%
#' hist()
#'
#' # or a boxplot of numeric values
#' septic_patients %>%
#' freq(age) %>%
#' boxplot()
#'
#' # or even a boxplot per group
#' septic_patients %>%
#' group_by(hospital_id) %>%
#' freq(age) %>%
#' boxplot()
#'
#' # or print all points to a regular plot
#' septic_patients %>%
@ -183,22 +193,22 @@
#' # check differences between frequency tables
#' diff(freq(septic_patients$TMP),
#' freq(septic_patients$SXT))
frequency_tbl <- function(x,
...,
sort.count = TRUE,
nmax = getOption("max.print.freq"),
na.rm = TRUE,
row.names = TRUE,
markdown = !interactive(),
digits = 2,
quote = FALSE,
header = TRUE,
title = NULL,
na = "<NA>",
droplevels = TRUE,
sep = " ",
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark != ",", ",", ".")) {
freq <- function(x,
...,
sort.count = TRUE,
nmax = getOption("max.print.freq"),
na.rm = TRUE,
row.names = TRUE,
markdown = !interactive(),
digits = 2,
quote = FALSE,
header = TRUE,
title = NULL,
na = "<NA>",
droplevels = TRUE,
sep = " ",
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark != ",", ",", ".")) {
mult.columns <- 0
x.group = character(0)
@ -544,7 +554,7 @@ frequency_tbl <- function(x,
# }
structure(.Data = df,
class = c("frequency_tbl", class(df)),
class = unique(c("freq", class(df))),
header = header_list,
opt = list(title = title,
data = x.name,
@ -565,7 +575,11 @@ frequency_tbl <- function(x,
#' @rdname freq
#' @export
freq <- frequency_tbl
frequency_tbl <- freq
is.freq <- function(f) {
any(c("freq", "frequency_tbl") %in% class(f))
}
#' @importFrom crayon silver green red
#' @importFrom dplyr %>%
@ -639,13 +653,7 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
# class and mode
if (is.null(header$columns)) {
# if (markdown == TRUE) {
# header$class <- paste0("`", header$class, "`")
# }
if (!header$mode %in% header$class) {
# if (markdown == TRUE) {
# header$mode <- paste0("`", header$mode, "`")
# }
header$class <- header$class %>% rev() %>% paste(collapse = " > ") %>% paste0(silver(paste0(" (", header$mode, ")")))
} else {
header$class <- header$class %>% rev() %>% paste(collapse = " > ")
@ -654,9 +662,6 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
}
# levels
if (!is.null(header$levels)) {
# if (markdown == TRUE) {
# header$levels <- paste0("`", header$levels, "`")
# }
if (header$ordered == TRUE) {
levels_text <- paste0(header$levels, collapse = " < ")
} else {
@ -733,7 +738,7 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
#' @export
#' @importFrom dplyr top_n pull
top_freq <- function(f, n) {
if (!"frequency_tbl" %in% class(f)) {
if (!is.freq(f)) {
stop("`top_freq` can only be applied to frequency tables", call. = FALSE)
}
if (!is.numeric(n) | length(n) != 1L) {
@ -751,7 +756,7 @@ top_freq <- function(f, n) {
#' @rdname freq
#' @export
header <- function(f, property = NULL) {
if (!"frequency_tbl" %in% class(f)) {
if (!is.freq(f)) {
stop("`header` can only be applied to frequency tables", call. = FALSE)
}
if (is.null(property)) {
@ -765,13 +770,12 @@ header <- function(f, property = NULL) {
}
#' @noRd
#' @exportMethod diff.frequency_tbl
#' @exportMethod diff.freq
#' @importFrom dplyr %>% full_join mutate
#' @export
diff.frequency_tbl <- function(x, y, ...) {
diff.freq <- function(x, y, ...) {
# check classes
if (!"frequency_tbl" %in% class(x)
| !"frequency_tbl" %in% class(y)) {
if (!is.freq(x) | !is.freq(y)) {
stop("Both x and y must be a frequency table.")
}
@ -817,21 +821,34 @@ diff.frequency_tbl <- function(x, y, ...) {
}
#' @rdname freq
#' @exportMethod print.frequency_tbl
#' @exportMethod print.freq
#' @importFrom knitr kable
