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(v1.3.0.9000) support across() in as.rsi()

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dr. M.S. (Matthijs) Berends 2020-08-10 11:44:58 +02:00
parent 791bb6d33f
commit 0d9602a6a9
31 changed files with 378 additions and 141 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.3.0 Version: 1.3.0.9000
Date: 2020-07-31 Date: 2020-08-10
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

16
NEWS.md
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@ -1,5 +1,19 @@
# AMR 1.3.0 # AMR 1.3.0.9000
## <small>Last updated: 10 August 2020</small>
### Changed
* Support for using `dplyr`'s `across()` in `as.rsi()` to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.
```r
# until dplyr 1.0.0
your_data %>% mutate_if(is.mic, as.rsi)
your_data %>% mutate_if(is.disk, as.rsi)
# since dplyr 1.0.0
your_data %>% mutate(across(where(is.mic), as.rsi))
your_data %>% mutate(across(where(is.disk), as.rsi))
```
# AMR 1.3.0
### New ### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally

12
R/aa_helper_functions.R
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@ -202,11 +202,19 @@ stop_ifnot_installed <- function(package) {
return(invisible()) return(invisible())
} }
import_fn <- function(name, pkg) { import_fn <- function(name, pkg, error_on_fail = TRUE) {
if (isTRUE(error_on_fail)) {
stop_ifnot_installed(pkg) stop_ifnot_installed(pkg)
}
tryCatch( tryCatch(
get(name, envir = asNamespace(pkg)), get(name, envir = asNamespace(pkg)),
error = function(e) stop_("an error occurred in import_fn() while using this function", call = FALSE)) error = function(e) {
if (isTRUE(error_on_fail)) {
stop_("function ", name, "() not found in package '", pkg, "'. Please contact the maintainers of the AMR package at https://github.com/msberends/AMR/issues.", call = FALSE)
} else {
return(NULL)
}
})
} }
stop_ <- function(..., call = TRUE) { stop_ <- function(..., call = TRUE) {

