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v1.8.1
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6
.github/workflows/check.yaml
vendored
6
.github/workflows/check.yaml
vendored
@ -57,8 +57,8 @@ jobs:
|
||||
- {os: macOS-latest, r: '3.6', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.5', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.4', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.3', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.2', allowfail: false}
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# - {os: macOS-latest, r: '3.3', allowfail: false}
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# - {os: macOS-latest, r: '3.2', allowfail: false}
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# - {os: macOS-latest, r: '3.1', allowfail: true}
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||||
# - {os: macOS-latest, r: '3.0', allowfail: true}
|
||||
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
@ -77,7 +77,7 @@ jobs:
|
||||
- {os: windows-latest, r: '3.6', allowfail: false}
|
||||
- {os: windows-latest, r: '3.5', allowfail: false}
|
||||
- {os: windows-latest, r: '3.4', allowfail: false}
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||||
- {os: windows-latest, r: '3.3', allowfail: false}
|
||||
# - {os: windows-latest, r: '3.3', allowfail: false}
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||||
# - {os: windows-latest, r: '3.2', allowfail: true}
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||||
# - {os: windows-latest, r: '3.1', allowfail: true}
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||||
# - {os: windows-latest, r: '3.0', allowfail: true}
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||||
|
||||
@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.8.1
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Date: 2022-03-17
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Version: 1.8.1.9010
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Date: 2022-05-16
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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||||
|
||||
@ -50,7 +50,6 @@ S3method(any,mic)
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S3method(as.data.frame,ab)
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S3method(as.data.frame,mo)
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S3method(as.double,mic)
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S3method(as.integer,mic)
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S3method(as.list,custom_eucast_rules)
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S3method(as.list,custom_mdro_guideline)
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S3method(as.matrix,mic)
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|
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18
NEWS.md
18
NEWS.md
@ -1,8 +1,20 @@
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# `AMR` 1.8.1.9010
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## <small>Last updated: 16 May 2022</small>
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|
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### New
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* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
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|
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### Changed
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* Fix for `as.rsi()` on certain EUCAST breakpoints for MIC values
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* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
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* `droplevels()` on MIC will now return a common `factor` at default and will lose the `<mic>` class. Use `droplevels(..., as.mic = TRUE)` to keep the `<mic>` class.
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* Small fix for using `ab_from_text()`
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* Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
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* Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`
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|
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|
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# `AMR` 1.8.1
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|
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|
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All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
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|
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### Changed
|
||||
* Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
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* Support for antibiotic interpretations of the MIPS laboratory system: `"U"` for S ('susceptible urine'), `"D"` for I ('susceptible dose-dependent')
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|
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@ -638,7 +638,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
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if (isTRUE(initial_captital)) {
|
||||
v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
|
||||
}
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||||
if (length(v) == 1) {
|
||||
if (length(v) <= 1) {
|
||||
return(paste0(quotes, v, quotes))
|
||||
}
|
||||
if (identical(v, c("I", "R", "S"))) {
|
||||
|
||||
9
R/data.R
9
R/data.R
@ -251,7 +251,14 @@
|
||||
#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
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#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
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||||
#' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
|
||||
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
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||||
#' @details
|
||||
#' Overview of the data set:
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||||
#'
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||||
#' ```{r}
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#' head(rsi_translation)
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#' ```
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||||
#'
|
||||
#' The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @seealso [intrinsic_resistant]
|
||||
|
||||
28
R/mic.R
28
R/mic.R
@ -47,7 +47,8 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
|
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#' @rdname as.mic
|
||||
#' @param x a [character] or [numeric] vector
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#' @param na.rm a [logical] indicating whether missing values should be removed
|
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#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
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#' @param ... arguments passed on to methods
|
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#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
|
||||
#'
|
||||
#' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
|
||||
#'
|
||||
@ -86,6 +87,10 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
|
||||
#' ```
|
||||
#'
|
||||
#' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
|
||||
#'
|
||||
#' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).
|
||||
#'
|
||||
#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `<mic>` class.
|
||||
#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
|
||||
#' @aliases mic
|
||||
#' @export
|
||||
@ -196,7 +201,8 @@ all_valid_mics <- function(x) {
|
||||
}
|
||||
|
||||
#' @rdname as.mic
|
||||
#' @details `NA_mic_` is a missing value of the new `<mic>` class.
|
||||
#' @details `NA_mic_` is a missing value of the new `<mic>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
|
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#' @format NULL
|
||||
#' @export
|
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NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
|
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new_class = c("mic", "ordered", "factor"))
|
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@ -214,13 +220,6 @@ as.double.mic <- function(x, ...) {
|
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as.double(gsub("[<=>]+", "", as.character(x), perl = TRUE))
|
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}
|
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|
||||
#' @method as.integer mic
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#' @export
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#' @noRd
|
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as.integer.mic <- function(x, ...) {
|
||||
as.integer(gsub("[<=>]+", "", as.character(x), perl = TRUE))
|
||||
}
|
||||
|
||||
#' @method as.numeric mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
@ -228,11 +227,12 @@ as.numeric.mic <- function(x, ...) {
|
||||
as.numeric(gsub("[<=>]+", "", as.character(x), perl = TRUE))
|
||||
}
|
||||
|
||||
#' @rdname as.mic
|
||||
#' @method droplevels mic
|
||||
#' @param as.mic a [logical] to indicate whether the `<mic>` class should be kept, defaults to `FALSE`
|
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#' @export
|
||||
#' @noRd
|
||||
droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, as.mic = TRUE, ...) {
|
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x <- droplevels.factor(x, exclude = exclude, ...)
|
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droplevels.mic <- function(x, as.mic = FALSE, ...) {
|
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x <- droplevels.factor(x, ...)
|
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if (as.mic == TRUE) {
|
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class(x) <- c("mic", "ordered", "factor")
|
||||
}
|
||||
@ -260,7 +260,9 @@ type_sum.mic <- function(x, ...) {
|
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#' @export
|
||||
#' @noRd
|
||||
print.mic <- function(x, ...) {
|
||||
cat("Class <mic>\n")
|
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cat("Class <mic>",
|
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ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""),
|
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"\n", sep = "")
|
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print(as.character(x), quote = FALSE)
|
||||
att <- attributes(x)
|
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if ("na.action" %in% names(att)) {
|
||||
|
||||
@ -29,16 +29,16 @@
|
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#'
|
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#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
|
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#' @inheritSection lifecycle Stable Lifecycle
|
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#' @param path location of your reference file, see *Details*. Can be `""`, `NULL` or `FALSE` to delete the reference file.
|
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#' @param path location of your reference file, this can be any text file (comma-, tab- or pipe-separated) or an Excel file (see *Details*). Can also be `""`, `NULL` or `FALSE` to delete the reference file.
|
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#' @param destination destination of the compressed data file, default to the user's home directory.
|
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#' @rdname mo_source
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#' @name mo_source
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#' @aliases set_mo_source get_mo_source
|
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#' @details The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the `readxl` package installed.
|
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#'
|
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#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
|
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#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] or [`microorganisms$fullname`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
|
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#'
|
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#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an attribute to the compressed data file.
|
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#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an [attribute][base::attributes()] to the compressed data file.
|
||||
#'
|
||||
#' The function [get_mo_source()] will return the data set by reading `"mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the location and timestamp of the original file), it will call [set_mo_source()] to update the data file automatically if used in an interactive session.
|
||||
#'
|
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@ -46,15 +46,15 @@
|
||||
#'
|
||||
#' @section How to Setup:
|
||||
#'
|
||||
#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the [microorganisms] data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
|
||||
#' Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:
|
||||
#'
|
||||
#' ```
|
||||
#' | A | B |
|
||||
#' --|--------------------|--------------|
|
||||
#' 1 | Organisation XYZ | mo |
|
||||
#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
|
||||
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
|
||||
#' 4 | | |
|
||||
#' | A | B |
|
||||
#' --|--------------------|-----------------------|
|
||||
#' 1 | Organisation XYZ | mo |
|
||||
#' 2 | lab_mo_ecoli | Escherichia coli |
|
||||
#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
|
||||
#' 4 | | |
|
||||
#' ```
|
||||
#'
|
||||
#' We save it as `"home/me/ourcodes.xlsx"`. Now we have to set it as a source:
|
||||
@ -89,13 +89,13 @@
|
||||
#' If we edit the Excel file by, let's say, adding row 4 like this:
|
||||
#'
|
||||
#' ```
|
||||
#' | A | B |
|
||||
#' --|--------------------|--------------|
|
||||
#' 1 | Organisation XYZ | mo |
|
||||
#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
|
||||
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
|
||||
#' 4 | lab_Staph_aureus | B_STPHY_AURS |
|
||||
#' 5 | | |
|
||||
#' | A | B |
|
||||
#' --|--------------------|-----------------------|
|
||||
#' 1 | Organisation XYZ | mo |
|
||||
#' 2 | lab_mo_ecoli | Escherichia coli |
|
||||
#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
|
||||
#' 4 | lab_Staph_aureus | Staphylococcus aureus |
|
||||
#' 5 | | |
|
||||
#' ```
|
||||
#'
|
||||
#' ...any new usage of an MO function in this package will update your data file:
|
||||
@ -144,6 +144,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
|
||||
stop_ifnot(file.exists(path), "file not found: ", path)
|
||||
|
||||
df <- NULL
|
||||
if (path %like% "[.]rds$") {
|
||||
df <- readRDS(path)
|
||||
|
||||
@ -153,28 +154,34 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
df <- readxl::read_excel(path)
|
||||
|
||||
} else if (path %like% "[.]tsv$") {
|
||||
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
|
||||
|
||||
} else if (path %like% "[.]csv$") {
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE)
|
||||
|
||||
} else {
|
||||
# try comma first
|
||||
try(
|
||||
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE),
|
||||
silent = TRUE)
|
||||
if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
|
||||
# try tab
|
||||
try(
|
||||
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE),
|
||||
silent = TRUE)
|
||||
}
|
||||
if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
|
||||
# try pipe
|
||||
try(
|
||||
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = "|", stringsAsFactors = FALSE),
|
||||
silent = TRUE)
|
||||
}
|
||||
}
|
||||
|
||||
# check integrity
|
||||
if (is.null(df)) {
|
||||
stop_("the path '", path, "' could not be imported as a dataset.")