#' @importFrom dplyr n_distinct
#' @importFrom crayon bold silver
#' @export
print.frequency_tbl <- function(x,
nmax = getOption("max.print.freq", default = 15),
markdown = !interactive(),
header = TRUE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark != ",", ",", "."),
...) {
print.freq <- function(x,
nmax = getOption("max.print.freq", default = 15),
markdown = !interactive(),
header = TRUE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark != ",", ",", "."),
...) {
opt <- attr(x, "opt")
if (is.null(opt)) {
# selection of frequency table, return original class
class(x) <- class(x)[!class(x) %in% c("freq", "frequency_tbl")]
print(x)
return(invisible())
}
opt$header_txt <- header(x)
if (is.null(opt$nmax)) {
opt$nmax <- 0
}
if (is.null(opt$tbl_format)) {
opt$tbl_format <- "pandoc"
}
dots <- list(...)
if ("markdown" %in% names(dots)) {
@ -854,7 +871,7 @@ print.frequency_tbl <- function(x,
}
if (is.null(opt$title)) {
if (isTRUE(opt$data %like% "^a data.frame") & opt$tbl_format == "markdown") {
if (isTRUE(opt$data %like% "^a data.frame") & isTRUE(opt$tbl_format == "markdown")) {
opt$data <- gsub("data.frame", "`data.frame`", opt$data, fixed = TRUE)
}
if (!is.null(opt$data) & !is.null(opt$vars)) {
@ -883,21 +900,21 @@ print.frequency_tbl <- function(x,
title <- opt$title
}
if (!missing(nmax)) {
if (!missing(nmax) | is.null(opt$nmax)) {
opt$nmax <- nmax
opt$nmax.set <- TRUE
}
if (opt$nmax %in% c(0, Inf, NA, NULL)) {
if (isTRUE(opt$nmax %in% c(0, Inf, NA, NULL))) {
opt$nmax <- NROW(x)
opt$nmax.set <- FALSE
} else if (opt$nmax >= NROW(x)) {
} else if (isTRUE(opt$nmax >= NROW(x))) {
opt$nmax.set <- FALSE
}
if (!missing(decimal.mark)) {
if (!missing(decimal.mark) | is.null(opt$decimal.mark)) {
opt$decimal.mark <- decimal.mark
}
if (!missing(big.mark)) {
if (!missing(big.mark) | is.null(opt$big.mark)) {
opt$big.mark <- big.mark
}
if (!missing(header)) {
@ -905,9 +922,9 @@ print.frequency_tbl <- function(x,
}
# bold title
if (opt$tbl_format == "pandoc") {
if (isTRUE(opt$tbl_format == "pandoc")) {
title <- bold(title)
} else if (opt$tbl_format == "markdown") {
} else if (isTRUE(opt$tbl_format == "markdown")) {
title <- paste0("\n\n**", title, "** ") # two space for newline
}
@ -915,7 +932,7 @@ print.frequency_tbl <- function(x,
if (NROW(x) == 0 | isTRUE(all(is.na(x$item)))) {
cat("No observations")
if (isTRUE(all(is.na(x$item)))) {
if (isTRUE(all(is.na(x$item) | identical(x$item, "<NA>") | identical(x$item, "(NA)")))) {
cat(" - all values are missing (<NA>)")
}
cat(".\n")
@ -925,7 +942,7 @@ print.frequency_tbl <- function(x,
return(invisible())
}
if (opt$header == TRUE) {
if (isTRUE(opt$header == TRUE)) {
if (!is.null(opt$header_txt)) {
if (is.null(opt$digits)) {
opt$digits <- 2
@ -940,7 +957,7 @@ print.frequency_tbl <- function(x,
if (is.null(opt$na)) {
opt$na <- "<NA>"
}
if (opt$tbl_format == "markdown") {
if (isTRUE(opt$tbl_format == "markdown")) {
# no HTML tags
opt$na <- gsub("<", "(", opt$na, fixed = TRUE)
opt$na <- gsub(">", ")", opt$na, fixed = TRUE)
@ -951,7 +968,7 @@ print.frequency_tbl <- function(x,
x.unprinted <- base::sum(x[(opt$nmax + 1):nrow(x), "count"], na.rm = TRUE)
x.printed <- base::sum(x$count) - x.unprinted
if (nrow(x) > opt$nmax & opt$tbl_format != "markdown") {
if (nrow(x) > opt$nmax & isTRUE(opt$tbl_format != "markdown")) {
if (opt$nmax.set == TRUE) {
nmax <- opt$nmax
@ -1029,6 +1046,13 @@ print.frequency_tbl <- function(x,
cat("\n")
}
if (is.null(opt$row_names)) {
opt$row_names <- TRUE
}
if (is.null(opt$column_names)) {
opt$column_names <- colnames(x)
}
print(
knitr::kable(x,