131
R/rsi.R
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@ -21,11 +21,11 @@
#' Class 'rsi' #' Class 'rsi'
#' #'
#' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning. #' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Values that cannot be interpreted will be returned as `NA` with a warning.
#' @inheritSection lifecycle Stable lifecycle #' @inheritSection lifecycle Stable lifecycle
#' @rdname as.rsi #' @rdname as.rsi
#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres) #' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()] #' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()], will be determined automatically if the `dplyr` package is installed
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()] #' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See *Examples*. #' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate #' @inheritParams first_isolate
@ -34,15 +34,44 @@
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples* #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
#' @param ... parameters passed on to methods #' @param ... parameters passed on to methods
#' @details #' @details
#' When using [as.rsi()] on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class [`mic`] (using [as.mic()]) or class [`disk`] (using [as.disk()]), the data will be interpreted based on the guideline set with the `guideline` parameter. #' ## How it works
#' #'
#' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline. #' The [as.rsi()] function works in four ways:
#' #'
#' When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and will in this case return "S" or "I". #' 1. For **cleaning raw / untransformed data**. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as `"<0.25; S"` will be coerced to `"S"`. Combined interpretations for multiple test methods (as seen in laboratory records) such as `"S; S"` will be coerced to `"S"`, but a value like `"S; I"` will return `NA` with a warning that the input is unclear.
#'
#' 2. For **interpreting minimum inhibitory concentration (MIC) values** according to EUCAST or CLSI. You must clean your MIC values first using [as.mic()], that also gives your columns the new data class [`mic`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` parameter.
#' * Using `dplyr`, R/SI interpretation can be done very easily with either:
#' ```
#' your_data %>% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
#' your_data %>% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
#' ```
#' * Operators like "<=" will be stripped before interpretation. When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
#'
#' 3. For **interpreting disk diffusion diameters** according to EUCAST or CLSI. You must clean your disk zones first using [as.disk()], that also gives your columns the new data class [`disk`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` parameter.
#' * Using `dplyr`, R/SI interpretation can be done very easily with either:
#' ```
#' your_data %>% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
#' your_data %>% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
#' ```
#'
#' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(data)`.
#'
#' ## Supported guidelines
#'
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`.
#'
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
#'
#' ## After interpretation
#'
#' After using [as.rsi()], you can use the [eucast_rules()] defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'
#' ## Machine readable interpretation guidelines
#' #'
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. #' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
#' #'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism. #' ## Other
#' #'
#' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` parameter. #' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` parameter.
#' @section Interpretation of R and S/I: #' @section Interpretation of R and S/I:
@ -59,7 +88,7 @@
#' @return Ordered factor with new class [`rsi`] #' @return Ordered factor with new class [`rsi`]
#' @aliases rsi #' @aliases rsi
#' @export #' @export
#' @seealso [as.mic()] #' @seealso [as.mic()], [as.disk()], [as.mo()]
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' summary(example_isolates) # see all R/SI results at a glance #' summary(example_isolates) # see all R/SI results at a glance
@ -79,12 +108,12 @@
#' #'
#' # the dplyr way #' # the dplyr way
#' library(dplyr) #' library(dplyr)
#' df %>% mutate_at(vars(AMP:TOB), as.rsi)
#' df %>% mutate(across(AMP:TOB), as.rsi)
#' df %>% #' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli") #' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
#' #'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
#'
#' # to include information about urinary tract infections (UTI) #' # to include information about urinary tract infections (UTI)
#' data.frame(mo = "E. coli", #' data.frame(mo = "E. coli",
#' NIT = c("<= 2", 32), #' NIT = c("<= 2", 32),
@ -248,17 +277,42 @@ as.rsi.default <- function(x, ...) {
#' @rdname as.rsi #' @rdname as.rsi
#' @export #' @export
as.rsi.mic <- function(x, as.rsi.mic <- function(x,
mo, mo = NULL,
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
conserve_capped_values = FALSE, conserve_capped_values = FALSE,
...) { ...) {
stop_if(missing(mo),
'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n', # for dplyr's across()
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_column_dplyr)) {
# try to get current column, which will only be available when in across()
ab <- tryCatch(cur_column_dplyr(),
error = function(e) ab)
}
# for auto-determining mo
mo_var_found <- ""
if (is.null(mo)) {
peek_mask_dplyr <- import_fn("peek_mask", "dplyr", error_on_fail = FALSE)
if (!is.null(peek_mask_dplyr)) {
try({
df <- as.data.frame(peek_mask_dplyr()$across_cols(), stringsAsFactors = FALSE)
mo <- suppressMessages(search_type_in_df(df, "mo"))
if (!is.null(mo)) {
mo_var_found <- paste0(" based on column `", font_bold(mo), "`")
mo <- df[, mo, drop = TRUE]
}
}, silent = TRUE)
}
}
if (is.null(mo)) {
stop_('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use\n", "To transform certain columns with e.g. mutate_at(), use\n",
"`data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n\n", "`data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n\n",
"To tranform all MIC variables in a data set, use `as.rsi(data)` or `data %>% as.rsi()`.", call = FALSE) "To tranform all MIC variables in a data set, use `as.rsi(data)` or `data %>% as.rsi()`.", call = FALSE)
}
ab_coerced <- suppressWarnings(as.ab(ab)) ab_coerced <- suppressWarnings(as.ab(ab))
mo_coerced <- suppressWarnings(as.mo(mo)) mo_coerced <- suppressWarnings(as.mo(mo))
@ -276,7 +330,8 @@ as.rsi.mic <- function(x,
message(font_blue(paste0("=> Interpreting MIC values of `", font_bold(ab), "` (", message(font_blue(paste0("=> Interpreting MIC values of `", font_bold(ab), "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""), ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") using guideline ", font_bold(guideline_coerced), " ... ")), ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
" according to ", font_bold(guideline_coerced), " ... ")),
appendLF = FALSE) appendLF = FALSE)
result <- exec_as.rsi(method = "mic", result <- exec_as.rsi(method = "mic",
x = x, x = x,
@ -291,16 +346,41 @@ as.rsi.mic <- function(x,
#' @rdname as.rsi #' @rdname as.rsi
#' @export #' @export
as.rsi.disk <- function(x, as.rsi.disk <- function(x,
mo, mo = NULL,
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
...) { ...) {
stop_if(missing(mo),
'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n', # for dplyr's across()
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_column_dplyr)) {
# try to get current column, which will only be available when in across()
ab <- tryCatch(cur_column_dplyr(),
error = function(e) ab)
}
# for auto-determining mo
mo_var_found <- ""
if (is.null(mo)) {
peek_mask_dplyr <- import_fn("peek_mask", "dplyr", error_on_fail = FALSE)
if (!is.null(peek_mask_dplyr)) {
try({
df <- as.data.frame(peek_mask_dplyr()$across_cols(), stringsAsFactors = FALSE)
mo <- suppressMessages(search_type_in_df(df, "mo"))
if (!is.null(mo)) {
mo_var_found <- paste0(" based on column `", font_bold(mo), "`")
mo <- df[, mo, drop = TRUE]
}
}, silent = TRUE)
}
}
if (is.null(mo)) {
stop_('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use\n", "To transform certain columns with e.g. mutate_at(), use\n",
"`data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n\n", "`data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n\n",
"To tranform all disk diffusion zones in a data set, use `as.rsi(data)` or `data %>% as.rsi()`.", call = FALSE) "To tranform all disk diffusion zones in a data set, use `as.rsi(data)` or `data %>% as.rsi()`.", call = FALSE)
}
ab_coerced <- suppressWarnings(as.ab(ab)) ab_coerced <- suppressWarnings(as.ab(ab))
mo_coerced <- suppressWarnings(as.mo(mo)) mo_coerced <- suppressWarnings(as.mo(mo))
@ -573,12 +653,21 @@ summary.rsi <- function(object, ...) {
S <- sum(x == "S", na.rm = TRUE) S <- sum(x == "S", na.rm = TRUE)
I <- sum(x == "I", na.rm = TRUE) I <- sum(x == "I", na.rm = TRUE)
R <- sum(x == "R", na.rm = TRUE) R <- sum(x == "R", na.rm = TRUE)
pad <- function(x) {
if (x == "0%") {
x <- " 0.0%"
}
if (nchar(x) < 5) {
x <- paste0(rep(" ", 5 - nchar(x)), x)
}
x
}
value <- c( value <- c(
"Class" = "rsi", "Class" = "rsi",
"%R" = paste0(percentage(R / n), " (n=", R, ")"), "%R" = paste0(pad(percentage(R / n, digits = 1)), " (n=", R, ")"),
"%SI" = paste0(percentage((S + I) / n), " (n=", S + I, ")"), "%SI" = paste0(pad(percentage((S + I) / n, digits = 1)), " (n=", S + I, ")"),
"- %S" = paste0(percentage(S / n), " (n=", S, ")"), "- %S" = paste0(pad(percentage(S / n, digits = 1)), " (n=", S, ")"),
"- %I" = paste0(percentage(I / n), " (n=", I, ")") "- %I" = paste0(pad(percentage(I / n, digits = 1)), " (n=", I, ")")
) )
class(value) <- c("summaryDefault", "table") class(value) <- c("summaryDefault", "table")
value value

