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(v0.7.1.9059) bug_drug_combinations

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dr. M.S. (Matthijs) Berends 2019-08-25 22:53:22 +02:00
parent 7c069145ac
commit e46cb0399f
23 changed files with 1081 additions and 230 deletions
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6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.1.9058 Version: 0.7.1.9059
Date: 2019-08-20 Date: 2019-08-25
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
@ -30,7 +30,7 @@ Depends:
R (>= 3.1.0) R (>= 3.1.0)
Imports: Imports:
backports, backports,
clean, clean (>= 1.1.0),
crayon (>= 1.3.0), crayon (>= 1.3.0),
data.table (>= 1.9.0), data.table (>= 1.9.0),
dplyr (>= 0.7.0), dplyr (>= 0.7.0),

10
NAMESPACE
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@ -23,6 +23,7 @@ S3method(c,ab)
S3method(c,mo) S3method(c,mo)
S3method(droplevels,mic) S3method(droplevels,mic)
S3method(droplevels,rsi) S3method(droplevels,rsi)
S3method(format,bugdrug)
S3method(freq,mo) S3method(freq,mo)
S3method(freq,rsi) S3method(freq,rsi)
S3method(kurtosis,data.frame) S3method(kurtosis,data.frame)
@ -37,6 +38,7 @@ S3method(plot,mic)
S3method(plot,resistance_predict) S3method(plot,resistance_predict)
S3method(plot,rsi) S3method(plot,rsi)
S3method(print,ab) S3method(print,ab)
S3method(print,bugdrug)
S3method(print,catalogue_of_life_version) S3method(print,catalogue_of_life_version)
S3method(print,disk) S3method(print,disk)
S3method(print,mic) S3method(print,mic)
@ -81,6 +83,7 @@ export(atc_online_groups)
export(atc_online_property) export(atc_online_property)
export(availability) export(availability)
export(brmo) export(brmo)
export(bug_drug_combinations)
export(catalogue_of_life_version) export(catalogue_of_life_version)
export(count_I) export(count_I)
export(count_IR) export(count_IR)
@ -108,6 +111,7 @@ export(filter_glycopeptides)
export(filter_macrolides) export(filter_macrolides)
export(filter_tetracyclines) export(filter_tetracyclines)
export(first_isolate) export(first_isolate)
export(freq)
export(full_join_microorganisms) export(full_join_microorganisms)
export(g.test) export(g.test)
export(geom_rsi) export(geom_rsi)
@ -197,6 +201,7 @@ exportMethods(c.ab)
exportMethods(c.mo) exportMethods(c.mo)
exportMethods(droplevels.mic) exportMethods(droplevels.mic)
exportMethods(droplevels.rsi) exportMethods(droplevels.rsi)
exportMethods(format.bugdrug)
exportMethods(freq.mo) exportMethods(freq.mo)
exportMethods(freq.rsi) exportMethods(freq.rsi)
exportMethods(kurtosis) exportMethods(kurtosis)
@ -206,6 +211,7 @@ exportMethods(kurtosis.matrix)
exportMethods(plot.mic) exportMethods(plot.mic)
exportMethods(plot.rsi) exportMethods(plot.rsi)
exportMethods(print.ab) exportMethods(print.ab)
exportMethods(print.bugdrug)
exportMethods(print.catalogue_of_life_version) exportMethods(print.catalogue_of_life_version)
exportMethods(print.disk) exportMethods(print.disk)
exportMethods(print.mic) exportMethods(print.mic)
@ -223,6 +229,7 @@ exportMethods(summary.mic)
exportMethods(summary.mo) exportMethods(summary.mo)
exportMethods(summary.rsi) exportMethods(summary.rsi)
importFrom(clean,freq) importFrom(clean,freq)
importFrom(clean,freq.default)
importFrom(clean,top_freq) importFrom(clean,top_freq)
importFrom(crayon,bgGreen) importFrom(crayon,bgGreen)
importFrom(crayon,bgRed) importFrom(crayon,bgRed)
@ -272,6 +279,7 @@ importFrom(dplyr,n_distinct)
importFrom(dplyr,n_groups) importFrom(dplyr,n_groups)
importFrom(dplyr,progress_estimated) importFrom(dplyr,progress_estimated)
importFrom(dplyr,pull) importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,row_number) importFrom(dplyr,row_number)
importFrom(dplyr,select) importFrom(dplyr,select)
importFrom(dplyr,select_if) importFrom(dplyr,select_if)
@ -300,6 +308,8 @@ importFrom(stats,glm)
importFrom(stats,lm) importFrom(stats,lm)
importFrom(stats,pchisq) importFrom(stats,pchisq)
importFrom(stats,predict) importFrom(stats,predict)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(utils,browseURL) importFrom(utils,browseURL)
importFrom(utils,installed.packages) importFrom(utils,installed.packages)
importFrom(utils,menu) importFrom(utils,menu)

20
NEWS.md
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@ -1,7 +1,7 @@
# AMR 0.7.1.9058 # AMR 0.7.1.9059
### Breaking ### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too. * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). The `freq()` function still works, since it is re-exported from the `clean` package to this `AMR` package. Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`: * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
```r ```r
first_isolate(..., include_unknown = TRUE) first_isolate(..., include_unknown = TRUE)
@ -9,6 +9,21 @@
For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default, since `as.mo("con") = "UNKNOWN"`. The function always shows a note with the number of 'unknown' microorganisms that were included or excluded. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default, since `as.mo("con") = "UNKNOWN"`. The function always shows a note with the number of 'unknown' microorganisms that were included or excluded.