|
||||
}
|
||||
check_validity_mo_source(df)
|
||||
|
||||
df <- subset(df, !is.na(mo))
|
||||
@ -187,7 +194,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
}
|
||||
|
||||
df <- as.data.frame(df, stringAsFactors = FALSE)
|
||||
df[, "mo"] <- set_clean_class(df[, "mo", drop = TRUE], c("mo", "character"))
|
||||
df[, "mo"] <- as.mo(df[, "mo", drop = TRUE])
|
||||
|
||||
# success
|
||||
if (file.exists(mo_source_destination)) {
|
||||
@ -275,9 +282,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
|
||||
return(FALSE)
|
||||
}
|
||||
}
|
||||
if (!all(x$mo %in% c("", microorganisms$mo), na.rm = TRUE)) {
|
||||
if (!all(x$mo %in% c("", microorganisms$mo, microorganisms$fullname), na.rm = TRUE)) {
|
||||
if (stop_on_error == TRUE) {
|
||||
invalid <- x[which(!x$mo %in% c("", microorganisms$mo)), , drop = FALSE]
|
||||
invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms$fullname)), , drop = FALSE]
|
||||
if (nrow(invalid) > 1) {
|
||||
plural <- "s"
|
||||
} else {
|
||||
|
||||
18
R/plot.R
18
R/plot.R
@ -79,7 +79,7 @@ plot.mic <- function(x,
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
guideline = "EUCAST",
|
||||
main = paste("MIC values of", deparse(substitute(x))),
|
||||
main = deparse(substitute(x)),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
@ -166,7 +166,7 @@ barplot.mic <- function(height,
|
||||
mo = NULL,
|
||||
ab = NULL,
|
||||
guideline = "EUCAST",
|
||||
main = paste("MIC values of", deparse(substitute(height))),
|
||||
main = deparse(substitute(height)),
|
||||
ylab = "Frequency",
|
||||
xlab = "Minimum Inhibitory Concentration (mg/L)",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
@ -299,7 +299,7 @@ fortify.mic <- function(object, ...) {
|
||||
#' @importFrom graphics barplot axis mtext legend
|
||||
#' @rdname plot
|
||||
plot.disk <- function(x,
|
||||
main = paste("Disk zones of", deparse(substitute(x))),
|
||||
main = deparse(substitute(x)),
|
||||
ylab = "Frequency",
|
||||
xlab = "Disk diffusion diameter (mm)",
|
||||
mo = NULL,
|
||||
@ -386,7 +386,7 @@ plot.disk <- function(x,
|
||||
#' @export
|
||||
#' @noRd
|
||||
barplot.disk <- function(height,
|
||||
main = paste("Disk zones of", deparse(substitute(height))),
|
||||
main = deparse(substitute(height)),
|
||||
ylab = "Frequency",
|
||||
xlab = "Disk diffusion diameter (mm)",
|
||||
mo = NULL,
|
||||
@ -525,7 +525,7 @@ fortify.disk <- function(object, ...) {
|
||||
plot.rsi <- function(x,
|
||||
ylab = "Percentage",
|
||||
xlab = "Antimicrobial Interpretation",
|
||||
main = paste("Resistance Overview of", deparse(substitute(x))),
|
||||
main = deparse(substitute(x)),
|
||||
...) {
|
||||
meet_criteria(ylab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
||||
@ -576,7 +576,7 @@ plot.rsi <- function(x,
|
||||
#' @export
|
||||
#' @noRd
|
||||
barplot.rsi <- function(height,
|
||||
main = paste("Resistance Overview of", deparse(substitute(height))),
|
||||
main = deparse(substitute(height)),
|
||||
xlab = "Antimicrobial Interpretation",
|
||||
ylab = "Frequency",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
@ -738,7 +738,11 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, f
|
||||
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
|
||||
guideline_txt <- ""
|
||||
} else {
|
||||
guideline_txt <- paste0("(", guideline, ")")
|
||||
guideline_txt <- guideline
|
||||
if (isTRUE(list(...)$uti)) {
|
||||
guideline_txt <- paste("UTIs,", guideline_txt)
|
||||
}
|
||||
guideline_txt <- paste0("(", guideline_txt, ")")
|
||||
}
|
||||
sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
|
||||
} else {
|
||||
|
||||
@ -34,7 +34,7 @@
|
||||
#' @param ... ignored, only in place to allow future extensions
|
||||
#' @details The base \R function [sample()] is used for generating values.
|
||||
#'
|
||||
#' Generated values are based on the latest EUCAST guideline implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
|
||||
#' Generated values are based on the EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` guideline as implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
|
||||
#' @return class `<mic>` for [random_mic()] (see [as.mic()]) and class `<disk>` for [random_disk()] (see [as.disk()])
|
||||
#' @name random
|
||||
#' @rdname random
|
||||
@ -89,6 +89,7 @@ random_rsi <- function(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) {
|
||||
}
|
||||
|
||||
random_exec <- function(type, size, mo = NULL, ab = NULL) {
|
||||
check_dataset_integrity()
|
||||
df <- rsi_translation %pm>%
|
||||
pm_filter(guideline %like% "EUCAST") %pm>%
|
||||
pm_arrange(pm_desc(guideline)) %pm>%
|
||||
|
||||
18
R/rsi.R
18
R/rsi.R
@ -33,7 +33,7 @@
|
||||
#' @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 searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
|
||||
#' @inheritParams first_isolate
|
||||
#' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
|
||||
#' @param guideline defaults to EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [rsi_translation] data set), supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`), see *Details*
|
||||
#' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
|
||||
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
|
||||
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
|
||||
@ -179,7 +179,7 @@
|
||||
#' example_isolates %>%
|
||||
#' mutate_if(is.rsi.eligible, as.rsi)
|
||||
#'
|
||||
#' # note: from dplyr 1.0.0 on, this will be:
|
||||
#' # since dplyr 1.0.0, this can also be:
|
||||
#' # example_isolates %>%
|
||||
#' # mutate(across(where(is.rsi.eligible), as.rsi))
|
||||
#' }
|
||||
@ -189,7 +189,7 @@ as.rsi <- function(x, ...) {
|
||||
}
|
||||
|
||||
#' @rdname as.rsi
|
||||
#' @details `NA_rsi_` is a missing value of the new `<rsi>` class.
|
||||
#' @details `NA_rsi_` is a missing value of the new `<rsi>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
|
||||
#' @export
|
||||
NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE),
|
||||
new_class = c("rsi", "ordered", "factor"))
|
||||
@ -818,18 +818,20 @@ exec_as.rsi <- function(method,
|
||||
if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
|
||||
new_rsi[i] <- NA_character_
|
||||
} else if (method == "mic") {
|
||||
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
|
||||
isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
|
||||
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^<[0-9]") ~ "S",
|
||||
isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^>[0-9]") ~ "R",
|
||||
# these basically call `<=.mic()` and `>=.mic()`:
|
||||
x[i] <= get_record$breakpoint_S ~ "S",
|
||||
x[i] >= get_record$breakpoint_R ~ "R",
|
||||
isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
|
||||
guideline_coerced %like% "EUCAST" & isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
|
||||
guideline_coerced %like% "CLSI" & isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
|
||||
# return "I" when not match the bottom or top
|
||||
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
|
||||
# and NA otherwise
|
||||
TRUE ~ NA_character_)
|
||||
} else if (method == "disk") {
|
||||
new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
|
||||
isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
|
||||
guideline_coerced %like% "EUCAST" & isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
|
||||
guideline_coerced %like% "CLSI" & isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
|
||||
# return "I" when not match the bottom or top
|
||||
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
|
||||
# and NA otherwise
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
Binary file not shown.