10
R/zzz.R
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@ -29,7 +29,15 @@
envir = asNamespace("AMR")) envir = asNamespace("AMR"))
} }
# maybe add survey later: "https://www.surveymonkey.com/r/AMR_for_R" .onAttach <- function(...) {
if (!interactive() || stats::runif(1) > 0.25 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
return()
}
packageStartupMessage("Thank you for using the AMR package! ",
"If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities:",
"\nhttps://msberends.github.io/AMR/survey.html",
"\n[ permanently turn this message off with: Sys.setenv(AMR_silentstart = TRUE) ]")
}
create_MO_lookup <- function() { create_MO_lookup <- function() {
MO_lookup <- AMR::microorganisms MO_lookup <- AMR::microorganisms

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

4
docs/articles/welcome_to_AMR.html
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@ -39,7 +39,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Welcome to the AMR package</h1> <h1 data-toc-skip>Welcome to the AMR package</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">31 July 2020</h4> <h4 class="date">10 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd"><code>vignettes/welcome_to_AMR.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<div class="hidden name"><code>welcome_to_AMR.Rmd</code></div> <div class="hidden name"><code>welcome_to_AMR.Rmd</code></div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

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docs/extra.css
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@ -237,3 +237,16 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
color: black; color: black;
font-weight: bold; font-weight: bold;
} }
.btn.btn-info.btn-amr {
background: #128f76;
color: #ffffff;
border-color: #128f76;
line-height: 1;
width: 100%;
font-weight: bold;
}
.btn.btn-info.btn-amr:hover {
background: #128f7645;
color: #2c3e50;
}

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@ -43,7 +43,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>
@ -192,7 +192,7 @@
</h1></div> </h1></div>
<blockquote> <blockquote>
<p><em>July 2020</em><br><span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> <strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br> <p><em>July 2020</em><br><span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> <strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br>
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!</p> Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! <br><a class="btn btn-info btn-amr">Take me to the 5-min survey!</a></p>
</blockquote> </blockquote>
<div id="what-is-amr-for-r" class="section level3"> <div id="what-is-amr-for-r" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