format = opt$tbl_format,
@ -1055,37 +1079,42 @@ print.frequency_tbl <- function(x,
}
#' @noRd
#' @exportMethod as.data.frame.frequency_tbl
#' @exportMethod print.frequency_tbl
#' @export
as.data.frame.frequency_tbl <- function(x, ...) {
print.frequency_tbl <- print.freq
#' @noRd
#' @exportMethod as.data.frame.freq
#' @export
as.data.frame.freq <- function(x, ...) {
attr(x, "package") <- NULL
attr(x, "opt") <- NULL
as.data.frame.data.frame(x, ...)
}
#' @exportMethod select.frequency_tbl
#' @exportMethod select.freq
#' @export
#' @importFrom dplyr select
#' @noRd
select.frequency_tbl <- function(.data, ...) {
select.freq <- function(.data, ...) {
select(as.data.frame(.data), ...)
}
#' @noRd
#' @exportMethod as_tibble.frequency_tbl
#' @exportMethod as_tibble.freq
#' @export
#' @importFrom dplyr as_tibble
as_tibble.frequency_tbl <- function(x, validate = TRUE, ..., rownames = NA) {
as_tibble.freq <- function(x, validate = TRUE, ..., rownames = NA) {
attr(x, "package") <- NULL
attr(x, "opt") <- NULL
as_tibble(x = as.data.frame(x), validate = validate, ..., rownames = rownames)
}
#' @noRd
#' @exportMethod hist.frequency_tbl
#' @exportMethod hist.freq
#' @export
#' @importFrom graphics hist
hist.frequency_tbl <- function(x, breaks = "Sturges", main = NULL, xlab = NULL, ...) {
hist.freq <- function(x, breaks = "Sturges", main = NULL, xlab = NULL, ...) {
opt <- attr(x, "opt")
if (!class(x$item) %in% c("numeric", "double", "integer", "Date")) {
stop("`x` must be numeric or Date.", call. = FALSE)
@ -1112,9 +1141,56 @@ hist.frequency_tbl <- function(x, breaks = "Sturges", main = NULL, xlab = NULL,
}
#' @noRd
#' @exportMethod plot.frequency_tbl
#' @exportMethod boxplot.freq
#' @export
plot.frequency_tbl <- function(x, y, ...) {
#' @importFrom graphics boxplot
boxplot.freq <- function(x, main = NULL, xlab = NULL, ...) {
opt <- attr(x, "opt")
x.bak <- x
if (!class(x$item) %in% c("numeric", "double", "integer", "Date")) {
stop("`x` must be numeric or Date.", call. = FALSE)
}
if (!is.null(opt$vars)) {
title <- opt$vars
} else if (!is.null(opt$data)) {
title <- opt$data
} else {
title <- "frequency table"
}
if (class(x$item) == "Date") {
x <- as.Date(as.vector(x), origin = "1970-01-01")
} else {
x <- as.vector(x)
}
if (is.null(main)) {
main <- paste("Boxplot of", title)
}
if (is.null(xlab)) {
xlab <- title
}
if (!is.null(opt$group_var) & isTRUE(length(opt$group_var) > 0)) {
# support for grouped frequency table
x.new <- data.frame(group = character(0), item = character(0))
for (i in 1:nrow(x.bak)) {
if (x.bak[i, "group"] == "") {
x.bak[i, "group"] <- x.bak[i - 1, "group"]
}
for (j in 1:x.bak[i, "count"]) {
x.new <- rbind(x.new,
data.frame(group = x.bak[i, "group"],
item = x.bak[i, "item"]))
}
}
boxplot(item ~ group, data = x.bak, main = main, ylab = xlab, xlab = opt$group_var, ...)
} else {
boxplot(x, main = main, xlab = xlab, ...)
}
}
#' @noRd
#' @exportMethod plot.freq
#' @export
plot.freq <- function(x, y, ...) {
opt <- attr(x, "opt")
if (!is.null(opt$vars)) {
title <- opt$vars
@ -1125,16 +1201,16 @@ plot.frequency_tbl <- function(x, y, ...) {
}
#' @noRd
#' @exportMethod as.vector.frequency_tbl
#' @exportMethod as.vector.freq
#' @export
as.vector.frequency_tbl <- function(x, mode = "any") {
as.vector.freq <- function(x, mode = "any") {
as.vector(rep(x$item, x$count), mode = mode)
}
#' @noRd
#' @exportMethod format.frequency_tbl
#' @exportMethod format.freq
#' @export
format.frequency_tbl <- function(x, digits = 1, ...) {
format.freq <- function(x, digits = 1, ...) {
opt <- attr(x, "opt")
if (opt$nmax.set == TRUE) {
nmax <- opt$nmax