### New ### New
* Function `bug_drug_combinations()` to quickly get a `data.frame` with the antimicrobial resistance of any bug-drug combination in a data set:
```r
x <- bug_drug_combinations(septic_patients)
x
#> ab mo S I R total
#> 1 AMC B_ESCHR_COL 332 74 61 467
#> 2 AMC B_KLBSL_PNE 49 3 6 58
#> 3 AMC B_PROTS_MIR 28 7 1 36
#> 4 AMC B_PSDMN_AER 0 0 30 30
#> 5 AMC B_STPHY_AUR 234 0 1 235
```
You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R `format()` function:
```r
format(x)
```
* Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for `portion_*` functions or `count_*` functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter `only_all_tested` (**which defaults to `FALSE`**) replaces the old `also_single_tested` and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the `portion` and `count` help pages), where the %SI is being determined: * Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for `portion_*` functions or `count_*` functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter `only_all_tested` (**which defaults to `FALSE`**) replaces the old `also_single_tested` and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the `portion` and `count` help pages), where the %SI is being determined:
```r ```r
@ -72,6 +87,7 @@
* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations * Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
* Improved `filter_ab_class()` to be more reliable and to support 5th generation cephalosporins * Improved `filter_ab_class()` to be more reliable and to support 5th generation cephalosporins
* Classes `ab` and `mo` will now be preserved in any subsetting * Classes `ab` and `mo` will now be preserved in any subsetting
* Function `availability()` now uses `portion_R()` instead of `portion_IR()`, to comply with EUCAST insights
#### Other #### Other
* Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors * Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors

25
R/availability.R
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@ -21,9 +21,10 @@
#' Check availability of columns #' Check availability of columns
#' #'
#' Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}. #' Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. \code{\link{portion_R}}.
#' @param tbl a \code{data.frame} or \code{list} #' @param tbl a \code{data.frame} or \code{list}
#' @param width number of characters to present the visual availability, defaults to filling the width of the console #' @param width number of characters to present the visual availability, defaults to filling the width of the console
#' @details The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{portion_R}}.
#' @return \code{data.frame} with column names of \code{tbl} as row names #' @return \code{data.frame} with column names of \code{tbl} as row names
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @export #' @export
@ -44,10 +45,10 @@
availability <- function(tbl, width = NULL) { availability <- function(tbl, width = NULL) {
x <- base::sapply(tbl, function(x) { 1 - base::sum(base::is.na(x)) / base::length(x) }) x <- base::sapply(tbl, function(x) { 1 - base::sum(base::is.na(x)) / base::length(x) })
n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)])) n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)]))
IR <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), portion_IR(x, minimum = 0), NA)) R <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), portion_R(x, minimum = 0), NA))
IR_print <- character(length(IR)) R_print <- character(length(R))
IR_print[!is.na(IR)] <- percent(IR[!is.na(IR)], round = 1, force_zero = TRUE) R_print[!is.na(R)] <- percent(R[!is.na(R)], round = 1, force_zero = TRUE)
IR_print[is.na(IR)] <- "" R_print[is.na(R)] <- ""
if (is.null(width)) { if (is.null(width)) {
width <- options()$width - width <- options()$width -
@ -63,14 +64,14 @@ availability <- function(tbl, width = NULL) {
width <- width / 2 width <- width / 2
} }
if (length(IR[is.na(IR)]) == ncol(tbl)) { if (length(R[is.na(R)]) == ncol(tbl)) {
width <- width * 2 + 10 width <- width * 2 + 10
} }
x_chars_IR <- strrep("#", round(width * IR, digits = 2)) x_chars_R <- strrep("#", round(width * R, digits = 2))
x_chars_S <- strrep("-", width - nchar(x_chars_IR)) x_chars_SI <- strrep("-", width - nchar(x_chars_R))
vis_resistance <- paste0("|", x_chars_IR, x_chars_S, "|") vis_resistance <- paste0("|", x_chars_R, x_chars_SI, "|")
vis_resistance[is.na(IR)] <- "" vis_resistance[is.na(R)] <- ""
x_chars <- strrep("#", round(x, digits = 2) / (1 / width)) x_chars <- strrep("#", round(x, digits = 2) / (1 / width))
x_chars_empty <- strrep("-", width - nchar(x_chars)) x_chars_empty <- strrep("-", width - nchar(x_chars))
@ -78,9 +79,9 @@ availability <- function(tbl, width = NULL) {
df <- data.frame(count = n, df <- data.frame(count = n,
available = percent(x, round = 1, force_zero = TRUE), available = percent(x, round = 1, force_zero = TRUE),
visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"), visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"),
resistant = IR_print, resistant = R_print,
visual_resistance = vis_resistance) visual_resistance = vis_resistance)
if (length(IR[is.na(IR)]) == ncol(tbl)) { if (length(R[is.na(R)]) == ncol(tbl)) {
df[,1:3] df[,1:3]
} else { } else {
df df

107
R/bug_drug_combinations.R Normal file
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@ -0,0 +1,107 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Determine bug-drug combinations
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
#' @inheritParams eucast_rules
#' @inheritParams rsi_df
#' @importFrom dplyr rename
#' @importFrom tidyr spread
#' @importFrom clean freq
#' @export
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website!