@ -252,7 +252,9 @@ changed_md5 <- function(object) {
|
||||
}
|
||||
|
||||
# give official names to ABs and MOs
|
||||
rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
|
||||
rsi <- AMR::rsi_translation %>%
|
||||
mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
|
||||
mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
|
||||
if (changed_md5(rsi)) {
|
||||
usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('/data-raw/')}"))
|
||||
write_md5(rsi)
|
||||
@ -312,8 +314,8 @@ if (changed_md5(av)) {
|
||||
}
|
||||
|
||||
# give official names to ABs and MOs
|
||||
intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo),
|
||||
antibiotic = ab_name(intrinsic_resistant$ab),
|
||||
intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo, language = NULL),
|
||||
antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
|
||||
stringsAsFactors = FALSE)
|
||||
if (changed_md5(intrinsicR)) {
|
||||
usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('/data-raw/')}"))
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -24,6 +24,7 @@
|
||||
# ==================================================================== #
|
||||
|
||||
# This script runs in under a minute and renews all guidelines of CLSI and EUCAST!
|
||||
# Run it with source("data-raw/reproduction_of_rsi_translation.R")
|
||||
|
||||
library(dplyr)
|
||||
library(readr)
|
||||
@ -32,9 +33,9 @@ library(AMR)
|
||||
|
||||
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
|
||||
# and copy the folder C:\WHONET\Codes to data-raw/WHONET/Codes
|
||||
DRGLST <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"))
|
||||
DRGLST1 <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"))
|
||||
ORGLIST <- readr::read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"))
|
||||
DRGLST <- read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
|
||||
DRGLST1 <- read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"), show_col_types = FALSE)
|
||||
ORGLIST <- read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
|
||||
|
||||
# create data set for generic rules (i.e., AB-specific but not MO-specific)
|
||||
rsi_generic <- DRGLST %>%
|
||||
@ -128,11 +129,30 @@ rsi_translation[which(rsi_translation$breakpoint_R == 257), "breakpoint_R"] <- m
|
||||
rsi_translation[which(rsi_translation$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
|
||||
rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
|
||||
|
||||
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
|
||||
# EUCAST 2021 guideline: S <= 8 and R > 8
|
||||
# WHONET file: S <= 8 and R >= 16
|
||||
# this will make an MIC of 12 I, which should be R, so:
|
||||
eucast_mics <- which(rsi_translation$guideline %like% "EUCAST" &
|
||||
rsi_translation$method == "MIC" &
|
||||
log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0 &
|
||||
!is.na(rsi_translation$breakpoint_R))
|
||||
old_R <- rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE]
|
||||
old_S <- rsi_translation[eucast_mics, "breakpoint_S", drop = TRUE]
|
||||
new_R <- 2 ^ (log2(old_R) - 1)
|
||||
new_R[new_R < old_S | is.na(as.mic(new_R))] <- old_S[new_R < old_S | is.na(as.mic(new_R))]
|
||||
rsi_translation[eucast_mics, "breakpoint_R"] <- new_R
|
||||
eucast_disks <- which(rsi_translation$guideline %like% "EUCAST" &
|
||||
rsi_translation$method == "DISK" &
|
||||
rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0 &
|
||||
!is.na(rsi_translation$breakpoint_R))
|
||||
rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
|
||||
|
||||
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
|
||||
rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE)
|
||||
rsi_translation$disk_dose <- gsub("–", "-", rsi_translation$disk_dose, fixed = TRUE)
|
||||
|
||||
# save to package
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE)
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
|
||||
rm(rsi_translation)
|
||||
devtools::load_all(".")
|
||||
|
||||
@ -1 +1 @@
|
||||
d8083b68d4e492ea8e87c1eae4da4196
|
||||
75a10b41a8bd4f4788520f3407431e66
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because it is too large
Load Diff
Binary file not shown.
BIN
data-raw/v_12.0_Breakpoint_Tables.xlsx
Normal file
BIN
data-raw/v_12.0_Breakpoint_Tables.xlsx
Normal file
Binary file not shown.
Binary file not shown.
@ -43,7 +43,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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="Released version">1.8.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -57,7 +57,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -205,14 +205,12 @@ Content not found. Please use links in the navbar.
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -416,13 +416,11 @@ END OF TERMS AND CONDITIONS
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -192,7 +192,7 @@
|
||||
<h4 data-toc-skip class="author">Dr Matthijs
|
||||
Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">14 March 2022</h4>
|
||||
<h4 data-toc-skip class="date">11 mei 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||
@ -205,7 +205,7 @@ Berends</h4>
|
||||
website update since they are based on randomly created values and the
|
||||
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
|
||||
Markdown</a>. However, the methodology remains unchanged. This page was
|
||||
generated on 14 March 2022.</p>
|
||||
generated on 11 mei 2022.</p>
|
||||
<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h2>
|
||||
@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2022-03-14</td>
|
||||
<td align="center">2022-05-11</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2022-03-14</td>
|
||||
<td align="center">2022-05-11</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2022-03-14</td>
|
||||
<td align="center">2022-05-11</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -392,12 +392,12 @@ data set:</p>
|
||||
<col width="13%">
|
||||
<col width="13%">
|
||||
<col width="13%">
|
||||
<col width="28%">
|
||||
<col width="26%">
|
||||
<col width="5%">
|
||||
<col width="5%">
|
||||
<col width="5%">
|
||||
<col width="5%">
|
||||
<col width="8%">
|
||||
<col width="9%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">date</th>
|
||||
@ -412,69 +412,69 @@ data set:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-06-11</td>
|
||||
<td align="center">R8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-12-29</td>
|
||||
<td align="center">E9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-11-10</td>
|
||||
<td align="center">L4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2013-03-20</td>
|
||||
<td align="center">G10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-03-14</td>
|
||||
<td align="center">N6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-09-24</td>
|
||||
<td align="center">2012-05-19</td>
|
||||
<td align="center">T9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-09-16</td>
|
||||
<td align="center">D6</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-03-16</td>
|
||||
<td align="center">D10</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-05-04</td>
|
||||
<td align="center">S5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-06-06</td>
|
||||
<td align="center">N10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-05-12</td>
|
||||
<td align="center">R3</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -511,16 +511,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,365</td>
|
||||
<td align="right">51.83%</td>
|
||||
<td align="right">10,365</td>
|
||||
<td align="right">51.83%</td>
|
||||
<td align="right">10,452</td>
|
||||
<td align="right">52.26%</td>
|
||||
<td align="right">10,452</td>
|
||||
<td align="right">52.26%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,635</td>
|
||||
<td align="right">48.18%</td>
|
||||
<td align="right">9,548</td>
|
||||
<td align="right">47.74%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -630,9 +630,9 @@ takes into account the antimicrobial susceptibility test results using
|
||||
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
|
||||
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
||||
<span class="co"># 2</span>
|
||||
<span class="co"># => Found 10,676 'phenotype-based' first isolates (53.4% of total where a</span>
|
||||
<span class="co"># => Found 10,708 'phenotype-based' first isolates (53.5% of total where a</span>
|
||||
<span class="co"># microbial ID was available)</span></code></pre></div>
|
||||
<p>So only 53.4% is suitable for resistance analysis! We can now filter
|
||||
<p>So only 53.5% is suitable for resistance analysis! We can now filter
|
||||
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
|
||||
<code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||
@ -642,11 +642,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
|
||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
<p>So we end up with 10,676 isolates for analysis. Now our data looks
|
||||
<p>So we end up with 10,708 isolates for analysis. Now our data looks
|
||||
like:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
|
||||
<table class="table">
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="2%">
|
||||
<col width="9%">
|
||||
@ -659,7 +659,7 @@ like:</p>
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@ -681,58 +681,58 @@ like:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="center">2015-06-11</td>
|
||||
<td align="center">R8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="left">2</td>
|
||||
<td align="center">2014-09-16</td>
|
||||
<td align="center">D6</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">3</td>
|
||||
<td align="center">2011-11-10</td>
|
||||
<td align="center">L4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">4</td>
|
||||
<td align="center">2013-03-20</td>
|
||||
<td align="center">G10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">5</td>
|
||||
<td align="center">2010-03-14</td>
|
||||
<td align="center">N6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2011-06-06</td>
|
||||
<td align="center">N10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">6</td>
|
||||
<td align="center">2016-05-12</td>
|
||||
<td align="center">R3</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">8</td>
|
||||
<td align="center">2010-02-19</td>
|
||||
<td align="center">U1</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -745,35 +745,35 @@ like:</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">6</td>
|
||||
<td align="center">2010-09-24</td>
|
||||
<td align="center">T9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="left">11</td>
|
||||
<td align="center">2012-02-09</td>
|
||||
<td align="center">G7</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">10</td>
|
||||
<td align="center">2011-01-26</td>
|
||||
<td align="center">K5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="left">12</td>
|
||||
<td align="center">2012-04-12</td>
|
||||
<td align="center">Q10</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -809,8 +809,8 @@ readable:</p>
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 10,676<br>
|
||||
Available: 10,676 (100%, NA: 0 = 0%)<br>
|
||||
Length: 10,708<br>
|
||||
Available: 10,708 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -835,33 +835,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">4,677</td>
|
||||
<td align="right">43.81%</td>
|
||||
<td align="right">4,677</td>
|
||||
<td align="right">43.81%</td>
|
||||
<td align="right">4,664</td>
|
||||
<td align="right">43.56%</td>
|
||||
<td align="right">4,664</td>
|
||||
<td align="right">43.56%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">2,652</td>
|
||||
<td align="right">24.84%</td>
|
||||
<td align="right">7,329</td>
|
||||
<td align="right">68.65%</td>
|
||||
<td align="right">2,713</td>
|
||||
<td align="right">25.34%</td>
|
||||
<td align="right">7,377</td>
|
||||
<td align="right">68.89%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,144</td>
|
||||
<td align="right">20.08%</td>
|
||||
<td align="right">9,473</td>
|
||||
<td align="right">88.73%</td>
|
||||
<td align="right">2,154</td>
|
||||
<td align="right">20.12%</td>
|
||||
<td align="right">9,531</td>
|
||||
<td align="right">89.01%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,203</td>
|
||||
<td align="right">11.27%</td>
|
||||
<td align="right">10,676</td>
|
||||
<td align="right">1,177</td>
|
||||
<td align="right">10.99%</td>
|
||||
<td align="right">10,708</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -882,14 +882,14 @@ antibiotic class they are in:</p>