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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>

4
docs/articles/freq.html
View File

@ -40,7 +40,7 @@
</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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -736,7 +736,7 @@ Median: 31 July 2009 (47.39%)</p>
<p>A frequency table is actually a regular <code>data.frame</code>, with the exception that it contains an additional class.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">my_df &lt;-<span class="st"> </span>septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb11-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(my_df)</a></code></pre></div>
<p>[1] “frequency_tbl” “data.frame”</p>
<p>[1] “freq” “data.frame”</p>
<p>Because of this additional class, a frequency table prints like the examples above. But the object itself contains the complete table without a row limitation:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_df)</a></code></pre></div>
<p>[1] 74 5</p>

2
docs/articles/index.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>

2
docs/authors.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>

2
docs/index.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>

239
docs/news/index.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -287,6 +287,17 @@ Please create an issue in one of our repositories if you want additions in this
<ul>
<li>speed improvement for microbial IDs</li>
<li>fixed level names in markdown</li>
<li>
<p>support for boxplots:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># grouped boxplots:</span></a>
<a class="sourceLine" id="cb2-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-6" title="6"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-7" title="7"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-8" title="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
</li>
</ul>
</li>
<li>Removed all hardcoded EUCAST rules and replaced them with a new reference file: <code>./inst/eucast/eucast.tsv</code>
@ -367,32 +378,32 @@ This data is updated annually - check the included version with the new function
</li>
<li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb2-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb2-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb2-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
<a class="sourceLine" id="cb2-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
<a class="sourceLine" id="cb3-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
<a class="sourceLine" id="cb3-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
<a class="sourceLine" id="cb3-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
<a class="sourceLine" id="cb3-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
<a class="sourceLine" id="cb4-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
<a class="sourceLine" id="cb4-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
<a class="sourceLine" id="cb4-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
<a class="sourceLine" id="cb4-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
<a class="sourceLine" id="cb4-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
<a class="sourceLine" id="cb4-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
<a class="sourceLine" id="cb4-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
<a class="sourceLine" id="cb5-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
<a class="sourceLine" id="cb5-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
<a class="sourceLine" id="cb5-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
<a class="sourceLine" id="cb5-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
<a class="sourceLine" id="cb5-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
<a class="sourceLine" id="cb5-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
@ -404,20 +415,20 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
<a class="sourceLine" id="cb5-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
<a class="sourceLine" id="cb6-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
<a class="sourceLine" id="cb6-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
</li>
<li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
<a class="sourceLine" id="cb6-2" title="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb6-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
<a class="sourceLine" id="cb7-2" title="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb7-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb7-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb7-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
</li>
<li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
</li>
@ -446,33 +457,33 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<ul>
<li>
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
<a class="sourceLine" id="cb8-2" title="2"></a>
<a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
<a class="sourceLine" id="cb8-4" title="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
<a class="sourceLine" id="cb8-5" title="5"></a>
<a class="sourceLine" id="cb8-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
<a class="sourceLine" id="cb8-7" title="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
<a class="sourceLine" id="cb9-2" title="2"></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
<a class="sourceLine" id="cb9-4" title="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
<a class="sourceLine" id="cb9-5" title="5"></a>
<a class="sourceLine" id="cb9-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
<a class="sourceLine" id="cb9-7" title="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># equal:</span></a>
<a class="sourceLine" id="cb9-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb9-4" title="4"></a>
<a class="sourceLine" id="cb9-5" title="5"><span class="co"># also equal:</span></a>
<a class="sourceLine" id="cb9-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="co"># equal:</span></a>
<a class="sourceLine" id="cb10-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb10-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb10-4" title="4"></a>
<a class="sourceLine" id="cb10-5" title="5"><span class="co"># also equal:</span></a>
<a class="sourceLine" id="cb10-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb10-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
</li>
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
<a class="sourceLine" id="cb10-2" title="2"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb10-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
<a class="sourceLine" id="cb10-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
<a class="sourceLine" id="cb11-2" title="2"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb11-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