#' @examples
#' \donttest{
#' x <- bug_drug_combinations(septic_patients)
#' x
#' format(x)
#' }
bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
if (!is.data.frame(x)) {
stop("`x` must be a data frame.", call. = FALSE)
}
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
x <- x %>%
mutate(col_mo = x %>% pull(col_mo)) %>%
filter(mo %in% (clean::freq(mo) %>%
filter(count >= minimum) %>%
pull(item))) %>%
group_by(mo) %>%
AMR::rsi_df(translate_ab = FALSE, combine_SI = FALSE) %>%
select(-value) %>%
spread(interpretation, isolates) %>%
mutate(total = S + I + R) %>%
filter(total >= minimum) %>%
rename(ab = antibiotic)
structure(.Data = x, class = c("bugdrug", class(x)))
}
#' @importFrom dplyr everything rename
#' @importFrom tidyr spread
#' @exportMethod format.bugdrug
#' @export
format.bugdrug <- function(x, combine_SI = TRUE, add_ab_group = TRUE, ...) {
if (combine_SI == TRUE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I
}
y <- x %>%
mutate(mo = mo_name(mo),
txt = paste0(AMR:::percent(isolates / total, force_zero = TRUE),
" (", trimws(format(isolates, big.mark = ",")), "/",
trimws(format(total, big.mark = ",")), ")")) %>%
select(ab, mo, txt) %>%
spread(mo, txt) %>%
mutate_all(~ifelse(is.na(.), "", .)) %>%
mutate(ab = paste0(ab_name(ab), " (", as.ab(ab), ", ", ab_atc(ab), ")"),
ab_group = ab_group(ab)) %>%
select(ab_group, ab, everything()) %>%
arrange(ab_group, ab) %>%
mutate(ab_group = ifelse(ab_group != lag(ab_group) | is.na(lag(ab_group)), ab_group, ""))
if (add_ab_group == FALSE) {
y <- y %>% select(-ab_group)
}
y <- y %>% rename("Group" = ab_group,
"Antibiotic" = ab)
y
}
#' @exportMethod print.bugdrug
#' @export
#' @importFrom crayon blue
print.bugdrug <- function(x, ...) {
print(as.data.frame(x, stringsAsFactors = FALSE))
message(blue("NOTE: Use 'format()' on this result to get a format that is ready for export or printing."))
}

32
R/freq.R
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@ -19,23 +19,25 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. # # Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== # # ==================================================================== #
freq_def <- clean:::freq.default #' @importFrom clean freq
#' @export
clean::freq
#' @exportMethod freq.mo #' @exportMethod freq.mo
#' @importFrom dplyr n_distinct #' @importFrom dplyr n_distinct
#' @importFrom clean freq #' @importFrom clean freq.default
#' @export #' @export
#' @noRd #' @noRd
freq.mo <- function(x, ...) { freq.mo <- function(x, ...) {
# replace with freq.default() if next `clean` version is published on CRAN freq.default(x = x, ...,
freq_def(x = x, ..., .add_header = list(families = n_distinct(mo_family(x, language = NULL)),
.add_header = list(families = n_distinct(mo_family(x, language = NULL)), genera = n_distinct(mo_genus(x, language = NULL)),
genera = n_distinct(mo_genus(x, language = NULL)), species = n_distinct(paste(mo_genus(x, language = NULL),
species = n_distinct(paste(mo_genus(x, language = NULL), mo_species(x, language = NULL)))))
mo_species(x, language = NULL)))))
} }
#' @exportMethod freq.rsi #' @exportMethod freq.rsi
#' @importFrom clean freq #' @importFrom clean freq.default
#' @export #' @export
#' @noRd #' @noRd
freq.rsi <- function(x, ...) { freq.rsi <- function(x, ...) {
@ -43,12 +45,12 @@ freq.rsi <- function(x, ...) {
x_name <- gsub(".*[$]", "", x_name) x_name <- gsub(".*[$]", "", x_name)
ab <- suppressMessages(suppressWarnings(AMR::as.ab(x_name))) ab <- suppressMessages(suppressWarnings(AMR::as.ab(x_name)))
if (!is.na(ab)) { if (!is.na(ab)) {
freq_def(x = x, ..., freq.default(x = x, ...,
.add_header = list(Drug = paste0(ab_name(ab), " (", ab, ", ", ab_atc(ab), ")"), .add_header = list(Drug = paste0(ab_name(ab), " (", ab, ", ", ab_atc(ab), ")"),
group = ab_group(ab), group = ab_group(ab),
`%SI` = portion_SI(x, minimum = 0, as_percent = TRUE))) `%SI` = AMR::portion_SI(x, minimum = 0, as_percent = TRUE)))
} else { } else {
freq_def(x = x, ..., freq.default(x = x, ...,
.add_header = list(`%SI` = portion_SI(x, minimum = 0, as_percent = TRUE))) .add_header = list(`%SI` = AMR::portion_SI(x, minimum = 0, as_percent = TRUE)))
} }
} }

21
R/rsi_calc.R
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@ -169,6 +169,7 @@ rsi_calc <- function(...,
} }
#' @importFrom dplyr %>% summarise_if mutate select everything bind_rows #' @importFrom dplyr %>% summarise_if mutate select everything bind_rows
#' @importFrom tidyr gather
rsi_calc_df <- function(type, # "portion" or "count" rsi_calc_df <- function(type, # "portion" or "count"
data, data,
translate_ab = "name", translate_ab = "name",
@ -187,10 +188,10 @@ rsi_calc_df <- function(type, # "portion" or "count"
combine_SI <- FALSE combine_SI <- FALSE
} }
if (isTRUE(combine_SI) & isTRUE(combine_IR)) { if (isTRUE(combine_SI) & isTRUE(combine_IR)) {
stop("either `combine_SI` or `combine_IR` can be TRUE", call. = FALSE) stop("either `combine_SI` or `combine_IR` can be TRUE, not both", call. = FALSE)
} }
if (data %>% select_if(is.rsi) %>% ncol() == 0) { if (!any(sapply(data, is.rsi), na.rm = TRUE)) {
stop("No columns with class 'rsi' found. See ?as.rsi.", call. = FALSE) stop("No columns with class 'rsi' found. See ?as.rsi.", call. = FALSE)
} }
@ -198,7 +199,7 @@ rsi_calc_df <- function(type, # "portion" or "count"
translate_ab <- "name" translate_ab <- "name"
} }
get_summaryfunction <- function(int) { get_summaryfunction <- function(int, type) {
# look for portion_S, count_S, etc: # look for portion_S, count_S, etc:
int_fn <- get(paste0(type, "_", int), envir = asNamespace("AMR")) int_fn <- get(paste0(type, "_", int), envir = asNamespace("AMR"))
@ -218,11 +219,11 @@ rsi_calc_df <- function(type, # "portion" or "count"
select(interpretation, everything()) select(interpretation, everything())
} }
resS <- get_summaryfunction("S") resS <- get_summaryfunction("S", type)
resI <- get_summaryfunction("I") resI <- get_summaryfunction("I", type)
resR <- get_summaryfunction("R") resR <- get_summaryfunction("R", type)
resSI <- get_summaryfunction("SI") resSI <- get_summaryfunction("SI", type)
resIR <- get_summaryfunction("IR") resIR <- get_summaryfunction("IR", type)
data.groups <- group_vars(data) data.groups <- group_vars(data)
if (isFALSE(combine_SI) & isFALSE(combine_IR)) { if (isFALSE(combine_SI) & isFALSE(combine_IR)) {
@ -245,11 +246,11 @@ rsi_calc_df <- function(type, # "portion" or "count"
} }
res <- res %>% res <- res %>%
tidyr::gather(antibiotic, value, -interpretation, -data.groups) %>% gather(antibiotic, value, -interpretation, -data.groups) %>%
select(antibiotic, everything()) select(antibiotic, everything())
if (!translate_ab == FALSE) { if (!translate_ab == FALSE) {
res <- res %>% mutate(antibiotic = ab_property(antibiotic, property = translate_ab, language = language)) res <- res %>% mutate(antibiotic = AMR::ab_property(antibiotic, property = translate_ab, language = language))
} }
res res

1
R/rsi_df.R
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@ -21,7 +21,6 @@
#' @rdname portion #' @rdname portion
#' @rdname count #' @rdname count
#' @importFrom dplyr %>% select_if bind_rows summarise_if mutate group_vars select everything
#' @export #' @export
rsi_df <- function(data, rsi_df <- function(data,
translate_ab = "name", translate_ab = "name",

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9059</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9059</span>
</span> </span>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9059</span>
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9059</span>
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9059</span>
</span> </span>
</div> </div>
@ -225,15 +225,15 @@
</div> </div>
<div id="amr-0-7-1-9058" class="section level1"> <div id="amr-0-7-1-9059" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9058" class="anchor"></a>AMR 0.7.1.9058<small> Unreleased </small> <a href="#amr-0-7-1-9059" class="anchor"></a>AMR 0.7.1.9059<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3> <a href="#breaking" class="anchor"></a>Breaking</h3>
<ul> <ul>