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="10%">
|
||||
<col width="11%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="11%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@ -910,12 +910,12 @@ antibiotic class they are in:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-06-11</td>
|
||||
<td align="center">R8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2012-04-12</td>
|
||||
<td align="center">Q10</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
@ -925,39 +925,24 @@ antibiotic class they are in:</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-11-10</td>
|
||||
<td align="center">L4</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2011-03-17</td>
|
||||
<td align="center">Z4</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2013-03-20</td>
|
||||
<td align="center">G10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-09-24</td>
|
||||
<td align="center">T9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2010-09-07</td>
|
||||
<td align="center">P9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -969,31 +954,46 @@ antibiotic class they are in:</p>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-12-18</td>
|
||||
<td align="center">D8</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<tr class="even">
|
||||
<td align="center">2013-08-06</td>
|
||||
<td align="center">Z6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-02-20</td>
|
||||
<td align="center">K5</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-10-24</td>
|
||||
<td align="center">V7</td>
|
||||
<td align="center">2015-08-23</td>
|
||||
<td align="center">G1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
@ -1022,50 +1022,50 @@ different bug/drug combinations, you can use the
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">2208</td>
|
||||
<td align="center">135</td>
|
||||
<td align="center">2334</td>
|
||||
<td align="center">4677</td>
|
||||
<td align="center">2171</td>
|
||||
<td align="center">132</td>
|
||||
<td align="center">2361</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">3416</td>
|
||||
<td align="center">135</td>
|
||||
<td align="center">1126</td>
|
||||
<td align="center">4677</td>
|
||||
<td align="center">3389</td>
|
||||
<td align="center">168</td>
|
||||
<td align="center">1107</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3415</td>
|
||||
<td align="center">3428</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1262</td>
|
||||
<td align="center">4677</td>
|
||||
<td align="center">1236</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4110</td>
|
||||
<td align="center">4083</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">567</td>
|
||||
<td align="center">4677</td>
|
||||
<td align="center">581</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1203</td>
|
||||
<td align="center">1203</td>
|
||||
<td align="center">1177</td>
|
||||
<td align="center">1177</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">926</td>
|
||||
<td align="center">38</td>
|
||||
<td align="center">239</td>
|
||||
<td align="center">1203</td>
|
||||
<td align="center">935</td>
|
||||
<td align="center">30</td>
|
||||
<td align="center">212</td>
|
||||
<td align="center">1177</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1088,34 +1088,34 @@ different bug/drug combinations, you can use the
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4110</td>
|
||||
<td align="center">4083</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">567</td>
|
||||
<td align="center">4677</td>
|
||||
<td align="center">581</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">1083</td>
|
||||
<td align="center">1074</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">120</td>
|
||||
<td align="center">1203</td>
|
||||
<td align="center">103</td>
|
||||
<td align="center">1177</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">2348</td>
|
||||
<td align="center">2426</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">304</td>
|
||||
<td align="center">2652</td>
|
||||
<td align="center">287</td>
|
||||
<td align="center">2713</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">S. pneumoniae</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">2144</td>
|
||||
<td align="center">2144</td>
|
||||
<td align="center">2154</td>
|
||||
<td align="center">2154</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1147,7 +1147,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
||||
own:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
|
||||
<span class="co"># [1] 0.5491757</span></code></pre></div>
|
||||
<span class="co"># [1] 0.5473478</span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
|
||||
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||
@ -1162,19 +1162,19 @@ own:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5442031</td>
|
||||
<td align="center">0.5482456</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5462647</td>
|
||||
<td align="center">0.5499477</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5565553</td>
|
||||
<td align="center">0.5403687</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5569745</td>
|
||||
<td align="center">0.5464842</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1197,23 +1197,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5442031</td>
|
||||
<td align="center">3269</td>
|
||||
<td align="center">0.5482456</td>
|
||||
<td align="center">3192</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5462647</td>
|
||||
<td align="center">3815</td>
|
||||
<td align="center">0.5499477</td>
|
||||
<td align="center">3824</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5565553</td>
|
||||
<td align="center">1556</td>
|
||||
<td align="center">0.5403687</td>
|
||||
<td align="center">1573</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5569745</td>
|
||||
<td align="center">2036</td>
|
||||
<td align="center">0.5464842</td>
|
||||
<td align="center">2119</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1236,27 +1236,27 @@ therapies very easily:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7592474</td>
|
||||
<td align="center">0.8787684</td>
|
||||
<td align="center">0.9775497</td>
|
||||
<td align="center">0.7626501</td>
|
||||
<td align="center">0.8754288</td>
|
||||
<td align="center">0.9774871</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8013300</td>
|
||||
<td align="center">0.9002494</td>
|
||||
<td align="center">0.9758936</td>
|
||||
<td align="center">0.8198811</td>
|
||||
<td align="center">0.9124894</td>
|
||||
<td align="center">0.9821580</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7929864</td>
|
||||
<td align="center">0.8853695</td>
|
||||
<td align="center">0.9807692</td>
|
||||
<td align="center">0.7983782</td>
|
||||
<td align="center">0.8942130</td>
|
||||
<td align="center">0.9834132</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5247201</td>
|
||||
<td align="center">0.5329619</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5247201</td>
|
||||
<td align="center">0.5329619</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1284,23 +1284,23 @@ classes, use a antibiotic class selector such as
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital A</td>
|
||||
<td align="right">54.4%</td>
|
||||
<td align="right">26.2%</td>
|
||||
<td align="right">54.8%</td>
|
||||
<td align="right">28.0%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital B</td>
|
||||
<td align="right">54.6%</td>
|
||||
<td align="right">28.2%</td>
|
||||
<td align="right">55.0%</td>
|
||||
<td align="right">26.3%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital C</td>
|
||||
<td align="right">55.7%</td>
|
||||
<td align="right">26.6%</td>
|
||||
<td align="right">54.0%</td>
|
||||
<td align="right">26.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital D</td>
|
||||
<td align="right">55.7%</td>
|
||||
<td align="right">28.9%</td>
|
||||
<td align="right">54.6%</td>
|
||||
<td align="right">26.4%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1402,18 +1402,18 @@ classes) <code><mic></code> and <code><disk></code>:</p>
|
||||
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="va">mic_values</span>
|
||||
<span class="co"># Class <mic></span>
|
||||
<span class="co"># [1] 0.5 0.25 32 <=0.001 0.002 0.0625 0.025 256 1 </span>
|
||||
<span class="co"># [10] 1 0.25 0.25 1 128 0.125 256 0.025 0.002 </span>
|
||||
<span class="co"># [19] 128 0.25 0.5 <=0.001 0.01 256 0.25 0.0625 0.005 </span>
|
||||
<span class="co"># [28] 32 8 0.002 64 4 0.125 4 128 <=0.001</span>
|
||||
<span class="co"># [37] 32 1 4 0.002 0.25 0.5 16 0.25 128 </span>
|
||||
<span class="co"># [46] 256 0.01 16 0.25 0.002 0.5 16 128 0.5 </span>
|
||||
<span class="co"># [55] 0.005 128 64 0.25 2 4 16 16 2 </span>
|
||||
<span class="co"># [64] 0.0625 1 0.0625 8 0.5 <=0.001 8 4 0.002 </span>
|
||||
<span class="co"># [73] 16 0.002 0.5 0.01 <=0.001 128 0.025 0.025 0.01 </span>
|
||||
<span class="co"># [82] 4 0.25 64 4 0.25 32 0.0625 1 128 </span>
|
||||
<span class="co"># [91] <=0.001 <=0.001 0.005 8 0.25 0.25 64 16 0.01 </span>
|
||||
<span class="co"># [100] 128</span></code></pre></div>
|
||||
<span class="co"># [1] 4 4 <=0.001 2 256 32 32 0.002 4 </span>
|
||||
<span class="co"># [10] 0.002 0.125 0.005 <=0.001 4 0.002 128 16 32 </span>
|
||||
<span class="co"># [19] 256 8 256 0.25 0.025 0.25 0.002 64 <=0.001</span>
|
||||
<span class="co"># [28] 0.25 256 2 0.0625 2 0.25 0.01 0.005 2 </span>
|
||||
<span class="co"># [37] 0.0625 1 64 32 0.0625 0.002 0.0625 0.125 0.005 </span>
|
||||
<span class="co"># [46] 1 256 0.025 256 0.005 16 64 0.25 2 </span>
|
||||
<span class="co"># [55] 0.25 1 128 0.0625 0.005 0.5 0.5 <=0.001 0.025 </span>
|
||||
<span class="co"># [64] 2 64 0.005 0.0625 0.5 128 0.0625 8 4 </span>
|
||||
<span class="co"># [73] 0.002 128 0.01 <=0.001 2 64 64 128 32 </span>
|
||||
<span class="co"># [82] 0.005 256 64 0.0625 0.5 32 0.002 <=0.001 1 </span>
|
||||
<span class="co"># [91] 16 0.25 0.005 16 2 64 0.005 <=0.001 256 </span>
|
||||
<span class="co"># [100] 32</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
|
||||
@ -1449,10 +1449,10 @@ plotting:</p>
|
||||
<span class="co"># coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="va">disk_values</span>
|
||||
<span class="co"># Class <disk></span>
|
||||
<span class="co"># [1] 30 17 16 29 29 24 20 21 22 19 31 28 19 22 20 19 19 17 27 17 29 31 24 27 21</span>
|
||||
<span class="co"># [26] 18 19 29 22 20 22 31 28 23 24 24 25 20 17 29 17 31 20 29 31 27 18 27 23 22</span>
|
||||
<span class="co"># [51] 24 18 17 19 18 23 16 28 19 28 23 27 16 19 26 28 24 22 22 20 23 30 25 27 27</span>
|
||||
<span class="co"># [76] 18 31 21 27 30 23 24 26 19 19 23 17 17 28 16 23 26 27 29 22 27 17 27 28 21</span></code></pre></div>
|
||||
<span class="co"># [1] 28 27 24 30 31 28 30 27 21 22 18 28 20 25 29 18 31 20 31 28 26 31 25 30 29</span>
|
||||
<span class="co"># [26] 21 20 25 24 29 23 26 27 26 20 18 29 21 17 31 18 30 30 26 19 17 18 23 30 31</span>
|
||||
<span class="co"># [51] 24 22 27 29 17 27 29 20 31 30 19 28 30 21 21 19 19 25 24 30 29 19 21 27 22</span>
|
||||
<span class="co"># [76] 30 17 26 21 18 31 29 26 21 23 31 27 30 19 18 20 20 23 28 25 24 31 18 17 28</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
|
||||
@ -1531,14 +1531,12 @@ really different.</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
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for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
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@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -425,14 +425,12 @@ reading</em>, is basically a form of imputation, and is part of the
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -422,18 +422,18 @@ names or codes, this would have worked exactly the same way:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 I S I I S S</span>
|
||||
<span class="co"># 2 R S I S R R</span>
|
||||
<span class="co"># 3 I R I S R S</span>
|
||||
<span class="co"># 4 I I I R S R</span>
|
||||
<span class="co"># 5 R S I R S I</span>
|
||||
<span class="co"># 6 S S I S R R</span>
|
||||
<span class="co"># 1 R I R R I S</span>
|
||||
<span class="co"># 2 I I S S R S</span>
|
||||
<span class="co"># 3 I S R R S R</span>
|
||||
<span class="co"># 4 R I S R R I</span>
|
||||
<span class="co"># 5 R I I I R I</span>
|
||||
<span class="co"># 6 R I R S R I</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 R</span>
|
||||
<span class="co"># 2 I</span>