<a class="sourceLine" id="cb11-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
</li>
<li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li>
@ -518,19 +529,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<a class="sourceLine" id="cb11-2" title="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb11-3" title="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb11-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb11-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb11-6" title="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb11-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb11-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb11-9" title="9"></a>
<a class="sourceLine" id="cb11-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb11-11" title="11">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb11-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb11-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<a class="sourceLine" id="cb12-2" title="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb12-3" title="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb12-6" title="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb12-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb12-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb12-9" title="9"></a>
<a class="sourceLine" id="cb12-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb12-11" title="11">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb12-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
</li>
<li>Header info is now available as a list, with the <code>header</code> function</li>
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@ -605,10 +616,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb12-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb12-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb12-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb13-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb13-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb13-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
</li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@ -621,15 +632,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb13-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb14-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb14-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb15-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb15-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li>
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
</li>
@ -709,18 +720,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb15-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb15-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb15-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb15-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb15-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb15-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb15-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb16-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb16-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb16-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb16-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb16-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb16-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb16-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb16-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb17-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb17-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</li>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul>
@ -731,18 +742,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb17-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb17-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb17-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb17-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb17-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb18-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb18-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb18-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb18-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb18-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb18-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb18-3" title="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb18-4" title="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb18-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb19-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb19-3" title="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb19-4" title="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb19-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
@ -770,12 +781,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb19-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb19-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb19-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb19-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb19-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb20-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb20-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb20-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb20-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb20-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@ -786,13 +797,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
<a class="sourceLine" id="cb20-2" title="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb20-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb20-4" title="4"></a>
<a class="sourceLine" id="cb20-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb20-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb20-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
<a class="sourceLine" id="cb21-2" title="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb21-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb21-4" title="4"></a>
<a class="sourceLine" id="cb21-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb21-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb21-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
</li>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
@ -806,12 +817,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb21-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb22-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb22-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb22-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb23-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb23-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
</ul>
</div>