<li>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the <code>freq()</code> function. The <a href="https://github.com/msberends/clean"><code>clean</code></a> package is available on CRAN and will be installed automatically when updating the <code>AMR</code> package, that now imports it. In a later stage, the <code><a href="../reference/skewness.html">skewness()</a></code> and <code><a href="../reference/kurtosis.html">kurtosis()</a></code> functions will be moved to the <code>clean</code> package too.</li> <li>Function <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>). The <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package to this <code>AMR</code> package. Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function. The <a href="https://github.com/msberends/clean"><code>clean</code></a> package is available on CRAN and will be installed automatically when updating the <code>AMR</code> package, that now imports it. In a later stage, the <code><a href="../reference/skewness.html">skewness()</a></code> and <code><a href="../reference/kurtosis.html">kurtosis()</a></code> functions will be moved to the <code>clean</code> package too.</li>
<li> <li>
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p> <p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(..., <span class="dt">include_unknown =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(..., <span class="dt">include_unknown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
@ -246,30 +246,43 @@
<a href="#new" class="anchor"></a>New</h3> <a href="#new" class="anchor"></a>New</h3>
<ul> <ul>
<li> <li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the antimicrobial resistance of any bug-drug combination in a data set:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(septic_patients)</a>
<a class="sourceLine" id="cb2-2" data-line-number="2">x</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co">#&gt; ab mo S I R total</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">#&gt; 1 AMC B_ESCHR_COL 332 74 61 467</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co">#&gt; 2 AMC B_KLBSL_PNE 49 3 6 58</span></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co">#&gt; 3 AMC B_PROTS_MIR 28 7 1 36</span></a>
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co">#&gt; 4 AMC B_PSDMN_AER 0 0 30 30</span></a>
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co">#&gt; 5 AMC B_STPHY_AUR 234 0 1 235</span></a></code></pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://www.rdocumentation.org/packages/base/topics/format">format()</a></code> function:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/format">format</a></span>(x)</a></code></pre></div>
</li>
<li>
<p>Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p> <p>Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="co"># -------------------------------------------------------------------------</span></a> <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co"># -------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></a> <a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co"># Antibiotic Antibiotic ----------------------- -----------------------</span></a> <a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co"># Antibiotic Antibiotic ----------------------- -----------------------</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># A B include as include as include as include as</span></a> <a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># A B include as include as include as include as</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># numerator denominator numerator denominator</span></a> <a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co"># numerator denominator numerator denominator</span></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># ---------- ---------- ---------- ----------- ---------- -----------</span></a> <a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># ---------- ---------- ---------- ----------- ---------- -----------</span></a>
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># S S X X X X</span></a> <a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># S S X X X X</span></a>
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># I S X X X X</span></a> <a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># I S X X X X</span></a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># R S X X X X</span></a> <a class="sourceLine" id="cb4-9" data-line-number="9"><span class="co"># R S X X X X</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># not tested S X X - -</span></a> <a class="sourceLine" id="cb4-10" data-line-number="10"><span class="co"># not tested S X X - -</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># S I X X X X</span></a> <a class="sourceLine" id="cb4-11" data-line-number="11"><span class="co"># S I X X X X</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># I I X X X X</span></a> <a class="sourceLine" id="cb4-12" data-line-number="12"><span class="co"># I I X X X X</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># R I X X X X</span></a> <a class="sourceLine" id="cb4-13" data-line-number="13"><span class="co"># R I X X X X</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># not tested I X X - -</span></a> <a class="sourceLine" id="cb4-14" data-line-number="14"><span class="co"># not tested I X X - -</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co"># S R X X X X</span></a> <a class="sourceLine" id="cb4-15" data-line-number="15"><span class="co"># S R X X X X</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="co"># I R X X X X</span></a> <a class="sourceLine" id="cb4-16" data-line-number="16"><span class="co"># I R X X X X</span></a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="co"># R R - X - X</span></a> <a class="sourceLine" id="cb4-17" data-line-number="17"><span class="co"># R R - X - X</span></a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># not tested R - - - -</span></a> <a class="sourceLine" id="cb4-18" data-line-number="18"><span class="co"># not tested R - - - -</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># S not tested X X - -</span></a> <a class="sourceLine" id="cb4-19" data-line-number="19"><span class="co"># S not tested X X - -</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># I not tested X X - -</span></a> <a class="sourceLine" id="cb4-20" data-line-number="20"><span class="co"># I not tested X X - -</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># R not tested - - - -</span></a> <a class="sourceLine" id="cb4-21" data-line-number="21"><span class="co"># R not tested - - - -</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># not tested not tested - - - -</span></a> <a class="sourceLine" id="cb4-22" data-line-number="22"><span class="co"># not tested not tested - - - -</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># -------------------------------------------------------------------------</span></a></code></pre></div> <a class="sourceLine" id="cb4-23" data-line-number="23"><span class="co"># -------------------------------------------------------------------------</span></a></code></pre></div>
<p>Since this is a major change, usage of the old <code>also_single_tested</code> will throw an informative error that it has been replaced by <code>only_all_tested</code>.</p> <p>Since this is a major change, usage of the old <code>also_single_tested</code> will throw an informative error that it has been replaced by <code>only_all_tested</code>.</p>
</li> </li>
</ul> </ul>
@ -291,11 +304,11 @@
<li>Improved the internal auto-guessing function for determining antibiotics in your data set (<code>AMR:::get_column_abx()</code>)</li> <li>Improved the internal auto-guessing function for determining antibiotics in your data set (<code>AMR:::get_column_abx()</code>)</li>
<li> <li>
<p>Added tibble printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using tibbles containing antibiotic columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p> <p>Added tibble printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using tibbles containing antibiotic columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a> <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a> <a class="sourceLine" id="cb5-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb3-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb5-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb5-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb5-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
</li> </li>
<li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li> <li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li>
<li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code> <li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code>
@ -318,7 +331,8 @@