|
||||
<span class="co"># 2 R</span>
|
||||
<span class="co"># 3 S</span>
|
||||
<span class="co"># 4 S</span>
|
||||
<span class="co"># 5 S</span>
|
||||
<span class="co"># 4 I</span>
|
||||
<span class="co"># 5 I</span>
|
||||
<span class="co"># 6 R</span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can
|
||||
use:</p>
|
||||
@ -455,7 +455,7 @@ use:</p>
|
||||
<span class="co"># management of drug-resistant tuberculosis</span>
|
||||
<span class="co"># Author(s): WHO (World Health Organization)</span>
|
||||
<span class="co"># Version: WHO/HTM/TB/2014.11, 2014</span>
|
||||
<span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></code></pre></div>
|
||||
<span class="co"># Source: https://www.who.int/publications/i/item/9789241548809</span></code></pre></div>
|
||||
<p>Create a frequency table of the results:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
|
||||
@ -487,40 +487,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3261</td>
|
||||
<td align="right">65.22%</td>
|
||||
<td align="right">3261</td>
|
||||
<td align="right">65.22%</td>
|
||||
<td align="right">3218</td>
|
||||
<td align="right">64.36%</td>
|
||||
<td align="right">3218</td>
|
||||
<td align="right">64.36%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">987</td>
|
||||
<td align="right">19.74%</td>
|
||||
<td align="right">4248</td>
|
||||
<td align="right">84.96%</td>
|
||||
<td align="right">979</td>
|
||||
<td align="right">19.58%</td>
|
||||
<td align="right">4197</td>
|
||||
<td align="right">83.94%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">437</td>
|
||||
<td align="right">8.74%</td>
|
||||
<td align="right">4685</td>
|
||||
<td align="right">93.70%</td>
|
||||
<td align="right">458</td>
|
||||
<td align="right">9.16%</td>
|
||||
<td align="right">4655</td>
|
||||
<td align="right">93.10%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">218</td>
|
||||
<td align="right">4.36%</td>
|
||||
<td align="right">4903</td>
|
||||
<td align="right">98.06%</td>
|
||||
<td align="right">237</td>
|
||||
<td align="right">4.74%</td>
|
||||
<td align="right">4892</td>
|
||||
<td align="right">97.84%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">97</td>
|
||||
<td align="right">1.94%</td>
|
||||
<td align="right">108</td>
|
||||
<td align="right">2.16%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -539,14 +539,12 @@ Unique: 5</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -213,7 +213,7 @@ is currently being developed.</strong></p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="co"># Rows: 2,000</span>
|
||||
<span class="co"># Columns: 49</span>
|
||||
<span class="co"># $ date <span style="color: #949494; font-style: italic;"><date></span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
|
||||
@ -305,7 +305,7 @@ function:</p>
|
||||
<span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span>
|
||||
<span class="co"># Importance of components:</span>
|
||||
<span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span>
|
||||
<span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.121e-17</span>
|
||||
<span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.674e-17</span>
|
||||
<span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span>
|
||||
<span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
|
||||
<pre><code><span class="co"># Groups (n=4, named as 'order'):</span>
|
||||
@ -348,14 +348,12 @@ automatically adds the right labels and even groups:</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
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@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -192,7 +192,7 @@
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs
|
||||
Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">14 March 2022</h4>
|
||||
<h4 data-toc-skip class="date">11 mei 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||||
@ -272,7 +272,7 @@ data using a custom made website. The webdesign knowledge needed
|
||||
<li>
|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
|
||||
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">439,954
|
||||
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">447,735
|
||||
R-related questions</a> have already been asked on this platform (that
|
||||
covers questions and answers for any programming language). In my own
|
||||
experience, most questions are answered within a couple of
|
||||
@ -511,14 +511,12 @@ yourself:</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -436,14 +436,12 @@ using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
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@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Benchmarks</h1>
|
||||
@ -198,30 +198,14 @@
|
||||
|
||||
|
||||
|
||||
<p>One of the most important features of this package is the complete
|
||||
microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (CoL) and
|
||||
the <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
|
||||
Standing in Nomenclature</a> (LPSN). We created a function
|
||||
<code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid
|
||||
microbial ID by using intelligent rules combined with the microbial
|
||||
taxonomy.</p>
|
||||
<p>Using the <code>microbenchmark</code> package, we can review the
|
||||
calculation performance of this function. Its function
|
||||
<code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions
|
||||
independently of each other and measures their time-to-result.</p>
|
||||
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (CoL) and the <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN). We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the microbial taxonomy.</p>
|
||||
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
|
||||
<p>In the next test, we try to ‘coerce’ different input values into the
|
||||
microbial code of <em>Staphylococcus aureus</em>. Coercion is a
|
||||
computational process of forcing output based on an input. For
|
||||
microorganism names, coercing user input to taxonomically valid
|
||||
microorganism names is crucial to ensure correct interpretation and to
|
||||
enable grouping based on taxonomic properties.</p>
|
||||
<p>The actual result is the same every time: it returns its
|
||||
microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
|
||||
<em>Bacteria</em>, its taxonomic kingdom).</p>
|
||||
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
|
||||
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, its taxonomic kingdom).</p>
|
||||
<p>But the calculation time differs a lot:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">S.aureus</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>
|
||||
@ -238,42 +222,29 @@ microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 12.0 13.0 17.0 14.0 15 53 25</span>
|
||||
<span class="co"># as.mo("stau") 51.0 59.0 74.0 71.0 90 97 25</span>
|
||||
<span class="co"># as.mo("STAU") 53.0 60.0 77.0 87.0 91 96 25</span>
|
||||
<span class="co"># as.mo("staaur") 11.0 13.0 16.0 14.0 15 48 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 13.0 14.0 19.0 15.0 16 48 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 28.0 31.0 48.0 59.0 63 70 25</span>
|
||||
<span class="co"># as.mo("S aureus") 28.0 29.0 42.0 33.0 58 83 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.9 4.1 6.1 4.4 5 43 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 270.0 270.0 270 390 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 190.0 200.0 200.0 220 240 25</span>
|
||||
<span class="co"># as.mo("MRSA") 13.0 13.0 19.0 14.0 15 50 25</span>
|
||||
<span class="co"># as.mo("VISA") 21.0 22.0 29.0 24.0 27 61 25</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 19.0 20.0 25.0 20.0 26.0 55 25</span>
|
||||
<span class="co"># as.mo("stau") 94.0 95.0 110.0 100.0 130.0 140 25</span>
|
||||
<span class="co"># as.mo("STAU") 92.0 97.0 110.0 110.0 120.0 140 25</span>
|
||||
<span class="co"># as.mo("staaur") 19.0 19.0 24.0 20.0 21.0 56 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 19.0 20.0 21.0 20.0 20.0 49 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 54.0 57.0 72.0 64.0 86.0 96 25</span>
|
||||
<span class="co"># as.mo("S aureus") 55.0 55.0 72.0 57.0 90.0 100 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 5.6 5.7 8.5 5.8 6.2 40 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 360.0 370.0 400.0 400.0 420.0 550 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 280.0 290.0 300.0 300.0 320.0 350 25</span>
|
||||
<span class="co"># as.mo("MRSA") 19.0 20.0 24.0 20.0 21.0 51 25</span>
|
||||
<span class="co"># as.mo("VISA") 34.0 34.0 48.0 36.0 65.0 73 25</span></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds
|
||||
(thousands of seconds). A value of 5 milliseconds means it can determine
|
||||
200 input values per second. It case of 200 milliseconds, this is only 5
|
||||
input values per second. It is clear that accepted taxonomic names are
|
||||
extremely fast, but some variations are up to 61 times slower to
|
||||
determine.</p>
|
||||
<p>To improve performance, we implemented two important algorithms to
|
||||
save unnecessary calculations: <strong>repetitive results</strong> and
|
||||
<strong>already precalculated results</strong>.</p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 69 times slower to determine.</p>
|
||||
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
|
||||
</h3>
|
||||
<p>Repetitive results are values that are present more than once in a
|
||||
vector. Unique values will only be calculated once by
|
||||
<code><a href="../reference/as.mo.html">as.mo()</a></code>. So running
|
||||
<code>as.mo(c("E. coli", "E. coli"))</code> will check the value
|
||||
<code>"E. coli"</code> only once.</p>
|
||||
<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a
|
||||
helper function that returns the full microbial name (genus, species and
|
||||
possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
|
||||
<p>Repetitive results are values that are present more than once in a vector. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. So running <code>as.mo(c("E. coli", "E. coli"))</code> will check the value <code>"E. coli"</code> only once.</p>
|
||||
<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># start with the example_isolates data set</span>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
@ -287,8 +258,8 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
|
||||
<span class="co"># what do these values look like? They are of class <mo>:</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="co"># Class <mo></span>
|
||||
<span class="co"># [1] B_ACNTB B_ESCHR_COLI B_STRPT_GRPC B_STPHY_HMNS B_STPHY_CONS</span>
|
||||
<span class="co"># [6] B_ESCHR_COLI</span>
|
||||
<span class="co"># [1] B_ENTRBC_CLOC B_ESCHR_COLI B_STRPT_PYGN B_STPHY_AURS B_ESCHR_COLI </span>
|
||||
<span class="co"># [6] B_STRPT_PNMN</span>
|
||||
|
||||
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
@ -301,38 +272,28 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
|
||||
<span class="co"># now let's see:</span>
|
||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 200 204 265 225 320 392 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items
|
||||
consisting of 90 unique values only takes 0.225 seconds. That is 112
|
||||
nanoseconds on average. You only lose time on your unique input
|
||||
values.</p>
|
||||
<span class="co"># mo_name(x) 259 264 357 299 451 509 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.299 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
|
||||
</h3>
|
||||
<p>What about precalculated results? If the input is an already
|
||||
precalculated result of a helper function such as
|
||||
<code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other
|
||||
words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it
|
||||
will return the results immediately (see ‘C’ below):</p>
|
||||
<p>What about precalculated results? If the input is an already precalculated result of a helper function such as <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it will return the results immediately (see ‘C’ below):</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
|
||||
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 8.35 8.84 9.10 9.01 9.32 10.20 10</span>
|
||||
<span class="co"># B 23.00 24.70 30.30 25.00 26.90 72.70 10</span>
|
||||
<span class="co"># C 2.05 2.07 2.44 2.41 2.83 3.05 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to
|
||||