57
docs/reference/age_groups.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -273,7 +273,7 @@
<li><p>A numeric vector. A vector of e.g. <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(10, 20)</a></code> will split on 0-9, 10-19 and 20+. A value of only <code>50</code> will split on 0-49 and 50+.
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).</p></li>
<li><p>A character:</p><ul>
<li><p><code>"children"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
<li><p><code>"children"</code> or <code>"kids"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
<li><p><code>"elderly"</code> or <code>"seniors"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(65, 75, 85)</a></code>. This will split on 0-64, 65-74, 75-84, 85+.</p></li>
<li><p><code>"fives"</code>, equivalent of: <code>1:20 * 5</code>. This will split on 0-4, 5-9, 10-14, ..., 90-94, 95-99, 100+.</p></li>
<li><p><code>"tens"</code>, equivalent of: <code>1:10 * 10</code>. This will split on 0-9, 10-19, 20-29, ... 80-89, 90-99, 100+.</p></li>
@ -291,39 +291,38 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>ages</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
<pre class="examples"># NOT RUN {
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
<span class='co'># split into 0-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)
# split into 0-49 and 50+
age_groups(ages, 50)
<span class='co'># split into 0-19, 20-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
# split into 0-19, 20-49 and 50+
age_groups(ages, c(20, 50))
<span class='co'># split into groups of ten years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)
# split into groups of ten years
age_groups(ages, 1:10 * 10)
age_groups(ages, split_at = "tens")
<span class='co'># split into groups of five years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)
# split into groups of five years
age_groups(ages, 1:20 * 5)
age_groups(ages, split_at = "fives")
<span class='co'># split specifically for children</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)
<span class='co'># same:</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
# split specifically for children
age_groups(ages, "children")
# same:
age_groups(ages, c(1, 2, 4, 6, 13, 17))
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span></pre>
# resistance of ciprofloxacine per age group
library(dplyr)
septic_patients %>%
filter_first_isolate) %>%
filter(mo == as.mo("E. coli")) %>%
group_by(age_group = age_groups(age)) %>%
select(age_group, CIP) %>%
ggplot_rsi(x = "age_group")
# }
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>

24
docs/reference/eucast_rules.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -311,15 +311,17 @@
<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>Available abbrevations of the column containing antibiotics in the form '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)':</p>
<p><strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<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><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>),
<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>CAP</strong>: capreomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30'>J04AB30</a>),
<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
@ -331,26 +333,28 @@
<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>ETH</strong>: ethambutol (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK02'>J04AK02</a>),
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XD01'>J01XD01</a>),
<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01XD01</a>),
<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
@ -358,14 +362,18 @@
<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>NOV</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01CF04</a>),
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>PZA</strong>: pyrazinamide (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK01'>J04AK01</a>),
<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>RIF</strong>: rifampin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),

36
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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -250,27 +250,27 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</div>
<pre class="usage"><span class='fu'>frequency_tbl</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>na</span> <span class='kw'>=</span> <span class='st'>"&lt;NA&gt;"</span>, <span class='kw'>droplevels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" "</span>, <span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>),
<span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span> <span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>))
<span class='fu'>freq</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>),
<pre class="usage"><span class='fu'>freq</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>),
<span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(),
<span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>na</span> <span class='kw'>=</span> <span class='st'>"&lt;NA&gt;"</span>, <span class='kw'>droplevels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" "</span>,
<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span>
<span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>))
<span class='fu'>frequency_tbl</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>na</span> <span class='kw'>=</span> <span class='st'>"&lt;NA&gt;"</span>, <span class='kw'>droplevels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" "</span>, <span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>),
<span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span> <span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>))
<span class='fu'>top_freq</span>(<span class='no'>f</span>, <span class='no'>n</span>)
<span class='fu'>header</span>(<span class='no'>f</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='co'># S3 method for frequency_tbl</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>,
<span class='kw'>default</span> <span class='kw'>=</span> <span class='fl'>15</span>), <span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='co'># S3 method for freq</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>, <span class='kw'>default</span> <span class='kw'>=</span> <span class='fl'>15</span>),
<span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span>
<span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>), <span class='no'>...</span>)</pre>
@ -361,7 +361,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A <code>data.frame</code> (with an additional class <code>"frequency_tbl"</code>) with five columns: <code>item</code>, <code>count</code>, <code>percent</code>, <code>cum_count</code> and <code>cum_percent</code>.</p>
<p>A <code>data.frame</code> (with an additional class <code>"freq"</code>) with five columns: <code>item</code>, <code>count</code>, <code>percent</code>, <code>cum_count</code> and <code>cum_percent</code>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@ -452,6 +452,16 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/hist'>hist</a></span>()
<span class='co'># or a boxplot of numeric values</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/boxplot'>boxplot</a></span>()
<span class='co'># or even a boxplot per group</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>age</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/boxplot'>boxplot</a></span>()
<span class='co'># or print all points to a regular plot</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>