<li>The <code>antibiotics</code> data set is now sorted by name and all cephalosporins now have their generation between brackets</li> <li>The <code>antibiotics</code> data set is now sorted by name and all cephalosporins now have their generation between brackets</li>
<li>Speed improvement for <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30 times faster for antibiotic abbreviations</li> <li>Speed improvement for <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30 times faster for antibiotic abbreviations</li>
<li>Improved <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> to be more reliable and to support 5th generation cephalosporins</li> <li>Improved <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> to be more reliable and to support 5th generation cephalosporins</li>
<li><p>Classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting</p></li> <li>Classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting</li>
<li><p>Function <code><a href="../reference/availability.html">availability()</a></code> now uses <code><a href="../reference/portion.html">portion_R()</a></code> instead of <code><a href="../reference/portion.html">portion_IR()</a></code>, to comply with EUCAST insights</p></li>
</ul> </ul>
<div id="other" class="section level4"> <div id="other" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
@ -339,14 +353,14 @@
<ul> <ul>
<li> <li>
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p> <p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a> <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(AMX, CIP) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb6-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(AMX, CIP) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a> <a class="sourceLine" id="cb6-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a> <a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a> <a class="sourceLine" id="cb6-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a> <a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a> <a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div> <a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
</li> </li>
<li> <li>
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p> <p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
@ -364,12 +378,12 @@
<li>UPEC (Uropathogenic <em>E. coli</em>)</li> <li>UPEC (Uropathogenic <em>E. coli</em>)</li>
</ul> </ul>
<p>All these lead to the microbial ID of <em>E. coli</em>:</p> <p>All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a> <a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a> <a class="sourceLine" id="cb7-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a> <a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a> <a class="sourceLine" id="cb7-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div> <a class="sourceLine" id="cb7-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
</li> </li>
<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li> <li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li> <li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
@ -461,21 +475,21 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li> <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code>rsi()</code> <li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code>rsi()</code>
</li> </li>
<li>Frequency tables (<code>freq()</code>): <li>Frequency tables (<code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code>):
<ul> <ul>
<li>speed improvement for microbial IDs</li> <li>speed improvement for microbial IDs</li>
<li>fixed factor level names for R Markdown</li> <li>fixed factor level names for R Markdown</li>
<li>when all values are unique it now shows a message instead of a warning</li> <li>when all values are unique it now shows a message instead of a warning</li>
<li> <li>
<p>support for boxplots:</p> <p>support for boxplots:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="st"> </span><span class="kw">freq</span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb8-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-3" data-line-number="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="cb8-3" data-line-number="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="cb6-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a> <a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb8-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb8-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="st"> </span><span class="kw">freq</span>(age) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb8-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="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> <a class="sourceLine" id="cb8-8" data-line-number="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> </li>
</ul> </ul>
</li> </li>
@ -485,7 +499,7 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em> <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li> </li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li> <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code> <li>Fix for <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> for when all values are <code>NA</code>
</li> </li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li> <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -560,32 +574,32 @@ This data is updated annually - check the included version with the new function
</li> </li>
<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> <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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a> <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a> <a class="sourceLine" id="cb9-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb9-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb9-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb9-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb9-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb7-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb9-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb7-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a> <a class="sourceLine" id="cb9-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
<a class="sourceLine" id="cb7-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a> <a class="sourceLine" id="cb9-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
<a class="sourceLine" id="cb7-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a> <a class="sourceLine" id="cb9-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb9-11" data-line-number="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> <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="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><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> <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><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="cb8-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a> <a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
<a class="sourceLine" id="cb8-3" data-line-number="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="cb10-3" data-line-number="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="cb8-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div> <a class="sourceLine" id="cb10-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
</li> </li>
<li> <li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p> <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">ab_property -&gt;<span class="st"> </span><span class="kw">atc_property</span>()</a> <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">ab_property -&gt;<span class="st"> </span><span class="kw">atc_property</span>()</a>
<a class="sourceLine" id="cb9-2" data-line-number="2">ab_name -&gt;<span class="st"> </span><span class="kw">atc_name</span>()</a> <a class="sourceLine" id="cb11-2" data-line-number="2">ab_name -&gt;<span class="st"> </span><span class="kw">atc_name</span>()</a>
<a class="sourceLine" id="cb9-3" data-line-number="3">ab_official -&gt;<span class="st"> </span><span class="kw">atc_official</span>()</a> <a class="sourceLine" id="cb11-3" data-line-number="3">ab_official -&gt;<span class="st"> </span><span class="kw">atc_official</span>()</a>
<a class="sourceLine" id="cb9-4" data-line-number="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a> <a class="sourceLine" id="cb11-4" data-line-number="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