158
docs/news/index.html
View File

@ -81,7 +81,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>
@ -229,9 +229,35 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1309000" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9000">
<a href="#amr-1309000" class="anchor"></a>AMR 1.3.0.9000<small> Unreleased </small>
</h1>
<div id="last-updated-10-august-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-10-august-2020" class="anchor"></a><small>Last updated: 10 August 2020</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.</p>
<div class="sourceCode" id="cb1"><pre class="r"><span class="co"># until dplyr 1.0.0</span>
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate_if</span>(<span class="no">is.mic</span>, <span class="no">as.rsi</span>)
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate_if</span>(<span class="no">is.disk</span>, <span class="no">as.rsi</span>)
<span class="co"># since dplyr 1.0.0</span>
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(<span class="no">is.mic</span>), <span class="no">as.rsi</span>))
<span class="no">your_data</span> <span class="kw">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(<span class="no">is.disk</span>), <span class="no">as.rsi</span>))</pre></div>
</li>
</ul>
</div>
</div>
</div>
<div id="amr-130" class="section level1"> <div id="amr-130" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0"> <h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> Unreleased </small> <a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small>
</h1> </h1>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -240,7 +266,7 @@
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li> <li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li> <li>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p> <p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span> <span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
<span class="no">example_isolates</span> <span class="kw">%&gt;%</span> <span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
@ -255,9 +281,9 @@
<li><p>Added parameter <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li> <li><p>Added parameter <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
</ul> </ul>
</div> </div>
<div id="changed" class="section level3"> <div id="changed-1" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3> <a href="#changed-1" class="anchor"></a>Changed</h3>
<ul> <ul>
<li> <li>
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p> <p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
@ -331,9 +357,9 @@
</li> </li>
</ul> </ul>
</div> </div>
<div id="changed-1" class="section level3"> <div id="changed-2" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h3> <a href="#changed-2" class="anchor"></a>Changed</h3>
<ul> <ul>
<li>Taxonomy: <li>Taxonomy:
<ul> <ul>
@ -386,9 +412,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li> <li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
</ul> </ul>
</div> </div>
<div id="changed-2" class="section level3"> <div id="changed-3" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed-2" class="anchor"></a>Changed</h3> <a href="#changed-3" class="anchor"></a>Changed</h3>
<ul> <ul>
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally): <li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
<ul> <ul>
@ -420,14 +446,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="1.0.1"> <h1 class="page-header" data-toc-text="1.0.1">
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small> <a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small>
</h1> </h1>
<div id="changed-3" class="section level3"> <div id="changed-4" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed-3" class="anchor"></a>Changed</h3> <a href="#changed-4" class="anchor"></a>Changed</h3>
<ul> <ul>
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li> <li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li> <li>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p> <p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb2"><pre class="r"><span class="no">yourdata</span> <span class="kw">%&gt;%</span> <div class="sourceCode" id="cb3"><pre class="r"><span class="no">yourdata</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="st">"E. coli"</span>) <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="st">"E. coli"</span>)
<span class="no">yourdata</span> <span class="kw">%&gt;%</span> <span class="no">yourdata</span> <span class="kw">%&gt;%</span>
@ -454,7 +480,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul> <ul>
<li> <li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p> <p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
<div class="sourceCode" id="cb3"><pre class="r"><span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>) <div class="sourceCode" id="cb4"><pre class="r"><span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
<span class="co">#&gt; [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span> <span class="co">#&gt; [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>) <span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)
<span class="co">#&gt; [1] "Ampicillin"</span> <span class="co">#&gt; [1] "Ampicillin"</span>
@ -463,7 +489,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li> </li>
<li> <li>
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p> <p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
<div class="sourceCode" id="cb4"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>) <div class="sourceCode" id="cb5"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
<span class="co">#&gt; [1] 115329001 3092008 113961008</span> <span class="co">#&gt; [1] 115329001 3092008 113961008</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>) <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>)
<span class="co">#&gt; [1] "Staphylococcus aureus"</span> <span class="co">#&gt; [1] "Staphylococcus aureus"</span>
@ -526,9 +552,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul> <ul>
<li> <li>
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p> <p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
<div class="sourceCode" id="cb5"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="no">...</span></pre></div> <div class="sourceCode" id="cb6"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="no">...</span></pre></div>
<p>then please adjust this to:</p> <p>then please adjust this to:</p>
<div class="sourceCode" id="cb6"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacterales"</span>) <span class="no">...</span></pre></div> <div class="sourceCode" id="cb7"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacterales"</span>) <span class="no">...</span></pre></div>
</li> </li>
</ul> </ul>
</li> </li>
@ -540,7 +566,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul> <ul>
<li> <li>
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p> <p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
<div class="sourceCode" id="cb7"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <div class="sourceCode" id="cb8"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="no">example_isolates</span> <span class="kw">%&gt;%</span> <span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">bug</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">bug</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="kw">amoxicillin</span> <span class="kw">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>), <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="kw">amoxicillin</span> <span class="kw">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>),
@ -567,7 +593,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li> <li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
<li> <li>
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p> <p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
<div class="sourceCode" id="cb8"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>, <div class="sourceCode" id="cb9"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
<span class="st">"staphylokok aureuz"</span>)) <span class="st">"staphylokok aureuz"</span>))
<span class="co">#&gt; Warning: </span> <span class="co">#&gt; Warning: </span>
<span class="co">#&gt; Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span> <span class="co">#&gt; Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
@ -624,12 +650,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul> <ul>
<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="cb9"><pre class="r"><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">...</span>, <span class="kw">include_unknown</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></div> <div class="sourceCode" id="cb10"><pre class="r"><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">...</span>, <span class="kw">include_unknown</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></div>
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p> <p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
</li> </li>
<li> <li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p> <p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
<div class="sourceCode" id="cb10"><pre class="r"><span class="co"># how it works in base R:</span> <div class="sourceCode" id="cb11"><pre class="r"><span class="co"># how it works in base R:</span>
<span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>) <span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
<span class="no">x</span>[<span class="fl">1</span>] <span class="kw">&lt;-</span> <span class="st">"B"</span> <span class="no">x</span>[<span class="fl">1</span>] <span class="kw">&lt;-</span> <span class="st">"B"</span>
<span class="co">#&gt; Warning message:</span> <span class="co">#&gt; Warning message:</span>
@ -652,7 +678,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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 results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p> <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 results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<div class="sourceCode" id="cb11"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>) <div class="sourceCode" id="cb12"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>)
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span> <span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="no">x</span>[<span class="fl">1</span>:<span class="fl">4</span>, ] <span class="no">x</span>[<span class="fl">1</span>:<span class="fl">4</span>, ]
<span class="co">#&gt; mo ab S I R total</span> <span class="co">#&gt; mo ab S I R total</span>
@ -673,11 +699,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co">#&gt; 4 Gram-negative AMX 227 0 405 632</span> <span class="co">#&gt; 4 Gram-negative AMX 227 0 405 632</span>
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div> <span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></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://rdrr.io/r/base/format.html">format()</a></code> function:</p> <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://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<div class="sourceCode" id="cb12"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="no">x</span>, <span class="kw">combine_IR</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></div> <div class="sourceCode" id="cb13"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="no">x</span>, <span class="kw">combine_IR</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></div>