4
docs/reference/index.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -454,7 +454,7 @@
</tr><tr>
<td>
<p><code><a href="freq.html">frequency_tbl()</a></code> <code><a href="freq.html">freq()</a></code> <code><a href="freq.html">top_freq()</a></code> <code><a href="freq.html">header()</a></code> <code><a href="freq.html">print(<i>&lt;frequency_tbl&gt;</i>)</a></code> </p>
<p><code><a href="freq.html">freq()</a></code> <code><a href="freq.html">frequency_tbl()</a></code> <code><a href="freq.html">top_freq()</a></code> <code><a href="freq.html">header()</a></code> <code><a href="freq.html">print(<i>&lt;freq&gt;</i>)</a></code> </p>
</td>
<td><p>Frequency table</p></td>
</tr><tr>

24
docs/reference/mdro.html
View File

@ -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="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -312,15 +312,17 @@
<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>Available abbrevations of the column containing antibiotics in the form '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)':</p>
<p><strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<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><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>),
<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>CAP</strong>: capreomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30'>J04AB30</a>),
<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
@ -332,26 +334,28 @@
<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>ETH</strong>: ethambutol (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK02'>J04AK02</a>),
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XD01'>J01XD01</a>),
<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01XD01</a>),
<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
@ -359,14 +363,18 @@
<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>NOV</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01CF04</a>),
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>PZA</strong>: pyrazinamide (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK01'>J04AK01</a>),
<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>RIF</strong>: rifampin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),

20
man/eucast_rules.Rd
View File

@ -61,16 +61,18 @@ In the source code the file containing all rules is located \href{https://gitlab
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.
Available abbrevations of the column containing antibiotics in the form '\strong{antimicrobial ID}: name (\emph{ATC code})':
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:
\strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\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}),
\strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
\strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
\strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
\strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
\strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
\strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
\strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
\strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
\strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
@ -82,26 +84,28 @@ Available abbrevations of the column containing antibiotics in the form '\strong
\strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
\strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
\strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
\strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
\strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
\strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
\strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
\strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
\strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
\strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
\strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
\strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
\strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
\strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
\strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
\strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
\strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
\strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
\strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
\strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
\strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
\strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
\strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
\strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
\strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01XD01}),
\strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
\strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
\strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
@ -109,14 +113,18 @@ Available abbrevations of the column containing antibiotics in the form '\strong
\strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
\strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
\strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
\strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01CF04}),
\strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
\strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
\strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
\strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
\strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
\strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
\strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
\strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
\strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
\strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
\strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
\strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
\strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),