<a class="sourceLine" id="cb9-5" data-line-number="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a> <a class="sourceLine" id="cb11-5" data-line-number="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
<a class="sourceLine" id="cb9-6" data-line-number="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a> <a class="sourceLine" id="cb11-6" data-line-number="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
<a class="sourceLine" id="cb9-7" data-line-number="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div> <a class="sourceLine" id="cb11-7" data-line-number="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
These functions use <code><a href="../reference/AMR-deprecated.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> These functions use <code><a href="../reference/AMR-deprecated.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>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> <li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
@ -597,20 +611,20 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
<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>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> <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> <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="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="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> <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="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="cb10-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a> <a class="sourceLine" id="cb12-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div> <a class="sourceLine" id="cb12-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
</li> </li>
<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> <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="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a> <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="co"># or</span></a> <a class="sourceLine" id="cb13-2" data-line-number="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb11-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div> <a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
<p>is equal to:</p> <p>is equal to:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a> <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></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="cb14-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></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="cb12-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">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="cb14-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">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="cb12-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>only_firsts)</a></code></pre></div> <a class="sourceLine" id="cb14-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
</li> </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>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> </li>
@ -639,33 +653,33 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
<ul> <ul>
<li> <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> <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="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a> <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
<a class="sourceLine" id="cb13-2" data-line-number="2"></a> <a class="sourceLine" id="cb15-2" data-line-number="2"></a>
<a class="sourceLine" id="cb13-3" data-line-number="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="cb15-3" data-line-number="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="cb13-4" data-line-number="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a> <a class="sourceLine" id="cb15-4" data-line-number="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
<a class="sourceLine" id="cb13-5" data-line-number="5"></a> <a class="sourceLine" id="cb15-5" data-line-number="5"></a>
<a class="sourceLine" id="cb13-6" data-line-number="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="cb15-6" data-line-number="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="cb13-7" data-line-number="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div> <a class="sourceLine" id="cb15-7" data-line-number="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
</li> </li>
<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> <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="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1"><span class="co"># equal:</span></a> <div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="co"># equal:</span></a>
<a class="sourceLine" id="cb14-2" data-line-number="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="cb16-2" data-line-number="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="cb14-3" data-line-number="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="cb16-3" data-line-number="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="cb14-4" data-line-number="4"></a> <a class="sourceLine" id="cb16-4" data-line-number="4"></a>
<a class="sourceLine" id="cb14-5" data-line-number="5"><span class="co"># also equal:</span></a> <a class="sourceLine" id="cb16-5" data-line-number="5"><span class="co"># also equal:</span></a>
<a class="sourceLine" id="cb14-6" data-line-number="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="cb16-6" data-line-number="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="cb14-7" data-line-number="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> <a class="sourceLine" id="cb16-7" data-line-number="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> 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>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
</li> </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>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> <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> <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="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="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> <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="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="cb15-2" data-line-number="2"><span class="co"># Warning: </span></a> <a class="sourceLine" id="cb17-2" data-line-number="2"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb15-3" data-line-number="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="cb17-3" data-line-number="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="cb15-4" data-line-number="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div> <a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
</li> </li>
<li>Fix for vector containing only empty values</li> <li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li> <li>Finds better results when input is in other languages</li>
@ -707,23 +721,23 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
</ul> </ul>
</li> </li>
<li>Frequency tables (<code>freq()</code> function): <li>Frequency tables (<code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function):
<ul> <ul>
<li> <li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p> <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a> <div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<a class="sourceLine" id="cb16-2" data-line-number="2"><span class="co"># OLD WAY</span></a> <a class="sourceLine" id="cb18-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb16-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb18-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></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="cb18-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></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="cb16-5" data-line-number="5"><span class="st"> </span><span class="kw">freq</span>(genus)</a> <a class="sourceLine" id="cb18-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># NEW WAY</span></a> <a class="sourceLine" id="cb18-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb16-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb18-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb16-8" data-line-number="8"><span class="st"> </span><span class="kw">freq</span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a> <a class="sourceLine" id="cb18-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb16-9" data-line-number="9"></a> <a class="sourceLine" id="cb18-9" data-line-number="9"></a>