</li> </li>
<li> <li>
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility 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 antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility 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="cb13"><pre class="r"># -------------------------------------------------------------------- <div class="sourceCode" id="cb14"><pre class="r"># --------------------------------------------------------------------
# only_all_tested = FALSE only_all_tested = TRUE # only_all_tested = FALSE only_all_tested = TRUE
# ----------------------- ----------------------- # ----------------------- -----------------------
# Drug A Drug B include as include as include as include as # Drug A Drug B include as include as include as include as
@ -697,7 +723,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li> </li>
<li> <li>
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial 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><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial 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="cb14"><pre class="r"><span class="co"># (run this on your own console, as this page does not support colour printing)</span> <div class="sourceCode" id="cb15"><pre class="r"><span class="co"># (run this on your own console, as this page does not support colour printing)</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>) <span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="no">example_isolates</span> <span class="kw">%&gt;%</span> <span class="no">example_isolates</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">mo</span>:<span class="no">AMC</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">mo</span>:<span class="no">AMC</span>) <span class="kw">%&gt;%</span>
@ -705,9 +731,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li> </li>
</ul> </ul>
</div> </div>
<div id="changed-4" class="section level3"> <div id="changed-5" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed-4" class="anchor"></a>Changed</h3> <a href="#changed-5" class="anchor"></a>Changed</h3>
<ul> <ul>
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms. <li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
<ul> <ul>
@ -778,7 +804,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul> <ul>
<li> <li>
<p>Function <code><a href="../reference/proportion.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/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p> <p>Function <code><a href="../reference/proportion.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/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb15"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <div class="sourceCode" id="cb16"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">AMX</span>, <span class="no">CIP</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">AMX</span>, <span class="no">CIP</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>() <span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>()
<span class="co"># antibiotic interpretation value isolates</span> <span class="co"># antibiotic interpretation value isolates</span>
@ -803,7 +829,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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="cb16"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>) <div class="sourceCode" id="cb17"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
<span class="co"># B_ESCHR_COL</span> <span class="co"># B_ESCHR_COL</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>) <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
<span class="co"># "Escherichia coli"</span> <span class="co"># "Escherichia coli"</span>
@ -814,9 +840,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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>
</ul> </ul>
</div> </div>
<div id="changed-5" class="section level4"> <div id="changed-6" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-5" class="anchor"></a>Changed</h4> <a href="#changed-6" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> are now lowercase</li> <li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li> <li>Fixed bug in translation of microorganism names</li>
@ -863,9 +889,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li> <li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
</ul> </ul>
</div> </div>
<div id="changed-6" class="section level4"> <div id="changed-7" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-6" class="anchor"></a>Changed</h4> <a href="#changed-7" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li> <li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li> <li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
@ -906,7 +932,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>when all values are unique it now shows a message instead of a warning</p></li> <li><p>when all values are unique it now shows a message instead of a warning</p></li>
<li> <li>
<p>support for boxplots:</p> <p>support for boxplots:</p>
<div class="sourceCode" id="cb17"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <div class="sourceCode" id="cb18"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">age</span>) <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">age</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>() <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
<span class="co"># grouped boxplots:</span> <span class="co"># grouped boxplots:</span>
@ -948,9 +974,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.6.1"> <h1 class="page-header" data-toc-text="0.6.1">
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small> <a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
</h1> </h1>
<div id="changed-7" class="section level4"> <div id="changed-8" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-7" class="anchor"></a>Changed</h4> <a href="#changed-8" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code> <li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
</li> </li>
@ -999,7 +1025,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</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="cb18"><pre class="r"><span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>() <div class="sourceCode" id="cb19"><pre class="r"><span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>() <span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>() <span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>() <span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()
@ -1011,14 +1037,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>() <span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</pre></div> <span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</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="cb19"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>) <div class="sourceCode" id="cb20"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span> <span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>, <span class="kw">scope</span> <span class="kw">=</span> <span class="st">"all"</span>) <span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>, <span class="kw">scope</span> <span class="kw">=</span> <span class="st">"all"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></pre></div> <span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></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="cb20"><pre class="r"><span class="no">ab_property</span> <span class="kw">-&gt;</span> <span class="fu">atc_property</span>() <div class="sourceCode" id="cb21"><pre class="r"><span class="no">ab_property</span> <span class="kw">-&gt;</span> <span class="fu">atc_property</span>()
<span class="no">ab_name</span> <span class="kw">-&gt;</span> <span class="fu">atc_name</span>() <span class="no">ab_name</span> <span class="kw">-&gt;</span> <span class="fu">atc_name</span>()
<span class="no">ab_official</span> <span class="kw">-&gt;</span> <span class="fu">atc_official</span>() <span class="no">ab_official</span> <span class="kw">-&gt;</span> <span class="fu">atc_official</span>()
<span class="no">ab_trivial_nl</span> <span class="kw">-&gt;</span> <span class="fu">atc_trivial_nl</span>() <span class="no">ab_trivial_nl</span> <span class="kw">-&gt;</span> <span class="fu">atc_trivial_nl</span>()
@ -1037,17 +1063,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>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.</p></li> <li><p>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.</p></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://rdrr.io/r/base/plot.html">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://rdrr.io/r/base/plot.html">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="cb21"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="no">septic_patients</span>, <span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"amox"</span>) <div class="sourceCode" id="cb22"><pre class="r"><span class="no">x</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="no">septic_patients</span>, <span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"amox"</span>)
<span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">x</span>) <span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">x</span>)
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">x</span>)</pre></div> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">x</span>)</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="cb22"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">...</span>) <div class="sourceCode" id="cb23"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">...</span>)
<span class="co"># or</span> <span class="co"># or</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)</pre></div> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)</pre></div>
<p>is equal to:</p> <p>is equal to:</p>
<div class="sourceCode" id="cb23"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <div class="sourceCode" id="cb24"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">only_firsts</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">only_firsts</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">only_firsts</span> <span class="kw">==</span> <span class="fl">TRUE</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">only_firsts</span> <span class="kw">==</span> <span class="fl">TRUE</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">only_firsts</span>)</pre></div> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">only_firsts</span>)</pre></div>
@ -1056,9 +1082,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li> <li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul> </ul>
</div> </div>
<div id="changed-8" class="section level4"> <div id="changed-9" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-8" class="anchor"></a>Changed</h4> <a href="#changed-9" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>: <li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul> <ul>
@ -1078,7 +1104,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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="cb24"><pre class="r"><span class="co"># mo_fullname() uses as.mo() internally</span> <div class="sourceCode" id="cb25"><pre class="r"><span class="co"># mo_fullname() uses as.mo() internally</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>) <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)