<code>"Staphylococcus aureus"</code> takes 0.0024 seconds - it doesn’t
|
||||
even start calculating <em>if the result would be the same as the
|
||||
expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 11.90 12.10 13.0 13.50 13.70 13.80 10</span>
|
||||
<span class="co"># B 60.90 61.20 67.7 66.20 66.90 99.70 10</span>
|
||||
<span class="co"># C 2.91 2.94 3.2 3.32 3.38 3.46 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0033 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
@ -343,31 +304,23 @@ expected resulting value</em>. That goes for all helper functions:</p>
|
||||
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
|
||||
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.89 1.93 2.09 2.05 2.17 2.40 10</span>
|
||||
<span class="co"># B 1.89 1.93 2.08 2.00 2.19 2.63 10</span>
|
||||
<span class="co"># C 1.91 1.92 2.10 1.97 2.30 2.43 10</span>
|
||||
<span class="co"># D 1.90 1.94 2.21 2.02 2.53 2.88 10</span>
|
||||
<span class="co"># E 1.87 1.95 2.09 2.04 2.22 2.33 10</span>
|
||||
<span class="co"># F 1.84 1.91 1.97 1.92 2.04 2.14 10</span>
|
||||
<span class="co"># G 1.87 1.92 2.10 1.96 2.12 2.96 10</span>
|
||||
<span class="co"># H 1.90 1.96 2.12 2.06 2.21 2.47 10</span></code></pre></div>
|
||||
<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the
|
||||
function has zero knowledge about the actual microorganism, namely
|
||||
<em>S. aureus</em>. But since the result would be
|
||||
<code>"Firmicutes"</code> anyway, there is no point in calculating the
|
||||
result. And because this package contains all phyla of all known
|
||||
bacteria, it can just return the initial value immediately.</p>
|
||||
<span class="co"># A 2.92 2.93 3.02 2.94 3.02 3.40 10</span>
|
||||
<span class="co"># B 2.87 2.90 3.14 3.09 3.32 3.71 10</span>
|
||||
<span class="co"># C 2.91 2.94 3.15 3.12 3.33 3.46 10</span>
|
||||
<span class="co"># D 2.86 2.90 3.05 2.96 3.27 3.30 10</span>
|
||||
<span class="co"># E 2.87 2.88 3.03 2.96 3.16 3.29 10</span>
|
||||
<span class="co"># F 2.92 2.95 3.08 2.98 3.29 3.35 10</span>
|
||||
<span class="co"># G 2.89 2.96 3.04 2.99 3.11 3.29 10</span>
|
||||
<span class="co"># H 2.85 2.95 3.11 3.08 3.31 3.38 10</span></code></pre></div>
|
||||
<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="results-in-other-languages">Results in other languages<a class="anchor" aria-label="anchor" href="#results-in-other-languages"></a>
|
||||
</h3>
|
||||
<p>When the system language is non-English and supported by this
|
||||
<code>AMR</code> package, some functions will have a translated result.
|
||||
This almost does’t take extra time (compare “en” from the table below
|
||||
with the other languages):</p>
|
||||
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time (compare “en” from the table below with the other languages):</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">CoNS</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"CoNS"</span><span class="op">)</span>
|
||||
<span class="va">CoNS</span>
|
||||
@ -394,21 +347,20 @@ with the other languages):</p>
|
||||
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
|
||||
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># da 2.133 2.304 3.442 2.494 2.816 46.020 100</span>
|
||||
<span class="co"># de 2.128 2.312 3.068 2.520 2.699 53.220 100</span>
|
||||
<span class="co"># en 1.014 1.115 1.262 1.227 1.362 2.424 100</span>
|
||||
<span class="co"># es 2.133 2.338 2.981 2.570 2.737 43.770 100</span>
|
||||
<span class="co"># fr 1.986 2.149 3.139 2.377 2.567 41.610 100</span>
|
||||
<span class="co"># it 2.072 2.268 2.911 2.468 2.656 44.560 100</span>
|
||||
<span class="co"># nl 2.115 2.286 2.962 2.521 2.723 43.240 100</span>
|
||||
<span class="co"># pt 2.055 2.205 2.912 2.520 2.687 39.520 100</span>
|
||||
<span class="co"># ru 1.998 2.210 2.866 2.474 2.631 39.820 100</span>
|
||||
<span class="co"># sv 2.022 2.187 2.759 2.357 2.536 38.560 100</span></code></pre></div>
|
||||
<p>Currently supported languages are Danish, Dutch, English, French,
|
||||
German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
||||
<span class="co"># da 3.546 3.643 4.072 3.704 3.832 35.930 100</span>
|
||||
<span class="co"># de 3.597 3.659 4.422 3.734 3.839 36.400 100</span>
|
||||
<span class="co"># en 1.672 1.726 1.804 1.767 1.794 2.259 100</span>
|
||||
<span class="co"># es 3.609 3.685 4.496 3.760 3.843 36.540 100</span>
|
||||
<span class="co"># fr 3.484 3.567 3.725 3.654 3.713 6.281 100</span>
|
||||
<span class="co"># it 3.523 3.615 4.419 3.720 3.787 36.720 100</span>
|
||||
<span class="co"># nl 3.614 3.676 3.805 3.732 3.838 4.703 100</span>
|
||||
<span class="co"># pt 3.512 3.595 4.077 3.659 3.789 37.310 100</span>
|
||||
<span class="co"># ru 3.556 3.647 4.057 3.680 3.812 35.230 100</span>
|
||||
<span class="co"># sv 3.540 3.642 4.093 3.732 3.803 36.340 100</span></code></pre></div>
|
||||
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -422,14 +374,12 @@ German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 82 KiB After Width: | Height: | Size: 78 KiB |
@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -190,7 +190,7 @@
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">15 March 2022</h4>
|
||||
<h4 data-toc-skip class="date">16 May 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
@ -881,6 +881,173 @@ Dipivoxil, …</td>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
|
||||
</h2>
|
||||
<p>A data set with 20,318 rows and 11 columns, containing the following
|
||||
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
|
||||
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
|
||||
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 10 May 2022 19:42:39 UTC. Find more info about
|
||||
the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
|
||||
file</a> (49 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
|
||||
file</a> (0.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
|
||||
text file</a> (2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
|
||||
file</a> (4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
|
||||
file</a> (2.6 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
|
||||
file</a> (3.8 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
|
||||
</h3>
|
||||
<p>This data set contains interpretation rules for MIC values and disk
|
||||
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
|
||||
(2011-2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
|
||||
</h3>
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="8%">
|
||||
<col width="5%">
|
||||
<col width="3%">
|
||||
<col width="8%">
|
||||
<col width="14%">
|
||||
<col width="7%">
|
||||
<col width="3%">
|
||||
<col width="10%">
|
||||
<col width="8%">
|
||||
<col width="7%">
|
||||
<col width="8%">
|
||||
<col width="8%">
|
||||
<col width="4%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">guideline</th>
|
||||
<th align="center">method</th>
|
||||
<th align="center">site</th>
|
||||
<th align="center">mo</th>
|
||||
<th align="center">mo_name</th>
|
||||
<th align="center">rank_index</th>
|
||||
<th align="center">ab</th>
|
||||
<th align="center">ab_name</th>
|
||||
<th align="center">ref_tbl</th>
|
||||
<th align="center">disk_dose</th>
|
||||
<th align="center">breakpoint_S</th>
|
||||
<th align="center">breakpoint_R</th>
|
||||
<th align="center">uti</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">F_ASPRG_MGTS</td>
|
||||
<td align="center">Aspergillus fumigatus</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">AMB</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Aspergillus</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">4</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">F_ASPRG_NIGR</td>
|
||||
<td align="center">Aspergillus niger</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">AMB</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Aspergillus</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">4</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">F_CANDD</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center">3</td>
|
||||
<td align="center">AMB</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">F_CANDD_ALBC</td>
|
||||
<td align="center">Candida albicans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">AMB</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">F_CANDD_KRUS</td>
|
||||
<td align="center">Candida krusei</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">AMB</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">F_CANDD_PRPS</td>
|
||||
<td align="center">Candida parapsilosis</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">AMB</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
|
||||
</h2>
|
||||
<p>A data set with 134,956 rows and 2 columns, containing the following
|
||||
@ -895,7 +1062,7 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
|
||||
file</a> (78 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel
|
||||
file</a> (0.9 MB)<br>
|
||||
file</a> (1.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain
|
||||
text file</a> (5.1 MB)<br>
|
||||
@ -910,15 +1077,15 @@ file</a> (7.4 MB)<br>
|
||||
file</a> (10.2 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
|
||||
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
|
||||
</h3>
|
||||
<p>This data set contains all defined intrinsic resistance by EUCAST of
|
||||
all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST
|
||||
all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">‘EUCAST
|
||||
Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’
|
||||
v3.3</a> (2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
|
||||
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
|
||||
</h3>
|
||||
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
|
||||
<table class="table">
|
||||
@ -933,6 +1100,14 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Acetylspiramycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Amoxicillin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
@ -941,35 +1116,43 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Amoxicillin</td>
|
||||
<td align="center">Ampicillin/sulbactam</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Acetylspiramycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Avoparcin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Azithromycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Benzylpenicillin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cadazolid</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cephalothin</td>
|
||||
<td align="center">Cefadroxil</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cefadroxil</td>
|
||||
<td align="center">Cefazolin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Clindamycin</td>
|
||||
<td align="center">Cefoxitin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cephalexin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cephalothin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
@ -977,11 +1160,11 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cycloserine</td>
|
||||
<td align="center">Clindamycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cefazolin</td>
|
||||
<td align="center">Cycloserine</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
@ -1001,27 +1184,19 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cefoxitin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Fusidic acid</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Gamithromycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Josamycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Kitasamycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Cephalexin</td>
|
||||
<td align="center">Kitasamycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
@ -1033,31 +1208,39 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Meleumycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Midecamycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Miocamycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Meleumycin</td>
|
||||
<td align="center">Nafithromycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Midecamycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Norvancomycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Oleandomycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Oritavancin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Pirlimycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Benzylpenicillin</td>
|
||||
<td align="center">Primycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