32
man/freq.Rd
View File

@ -5,16 +5,9 @@
\alias{frequency_tbl}
\alias{top_freq}
\alias{header}
\alias{print.frequency_tbl}
\alias{print.freq}
\title{Frequency table}
\usage{
frequency_tbl(x, ..., sort.count = TRUE,
nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
markdown = !interactive(), digits = 2, quote = FALSE,
header = TRUE, title = NULL, na = "<NA>", droplevels = TRUE,
sep = " ", decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark != ",", ",", "."))
freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
digits = 2, quote = FALSE, header = TRUE, title = NULL,
@ -22,12 +15,19 @@ freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark !=
",", ",", "."))
frequency_tbl(x, ..., sort.count = TRUE,
nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
markdown = !interactive(), digits = 2, quote = FALSE,
header = TRUE, title = NULL, na = "<NA>", droplevels = TRUE,
sep = " ", decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark != ",", ",", "."))
top_freq(f, n)
header(f, property = NULL)
\method{print}{frequency_tbl}(x, nmax = getOption("max.print.freq",
default = 15), markdown = !interactive(), header = TRUE,
\method{print}{freq}(x, nmax = getOption("max.print.freq", default = 15),
markdown = !interactive(), header = TRUE,
decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark !=
",", ",", "."), ...)
}
@ -75,7 +75,7 @@ header(f, property = NULL)
\item{property}{property in header to return this value directly}
}
\value{
A \code{data.frame} (with an additional class \code{"frequency_tbl"}) with five columns: \code{item}, \code{count}, \code{percent}, \code{cum_count} and \code{cum_percent}.
A \code{data.frame} (with an additional class \code{"freq"}) with five columns: \code{item}, \code{count}, \code{percent}, \code{cum_count} and \code{cum_percent}.
}
\description{
Create a frequency table of a vector with items or a \code{data.frame}. Supports quasiquotation and markdown for reports. Best practice is: \code{data \%>\% freq(var)}.\cr
@ -173,6 +173,16 @@ septic_patients \%>\%
freq(age) \%>\%
hist()
# or a boxplot of numeric values
septic_patients \%>\%
freq(age) \%>\%
boxplot()
# or even a boxplot per group
septic_patients \%>\%
group_by(hospital_id) \%>\%
freq(age) \%>\%
boxplot()
# or print all points to a regular plot
septic_patients \%>\%

20
man/mdro.Rd
View File

@ -59,16 +59,18 @@ Other currently supported guidelines are:
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.
Available abbrevations of the column containing antibiotics in the form '\strong{antimicrobial ID}: name (\emph{ATC code})':
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:
\strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\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}),
\strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
\strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
\strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
\strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
\strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
\strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
\strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
\strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
\strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
\strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
@ -80,26 +82,28 @@ Available abbrevations of the column containing antibiotics in the form '\strong
\strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
\strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
\strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
\strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
\strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
\strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
\strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
\strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
\strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
\strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
\strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
\strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
\strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
\strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
\strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
\strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
\strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
\strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
\strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
\strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
\strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
\strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
\strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
\strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
\strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
\strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
\strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01XD01}),
\strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
\strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
\strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
@ -107,14 +111,18 @@ Available abbrevations of the column containing antibiotics in the form '\strong
\strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
\strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
\strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
\strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01CF04}),
\strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
\strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
\strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
\strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
\strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
\strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
\strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
\strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
\strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
\strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
\strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
\strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
\strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
\strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),

9
tests/testthat/test-freq.R
View File

@ -47,7 +47,10 @@ test_that("frequency table works", {
expect_output(print(freq(septic_patients$age, markdown = TRUE, title = "TITLE")))
# character
expect_output(suppressWarnings(print(freq(microorganisms$fullname))))
expect_output(print(freq(microorganisms$genus)))
expect_output(print(structure(freq(microorganisms$genus),
# check printing of old class:
class = c("frequency_tbl", "data.frame"))))
# mo
expect_output(print(freq(septic_patients$mo)))
# rsi
@ -121,9 +124,11 @@ test_that("frequency table works", {
# input must be freq tbl
expect_error(septic_patients %>% top_freq(1))
# charts from plot and hist, should not raise errors
# charts from plot, hist and boxplot, should not raise errors
plot(freq(septic_patients, age))
hist(freq(septic_patients, age))
boxplot(freq(septic_patients, age))
boxplot(freq(dplyr::group_by(septic_patients, gender), age))
# check vector
expect_identical(septic_patients %>%