<span class="co">#&gt; [1] "Staphylococcus aureus"</span> <span class="co">#&gt; [1] "Staphylococcus aureus"</span>
@ -1088,7 +1114,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</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="cb25"><pre class="r"><span class="co"># equal:</span> <div class="sourceCode" id="cb26"><pre class="r"><span class="co"># equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">TRUE</span>) <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">2</span>) <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">2</span>)
@ -1101,7 +1127,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>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.</p></li> <li><p>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.</p></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="cb26"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>) <div class="sourceCode" id="cb27"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>)
<span class="co"># Warning: </span> <span class="co"># Warning: </span>
<span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span> <span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
<span class="co">#&gt; [1] "(género desconocido)"</span></pre></div> <span class="co">#&gt; [1] "(género desconocido)"</span></pre></div>
@ -1149,7 +1175,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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="cb27"><pre class="r"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span> <div class="sourceCode" id="cb28"><pre class="r"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<span class="co"># OLD WAY</span> <span class="co"># OLD WAY</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%&gt;%</span>
@ -1207,9 +1233,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li> <li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
</ul> </ul>
</div> </div>
<div id="changed-9" class="section level4"> <div id="changed-10" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-9" class="anchor"></a>Changed</h4> <a href="#changed-10" class="anchor"></a>Changed</h4>
<ul> <ul>
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li> <li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li> <li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
@ -1231,7 +1257,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li> <li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></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="cb28"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span> <div class="sourceCode" id="cb29"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span> <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></pre></div> <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></pre></div>
@ -1246,13 +1272,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul> <ul>
<li> <li>
<p>Support for grouping variables, test with:</p> <p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb29"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <div class="sourceCode" id="cb30"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">gender</span>)</pre></div> <span class="fu">freq</span>(<span class="no">gender</span>)</pre></div>
</li> </li>
<li> <li>
<p>Support for (un)selecting columns:</p> <p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb30"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <div class="sourceCode" id="cb31"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span>
<span class="fu">freq</span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">hospital_id</span>) <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">count</span>, -<span class="no">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span></pre></div> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">count</span>, -<span class="no">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span></pre></div>
</li> </li>
@ -1330,7 +1356,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</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="cb31"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>) <div class="sourceCode" id="cb32"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] "Gram negative"</span> <span class="co"># [1] "Gram negative"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>) <span class="co"># German</span> <span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>) <span class="co"># German</span>
<span class="co"># [1] "Gramnegativ"</span> <span class="co"># [1] "Gramnegativ"</span>
@ -1339,7 +1365,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span> <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span>
<span class="co"># [1] "Streptococcus grupo A"</span></pre></div> <span class="co"># [1] "Streptococcus grupo A"</span></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="cb32"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>) <div class="sourceCode" id="cb33"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span> <span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
<span class="co"># [1] "Gram negative"</span></pre></div> <span class="co"># [1] "Gram negative"</span></pre></div>
</li> </li>
@ -1352,14 +1378,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li> <li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></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="cb33"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>) <div class="sourceCode" id="cb34"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] B_ESCHR_COL</span> <span class="co"># [1] B_ESCHR_COL</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>) <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)
<span class="co"># [1] B_STPHY_AUR</span> <span class="co"># [1] B_STPHY_AUR</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>) <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)
<span class="co"># [1] B_STRPTC_GRA</span></pre></div> <span class="co"># [1] B_STRPTC_GRA</span></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="cb34"><pre class="r"><span class="no">thousands_of_E_colis</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>) <div class="sourceCode" id="cb35"><pre class="r"><span class="no">thousands_of_E_colis</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
<span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">thousands_of_E_colis</span>), <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"s"</span>) <span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">thousands_of_E_colis</span>), <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"s"</span>)
<span class="co"># Unit: seconds</span> <span class="co"># Unit: seconds</span>
<span class="co"># min median max neval</span> <span class="co"># min median max neval</span>
@ -1384,14 +1410,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li> <li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
</ul> </ul>
</div> </div>
<div id="changed-10" class="section level4"> <div id="changed-11" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-10" class="anchor"></a>Changed</h4> <a href="#changed-11" class="anchor"></a>Changed</h4>
<ul> <ul>
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li> <li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></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="cb35"><pre class="r"><span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>) <div class="sourceCode" id="cb36"><pre class="r"><span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
<span class="co"># [1] "Mupirocin"</span> <span class="co"># [1] "Mupirocin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>)) <span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
<span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span> <span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span>
@ -1406,7 +1432,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li> <li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></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="cb36"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>() <div class="sourceCode" id="cb37"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>) <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
<span class="co"># which is the same as:</span> <span class="co"># which is the same as:</span>
<span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>) <span class="no">septic_patients</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>)
@ -1424,10 +1450,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li> <li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></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="cb37"><pre class="r"><span class="no">my_matrix</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="no">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">age</span>, <span class="no">gender</span>), <span class="kw">ncol</span> <span class="kw">=</span> <span class="fl">2</span>)) <div class="sourceCode" id="cb38"><pre class="r"><span class="no">my_matrix</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="no">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">age</span>, <span class="no">gender</span>), <span class="kw">ncol</span> <span class="kw">=</span> <span class="fl">2</span>))
<span class="fu">freq</span>(<span class="no">my_matrix</span>)</pre></div> <span class="fu">freq</span>(<span class="no">my_matrix</span>)</pre></div>
<p>For lists, subsetting is possible:</p> <p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb38"><pre class="r"><span class="no">my_list</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw">age</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">age</span>, <span class="kw">gender</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">gender</span>) <div class="sourceCode" id="cb39"><pre class="r"><span class="no">my_list</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw">age</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">age</span>, <span class="kw">gender</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">gender</span>)
<span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">age</span>) <span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">age</span>)
<span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">gender</span>)</pre></div> <span class="no">my_list</span> <span class="kw">%&gt;%</span> <span class="fu">freq</span>(<span class="no">gender</span>)</pre></div>
</li> </li>
@ -1518,9 +1544,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li> </li>
</ul> </ul>
</div> </div>
<div id="changed-11" class="section level4"> <div id="changed-12" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-11" class="anchor"></a>Changed</h4> <a href="#changed-12" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li> <li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
<li>More antibiotics added as parameters for EUCAST rules</li> <li>More antibiotics added as parameters for EUCAST rules</li>
@ -1604,9 +1630,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li> <li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
</ul> </ul>
</div> </div>
<div id="changed-12" class="section level4"> <div id="changed-13" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed-12" class="anchor"></a>Changed</h4> <a href="#changed-13" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li> <li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code> <li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>