<a class="sourceLine" id="cb16-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a> <a class="sourceLine" id="cb18-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb16-11" data-line-number="11">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb18-11" data-line-number="11">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb16-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb18-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb16-13" data-line-number="13"><span class="st"> </span><span class="kw">freq</span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div> <a class="sourceLine" id="cb18-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
</li> </li>
<li>Header info is now available as a list, with the <code>header</code> function</li> <li>Header info is now available as a list, with the <code>header</code> function</li>
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li> <li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@ -798,10 +812,10 @@ 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>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li> <li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p> <p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a> <div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a> <a class="sourceLine" id="cb19-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a> <a class="sourceLine" id="cb19-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div> <a class="sourceLine" id="cb19-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li> <li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li> <li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@ -810,19 +824,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code> <li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code>
</li> </li>
<li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li> <li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li>
<li>Frequency tables - <code>freq()</code>: <li>Frequency tables - <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code>:
<ul> <ul>
<li> <li>
<p>Support for grouping variables, test with:</p> <p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb20-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-3" data-line-number="3"><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div> <a class="sourceLine" id="cb20-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(gender)</a></code></pre></div>
</li> </li>
<li> <li>
<p>Support for (un)selecting columns:</p> <p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="st"> </span><span class="kw">freq</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></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> <a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li> </li>
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/Deprecated">hms::is.hms</a></code> <li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/Deprecated">hms::is.hms</a></code>
</li> </li>
@ -902,18 +916,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
</ul> </ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p> <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a> <div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a> <a class="sourceLine" id="cb22-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb20-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a> <a class="sourceLine" id="cb22-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb20-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a> <a class="sourceLine" id="cb22-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb20-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a> <a class="sourceLine" id="cb22-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb20-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a> <a class="sourceLine" id="cb22-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a> <a class="sourceLine" id="cb22-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div> <a class="sourceLine" id="cb22-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p> <p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a> <div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a> <a class="sourceLine" id="cb23-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div> <a class="sourceLine" id="cb23-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</li> </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 <li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul> <ul>
@ -924,18 +938,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
<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> <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="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a> <div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a> <a class="sourceLine" id="cb24-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb22-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a> <a class="sourceLine" id="cb24-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb22-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a> <a class="sourceLine" id="cb24-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb22-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a> <a class="sourceLine" id="cb24-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb22-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div> <a class="sourceLine" id="cb24-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p> <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="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a> <div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb23-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a> <a class="sourceLine" id="cb25-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb23-3" data-line-number="3"><span class="co"># Unit: seconds</span></a> <a class="sourceLine" id="cb25-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb23-4" data-line-number="4"><span class="co"># min median max neval</span></a> <a class="sourceLine" id="cb25-4" data-line-number="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb23-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div> <a class="sourceLine" id="cb25-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li> <li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like: <li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
@ -963,12 +977,12 @@ 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>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<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> <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="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a> <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb24-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a> <a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb24-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a> <a class="sourceLine" id="cb26-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb24-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a> <a class="sourceLine" id="cb26-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb24-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a> <a class="sourceLine" id="cb26-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb24-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div> <a class="sourceLine" id="cb26-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</li> </li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li> <li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li> <li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@ -979,13 +993,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
<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> <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="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></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> <div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></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="cb25-2" data-line-number="2"><span class="co"># which is the same as:</span></a> <a class="sourceLine" id="cb27-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb25-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a> <a class="sourceLine" id="cb27-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb25-4" data-line-number="4"></a> <a class="sourceLine" id="cb27-4" data-line-number="4"></a>