@ -1065,14 +1248,6 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Pirlimycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Primycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Quinupristin/dalfopristin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
@ -1093,15 +1268,15 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Ampicillin/sulbactam</td>
|
||||
<td align="center">Solithromycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Solithromycin</td>
|
||||
<td align="center">Spiramycin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Spiramycin</td>
|
||||
<td align="center">Tedizolid</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
@ -1109,15 +1284,7 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Thiacetazone</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Tilmicosin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Tildipirosin</td>
|
||||
<td align="center">Telavancin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
@ -1125,7 +1292,15 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Telavancin</td>
|
||||
<td align="center">Thiacetazone</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Tildipirosin</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Tilmicosin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
@ -1145,167 +1320,8 @@ v3.3</a> (2021).</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Tedizolid</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Vancomycin</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Enterobacter cloacae</td>
|
||||
<td align="center">Nafithromycin</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
|
||||
</h2>
|
||||
<p>A data set with 20,318 rows and 11 columns, containing the following
|
||||
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
|
||||
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
|
||||
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
|
||||
file</a> (39 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
|
||||
file</a> (0.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
|
||||
text file</a> (1.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
|
||||
file</a> (3.6 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
|
||||
file</a> (2.2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
|
||||
file</a> (3.4 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
|
||||
</h3>
|
||||
<p>This data set contains interpretation rules for MIC values and disk
|
||||
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
|
||||
(2011-2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
<col width="4%">
|
||||
<col width="16%">
|
||||
<col width="8%">
|
||||
<col width="11%">
|
||||
<col width="9%">
|
||||
<col width="8%">
|
||||
<col width="10%">
|
||||
<col width="10%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">guideline</th>
|
||||
<th align="center">method</th>
|
||||
<th align="center">site</th>
|
||||
<th align="center">mo</th>
|
||||
<th align="center">rank_index</th>
|
||||
<th align="center">ab</th>
|
||||
<th align="center">ref_tbl</th>
|
||||
<th align="center">disk_dose</th>
|
||||
<th align="center">breakpoint_S</th>
|
||||
<th align="center">breakpoint_R</th>
|
||||
<th align="center">uti</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Aspergillus fumigatus</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Aspergillus</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">4</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Aspergillus niger</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Aspergillus</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">4</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center">3</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Candida albicans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Candida krusei</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Candida parapsilosis</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">Amphotericin B</td>
|
||||
<td align="center">Candida</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
@ -1460,14 +1476,12 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9008</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -185,13 +185,11 @@
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
|
||||
@ -201,13 +201,8 @@
|
||||
<div class="section level2">
|
||||
<h2 id="needed-r-packages">Needed R packages<a class="anchor" aria-label="anchor" href="#needed-r-packages"></a>
|
||||
</h2>
|
||||
<p>As with many uses in R, we need some additional packages for AMR data
|
||||
analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr
|
||||
Hadley Wickham. The tidyverse tremendously improves the way we conduct
|
||||
data science - it allows for a very natural way of writing syntaxes and
|
||||
creating beautiful plots in R.</p>
|
||||
<p>Our <code>AMR</code> package depends on these packages and even
|
||||
extends their use and functions.</p>
|
||||
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
|
||||
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
|
||||
@ -219,34 +214,24 @@ extends their use and functions.</p>
|
||||
<div class="section level2">
|
||||
<h2 id="prediction-analysis">Prediction analysis<a class="anchor" aria-label="anchor" href="#prediction-analysis"></a>
|
||||
</h2>
|
||||
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>,
|
||||
which takes the same input as functions for <a href="./AMR.html">other
|
||||
AMR data analysis</a>. Based on a date column, it calculates cases per
|
||||
year and uses a regression model to predict antimicrobial
|
||||
resistance.</p>
|
||||
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
|
||||
<p>It is basically as easy as:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># or:</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> model <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>predict_TZP <span class="ot"><-</span> example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<p>The function will look for a date column itself if
|
||||
<code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model
|
||||
will be printed unless using
|
||||
<code>resistance_predict(..., info = FALSE)</code>.</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true"></a><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true"></a></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true"></a><span class="co"># or:</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true"></a>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true"></a> model <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true"></a></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true"></a>predict_TZP <-<span class="st"> </span>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true"></a> <span class="dt">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
|
||||
<pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre>
|
||||
<p>This text is only a printed summary - the actual result (output) of
|
||||
the function is a <code>data.frame</code> containing for each year: the
|
||||
number of observations, the actual observed resistance, the estimated
|
||||
resistance and the standard error below and above the estimation:</p>
|
||||
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">predict_TZP</span>
|
||||
<span class="co"># year value se_min se_max observations observed estimated</span>
|
||||
@ -281,18 +266,12 @@ resistance and the standard error below and above the estimation:</p>
|
||||
<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span>
|
||||
<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span>
|
||||
<span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></code></pre></div>
|
||||
<p>The function <code>plot</code> is available in base R, and can be
|
||||
extended by other packages to depend the output based on the type of
|
||||
input. We extended its function to cope with resistance predictions:</p>
|
||||
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
|
||||
<p>This is the fastest way to plot the result. It automatically adds the
|
||||
right axes, error bars, titles, number of available observations and
|
||||
type of model.</p>
|
||||
<p>We also support the <code>ggplot2</code> package with our custom
|
||||
function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing
|
||||
plots:</p>
|
||||
<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
|
||||
<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
|
||||
@ -304,9 +283,7 @@ plots:</p>
|
||||
<div class="section level3">
|
||||
<h3 id="choosing-the-right-model">Choosing the right model<a class="anchor" aria-label="anchor" href="#choosing-the-right-model"></a>
|
||||
</h3>
|
||||
<p>Resistance is not easily predicted; if we look at vancomycin
|
||||
resistance in Gram-positive bacteria, the spread (i.e. standard error)
|
||||
is enormous:</p>
|
||||
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
@ -314,13 +291,8 @@ is enormous:</p>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
|
||||
<p>Vancomycin resistance could be 100% in ten years, but might also stay
|
||||
around 0%.</p>
|
||||
<p>You can define the model with the <code>model</code> parameter. The
|
||||
model chosen above is a generalised linear regression model using a
|
||||
binomial distribution, assuming that a period of zero resistance was
|
||||
followed by a period of increasing resistance leading slowly to more and
|
||||
more resistance.</p>
|
||||
<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
|
||||
<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
|
||||
<p>Valid values are:</p>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
@ -336,8 +308,7 @@ more resistance.</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>
|
||||
<code>"binomial"</code> or <code>"binom"</code> or
|
||||
<code>"logit"</code>
|
||||
<code>"binomial"</code> or <code>"binom"</code> or <code>"logit"</code>
|
||||
</td>
|
||||
<td><code>glm(..., family = binomial)</code></td>
|
||||
<td>Generalised linear model with binomial distribution</td>
|
||||
@ -358,9 +329,7 @@ more resistance.</p>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>For the vancomycin resistance in Gram-positive bacteria, a linear
|
||||
model might be more appropriate since no binomial distribution is to be
|
||||
expected based on the observed years:</p>
|
||||
<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
@ -369,8 +338,7 @@ expected based on the observed years:</p>
|
||||
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
<p>This seems more likely, doesn’t it?</p>
|
||||
<p>The model itself is also available from the object, as an
|
||||
<code>attribute</code>:</p>
|
||||
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span>
|
||||
|
||||
@ -399,14 +367,12 @@ expected based on the observed years:</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
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@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
|
||||
@ -198,83 +198,33 @@
|
||||
|
||||
|
||||
|
||||
<p>Note: to keep the package size as small as possible, we only included
|
||||
this vignette on CRAN. You can read more vignettes on our website about
|
||||
how to conduct AMR data analysis, determine MDRO’s, find explanation of
|
||||
EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
|
||||
<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
|
||||
<hr>
|
||||
<p><code>AMR</code> is a free, open-source and independent R package
|
||||
(see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>)
|
||||
to simplify the analysis and prediction of Antimicrobial Resistance
|
||||
(AMR) and to work with microbial and antimicrobial data and properties,
|
||||
by using evidence-based methods. <strong>Our aim is to provide a
|
||||
standard</strong> for clean and reproducible antimicrobial resistance
|
||||
data analysis, that can therefore empower epidemiological analyses to
|
||||
continuously enable surveillance and treatment evaluation in any
|
||||
setting.</p>
|
||||
<p>After installing this package, R knows ~71,000 distinct microbial
|
||||
species and all ~570 antibiotic, antimycotic and antiviral drugs by name
|
||||
and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and
|
||||
knows all about valid R/SI and MIC values. It supports any data format,
|
||||
including WHONET/EARS-Net data.</p>
|
||||
<p>The <code>AMR</code> package is available in Danish, Dutch, English,
|
||||
French, German, Italian, Portuguese, Russian, Spanish and Swedish.