2
docs/pkgdown.yml
View File

@ -11,7 +11,7 @@ articles:
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-07-31T09:39Z last_built: 2020-08-10T09:44Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

2
docs/reference/ab_from_text.html
View File

@ -82,7 +82,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

2
docs/reference/ab_property.html
View File

@ -82,7 +82,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

2
docs/reference/antibiotic_class_selectors.html
View File

@ -82,7 +82,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

61
docs/reference/as.rsi.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Class 'rsi' — as.rsi" /> <meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." /> <meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Values that cannot be interpreted will be returned as NA with a warning." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>
@ -232,7 +232,7 @@
</div> </div>
<div class="ref-description"> <div class="ref-description">
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p> <p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Values that cannot be interpreted will be returned as <code>NA</code> with a warning.</p>
</div> </div>
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>) <pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
@ -244,7 +244,7 @@
<span class='co'># S3 method for mic</span> <span class='co'># S3 method for mic</span>
<span class='fu'>as.rsi</span>( <span class='fu'>as.rsi</span>(
<span class='no'>x</span>, <span class='no'>x</span>,
<span class='no'>mo</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)), <span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)),
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
@ -255,7 +255,7 @@
<span class='co'># S3 method for disk</span> <span class='co'># S3 method for disk</span>
<span class='fu'>as.rsi</span>( <span class='fu'>as.rsi</span>(
<span class='no'>x</span>, <span class='no'>x</span>,
<span class='no'>mo</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)), <span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)),
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
@ -289,7 +289,7 @@
</tr> </tr>
<tr> <tr>
<th>mo</th> <th>mo</th>
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td> <td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>, will be determined automatically if the <code>dplyr</code> package is installed</p></td>
</tr> </tr>
<tr> <tr>
<th>ab</th> <th>ab</th>
@ -318,12 +318,46 @@
<p>Ordered factor with new class <code>rsi</code></p> <p>Ordered factor with new class <code>rsi</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
<p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p> <h3>How it works</h3>
<p>When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and will in this case return "S" or "I".</p>
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.mic</span>, <span class='no'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='no'>is.mic</span>), <span class='no'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.disk</span>, <span class='no'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='no'>your_data</span> <span class='kw'>%&amp;gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='no'>is.disk</span>), <span class='no'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
</ol>
<h3>Supported guidelines</h3>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
<h3>After interpretation</h3>
<p>After using <code>as.rsi()</code>, you can use the <code><a href='eucast_rules.html'>eucast_rules()</a></code> defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<h3>Machine readable interpretation guidelines</h3>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p> <p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<h3>Other</h3>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p> <p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2> <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -352,7 +386,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p> <p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div> <div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span> <pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
@ -372,12 +406,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># the dplyr way</span> <span class='co'># the dplyr way</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>)
<span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>)
<span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>) <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>)
<span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.rsi</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='no'>.</span>$<span class='no'>microorganism</span>)
<span class='co'># to include information about urinary tract infections (UTI)</span> <span class='co'># to include information about urinary tract infections (UTI)</span>
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>, <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
<span class='kw'>NIT</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>), <span class='kw'>NIT</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

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@ -82,7 +82,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

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@ -81,7 +81,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

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@ -82,7 +82,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

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@ -81,7 +81,7 @@
</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">1.3.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9000</span>
</span> </span>
</div> </div>

2
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@ -3,6 +3,8 @@
> *July 2020*<br> > *July 2020*<br>
> <span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> **PLEASE TAKE PART IN OUR SURVEY!** > <span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> **PLEASE TAKE PART IN OUR SURVEY!**
> Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. **If you have a minute, please [anonymously fill in this short questionnaire](./survey.html)**. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! > Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. **If you have a minute, please [anonymously fill in this short questionnaire](./survey.html)**. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!
> <br>
> <a class="btn btn-info btn-amr">Take me to the 5-min survey!</a>
### What is `AMR` (for R)? ### What is `AMR` (for R)?