<a class="sourceLine" id="cb25-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a> <a class="sourceLine" id="cb27-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb25-6" data-line-number="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a> <a class="sourceLine" id="cb27-6" data-line-number="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb25-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div> <a class="sourceLine" id="cb27-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
</li> </li>
<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>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li> <li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
@ -999,12 +1013,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
<li> <li>
<p>Support for types (classes) list and matrix for <code>freq</code></p> <p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a> <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="kw">freq</span>(my_matrix)</a></code></pre></div> <a class="sourceLine" id="cb28-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p> <p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a> <div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb27-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">freq</span>(age)</a> <a class="sourceLine" id="cb29-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age)</a>
<a class="sourceLine" id="cb27-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div> <a class="sourceLine" id="cb29-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(gender)</a></code></pre></div>
</li> </li>
</ul> </ul>
</div> </div>
@ -1078,13 +1092,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul> <ul>
<li>A vignette to explain its usage</li> <li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li> <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code> <li>Support for <code>table</code> to use as input: <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq(table(x, y))</a></code>
</li> </li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://www.rdocumentation.org/packages/graphics/topics/hist">hist(freq(df$age))</a></code> <li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://www.rdocumentation.org/packages/graphics/topics/hist">hist(freq(df$age))</a></code>
</li> </li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code> <li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li> </li>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code> <li>Support for quasiquotation: <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li> </li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li> <li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li> <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
@ -1238,7 +1252,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9058">0.7.1.9058</a></li> <li><a href="#amr-0-7-1-9059">0.7.1.9059</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

14
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@ -47,7 +47,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Check availability of columns — availability" /> <meta property="og:title" content="Check availability of columns — availability" />
<meta property="og:description" content="Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. portion_IR." /> <meta property="og:description" content="Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. portion_R." />
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9059</span>
</span> </span>
</div> </div>
@ -230,7 +230,7 @@
<div class="ref-description"> <div class="ref-description">
<p>Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. <code><a href='portion.html'>portion_IR</a></code>.</p> <p>Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. <code><a href='portion.html'>portion_R</a></code>.</p>
</div> </div>
@ -253,6 +253,10 @@
<p><code>data.frame</code> with column names of <code>tbl</code> as row names</p> <p><code>data.frame</code> with column names of <code>tbl</code> as row names</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function returns a <code>data.frame</code> with columns <code>"resistant"</code> and <code>"visual_resistance"</code>. The values in that columns are calculated with <code><a href='portion.html'>portion_R</a></code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -283,6 +287,8 @@
<li><a href="#value">Value</a></li> <li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li> <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li> <li><a href="#examples">Examples</a></li>
@ -293,7 +299,7 @@
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<h1>Determine bug-drug combinations</h1>
<div class="hidden name"><code>bug_drug_combinations.Rd</code></div>
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<div class="ref-description">
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code>format</code> on the result to prettify it to a printable format, see Examples.</p>
</div>
<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
</tr>
<tr>
<th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr>
<tr>
<th>minimum</th>
<td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>septic_patients</span>)
<span class='no'>x</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>x</span>)
<span class='co'># }</span></pre>
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<h1>Objects exported from other packages</h1>
<div class="hidden name"><code>reexports.Rd</code></div>
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<p>These objects are imported from other packages. Follow the links
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<dt>clean</dt><dd><p><code><a href='https://www.rdocumentation.org/packages/clean/topics/freq'>freq</a></code></p></dd>
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<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/availability.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/availability.html</loc>
</url> </url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/bug_drug_combinations.html</loc>
</url>
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<loc>https://msberends.gitlab.io/AMR/reference/catalogue_of_life.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/catalogue_of_life.html</loc>
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@ -117,6 +120,9 @@
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/read.4D.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/read.4D.html</loc>
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<loc>https://msberends.gitlab.io/AMR/reference/resistance_predict.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/resistance_predict.html</loc>
</url> </url>

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@ -15,7 +15,10 @@ availability(tbl, width = NULL)
\code{data.frame} with column names of \code{tbl} as row names \code{data.frame} with column names of \code{tbl} as row names
} }
\description{ \description{
Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}. Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. \code{\link{portion_R}}.
}
\details{
The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{portion_R}}.
} }
\section{Read more on our website!}{ \section{Read more on our website!}{

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/bug_drug_combinations.R
\name{bug_drug_combinations}
\alias{bug_drug_combinations}
\title{Determine bug-drug combinations}
\source{
\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
}
\usage{
bug_drug_combinations(x, col_mo = NULL, minimum = 30)
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
}
\description{
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
}
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\examples{
\donttest{
x <- bug_drug_combinations(septic_patients)
x
format(x)
}
}

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/freq.R
\docType{import}
\name{reexports}
\alias{reexports}
\alias{freq}
\title{Objects exported from other packages}
\keyword{internal}
\description{
These objects are imported from other packages. Follow the links
below to see their documentation.
\describe{
\item{clean}{\code{\link[clean]{freq}}}
}}

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("bug_drug_combinations.R")
test_that("bug_drug_combinations works", {
b <- suppressWarnings(bug_drug_combinations(septic_patients))
expect_s3_class(b, "bugdrug")
expect_message(print(b))
expect_true(is.data.frame(format(b)))
})