55
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@ -18,7 +18,7 @@ is.rsi.eligible(x, threshold = 0.05)
\method{as.rsi}{mic}( \method{as.rsi}{mic}(
x, x,
mo, mo = NULL,
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
@ -28,7 +28,7 @@ is.rsi.eligible(x, threshold = 0.05)
\method{as.rsi}{disk}( \method{as.rsi}{disk}(
x, x,
mo, mo = NULL,
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
@ -51,7 +51,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}} \item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}} \item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}, will be determined automatically if the \code{dplyr} package is installed}
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}} \item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
@ -67,21 +67,53 @@ is.rsi.eligible(x, threshold = 0.05)
Ordered factor with new class \code{\link{rsi}} Ordered factor with new class \code{\link{rsi}}
} }
\description{ \description{
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning. Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Values that cannot be interpreted will be returned as \code{NA} with a warning.
} }
\details{ \details{
When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class \code{\link{mic}} (using \code{\link[=as.mic]{as.mic()}}) or class \code{\link{disk}} (using \code{\link[=as.disk]{as.disk()}}), the data will be interpreted based on the guideline set with the \code{guideline} parameter. \subsection{How it works}{
Supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using \code{"CLSI"} or \code{"EUCAST"} for input will automatically select the latest version of that guideline. The \code{\link[=as.rsi]{as.rsi()}} function works in four ways:
\enumerate{
\item For \strong{cleaning raw / untransformed data}. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as \code{"<0.25; S"} will be coerced to \code{"S"}. Combined interpretations for multiple test methods (as seen in laboratory records) such as \code{"S; S"} will be coerced to \code{"S"}, but a value like \code{"S; I"} will return \code{NA} with a warning that the input is unclear.
\item For \strong{interpreting minimum inhibitory concentration (MIC) values} according to EUCAST or CLSI. You must clean your MIC values first using \code{\link[=as.mic]{as.mic()}}, that also gives your columns the new data class \code{\link{mic}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} parameter.
\itemize{
\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
}
\item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
}
\item For \strong{interpreting disk diffusion diameters} according to EUCAST or CLSI. You must clean your disk zones first using \code{\link[=as.disk]{as.disk()}}, that also gives your columns the new data class \code{\link{disk}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} parameter.
\itemize{
\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
}
}
\item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(data)}.
}
}
When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and will in this case return "S" or "I". \subsection{Supported guidelines}{
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
}
\subsection{After interpretation}{
After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast_rules]{eucast_rules()}} defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
}
\subsection{Machine readable interpretation guidelines}{
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
}
After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism. \subsection{Other}{
The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} parameter. The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} parameter.
} }
}
\section{Interpretation of R and S/I}{ \section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}).
@ -128,12 +160,11 @@ as.rsi(df)
# the dplyr way # the dplyr way
library(dplyr) library(dplyr)
df \%>\% mutate_at(vars(AMP:TOB), as.rsi)
df \%>\% mutate(across(AMP:TOB), as.rsi)
df \%>\% df \%>\%
mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli") mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
df \%>\%
mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
# to include information about urinary tract infections (UTI) # to include information about urinary tract infections (UTI)
data.frame(mo = "E. coli", data.frame(mo = "E. coli",
NIT = c("<= 2", 32), NIT = c("<= 2", 32),
@ -190,5 +221,5 @@ is.rsi.eligible(WHONET$`First name`, threshold = 0.99) # succeeds
} }
} }
\seealso{ \seealso{
\code{\link[=as.mic]{as.mic()}} \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}}, \code{\link[=as.mo]{as.mo()}}
} }

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pkgdown/extra.css
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@ -237,3 +237,16 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
color: black; color: black;
font-weight: bold; font-weight: bold;
} }
.btn.btn-info.btn-amr {
background: #128f76;
color: #ffffff;
border-color: #128f76;
line-height: 1;
width: 100%;
font-weight: bold;
}
.btn.btn-info.btn-amr:hover {
background: #128f7645;
color: #2c3e50;
}

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pkgdown/logos/countries.png
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pkgdown/logos/countries_large.png
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8
tests/testthat/test-rsi.R
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@ -39,10 +39,10 @@ test_that("rsi works", {
expect_equal(summary(as.rsi(c("S", "R"))), expect_equal(summary(as.rsi(c("S", "R"))),
structure(c("Class" = "rsi", structure(c("Class" = "rsi",
"%R" = "50% (n=1)", "%R" = "50.0% (n=1)",
"%SI" = "50% (n=1)", "%SI" = "50.0% (n=1)",
"- %S" = "50% (n=1)", "- %S" = "50.0% (n=1)",
"- %I" = "0% (n=0)"), class = c("summaryDefault", "table"))) "- %I" = " 0.0% (n=0)"), class = c("summaryDefault", "table")))
expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)), expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
rep(FALSE, length(example_isolates))) rep(FALSE, length(example_isolates)))