|
||||
Antimicrobial drug (group) names and colloquial microorganism names are
|
||||
provided in these languages.</p>
|
||||
<p>This package is fully independent of any other R package and works on
|
||||
Windows, macOS and Linux with all versions of R since R-3.0 (April
|
||||
2013). <strong>It was designed to work in any setting, including those
|
||||
with very limited resources</strong>. Since its first public release in
|
||||
early 2018, this package has been downloaded from more than 175
|
||||
countries.</p>
|
||||
<p><code>AMR</code> is a free, open-source and independent R package (see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>The <code>AMR</code> package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
||||
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
|
||||
<p>This package can be used for:</p>
|
||||
<ul>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package
|
||||
contains all microbial (sub)species from the Catalogue of Life and List
|
||||
of Prokaryotic names with Standing in Nomenclature</li>
|
||||
<li>Interpreting raw MIC and disk diffusion values, based on the latest
|
||||
CLSI or EUCAST guidelines</li>
|
||||
<li>Retrieving antimicrobial drug names, doses and forms of
|
||||
administration from clinical health care records</li>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
|
||||
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</li>
|
||||
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</li>
|
||||
<li>Determining first isolates to be used for AMR data analysis</li>
|
||||
<li>Calculating antimicrobial resistance</li>
|
||||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant
|
||||
organisms (MDRO)</li>
|
||||
<li>Calculating (empirical) susceptibility of both mono therapy and
|
||||
combination therapies</li>
|
||||
<li>Predicting future antimicrobial resistance using regression
|
||||
models</li>
|
||||
<li>Getting properties for any microorganism (like Gram stain, species,
|
||||
genus or family)</li>
|
||||
<li>Getting properties for any antibiotic (like name, code of
|
||||
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
|
||||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</li>
|
||||
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies</li>
|
||||
<li>Predicting future antimicrobial resistance using regression models</li>
|
||||
<li>Getting properties for any microorganism (like Gram stain, species, genus or family)</li>
|
||||
<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
|
||||
<li>Plotting antimicrobial resistance</li>
|
||||
<li>Applying EUCAST expert rules</li>
|
||||
<li>Getting SNOMED codes of a microorganism, or getting properties of a
|
||||
microorganism based on a SNOMED code</li>
|
||||
<li>Getting LOINC codes of an antibiotic, or getting properties of an
|
||||
antibiotic based on a LOINC code</li>
|
||||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to
|
||||
translate MIC values and disk diffusion diameters to R/SI</li>
|
||||
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code</li>
|
||||
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code</li>
|
||||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</li>
|
||||
<li>Principal component analysis for AMR</li>
|
||||
</ul>
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI
|
||||
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
|
||||
publicly and freely available. We continually export our data sets to
|
||||
formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
|
||||
files that are machine-readable and suitable for input in any software
|
||||
program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all
|
||||
download links on our website</a>, which is automatically updated with
|
||||
every code change.</p>
|
||||
<p>This R package was created for both routine data analysis and
|
||||
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
|
||||
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
|
||||
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This
|
||||
R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
||||
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
|
||||
10.33612/diss.192486375</a>) but is actively and durably maintained (see
|
||||
<a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>)
|
||||
by two public healthcare organisations in the Netherlands.</p>
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is actively and durably maintained (see <a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>) by two public healthcare organisations in the Netherlands.</p>
|
||||
</div>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@ -287,14 +237,12 @@ by two public healthcare organisations in the Netherlands.</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -269,13 +269,11 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
335
docs/index.html
335
docs/index.html
@ -47,7 +47,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9010</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -61,7 +61,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -195,75 +195,23 @@
|
||||
<code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
|
||||
</h1></div>
|
||||
<blockquote>
|
||||
<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
|
||||
guideline for intrinsic resistance</a> (v3.3, October 2021) is now
|
||||
supported, the CLSI 2021 interpretation guideline is now supported, and
|
||||
our taxonomy tables have been updated as well (LPSN, 5 October
|
||||
2021).</p>
|
||||
<p>Update May 2022: EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="reference/as.rsi.html">as.rsi()</a></code>!</p>
|
||||
<p>Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
|
||||
</blockquote>
|
||||
<div class="section level3">
|
||||
<h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
|
||||
</h3>
|
||||
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction
|
||||
of Antimicrobial Resistance (AMR) and to work with microbial and
|
||||
antimicrobial data and properties, by using evidence-based methods.
|
||||
<strong>Our aim is to provide a standard</strong> for clean and
|
||||
reproducible AMR data analysis, that can therefore empower
|
||||
epidemiological analyses to continuously enable surveillance and
|
||||
treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct
|
||||
microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic
|
||||
and antiviral drugs</strong></a> by name and code (including ATC,
|
||||
WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about
|
||||
valid R/SI and MIC values. It supports any data format, including
|
||||
WHONET/EARS-Net data.</p>
|
||||
<p>The <code>AMR</code> package is available in
|
||||
<img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Danish,
|
||||
<img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Dutch,
|
||||
<img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
English,
|
||||
<img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
French,
|
||||
<img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
German,
|
||||
<img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Italian,
|
||||
<img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Portuguese,
|
||||
<img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Russian,
|
||||
<img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Spanish and
|
||||
<img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;">
|
||||
Swedish. Antimicrobial drug (group) names and colloquial microorganism
|
||||
names are provided in these languages.</p>
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent
|
||||
of any other R package</a> and works on Windows, macOS and Linux with
|
||||
all versions of R since R-3.0 (April 2013). <strong>It was designed to
|
||||
work in any setting, including those with very limited
|
||||
resources</strong>. It was created for both routine data analysis and
|
||||
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
|
||||
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
|
||||
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This
|
||||
R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
||||
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
|
||||
10.33612/diss.192486375</a>) but is <a href="./news">actively and
|
||||
durably maintained</a> by two public healthcare organisations in the
|
||||
Netherlands.</p>
|
||||
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>The <code>AMR</code> package is available in <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;"> Dutch, <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;"> English, <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;"> German, <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;"> Italian, <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;"> Spanish and <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;"> Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
|
||||
<div class="main-content" style="display: inline-block;">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
|
||||
<strong>Used in 175 countries</strong><br> Since its first public
|
||||
release in early 2018, this R package has been used in almost all
|
||||
countries in the world. Click the map to enlarge and to see the country
|
||||
names.
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
|
||||
</p>
|
||||
</div>
|
||||
<div class="section level5">
|
||||
<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable
|
||||
microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
|
||||
<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
|
||||
</h5>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
|
||||
@ -277,12 +225,7 @@ microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-am
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
|
||||
<span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>With only having defined a row filter on Gram-negative bacteria with
|
||||
intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code>
|
||||
and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on
|
||||
two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
|
||||
<code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the
|
||||
<code>AMR</code> package make sure you get what you meant:</p>
|
||||
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">bacteria</th>
|
||||
@ -396,14 +339,9 @@ two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html"
|
||||
<div class="section level4">
|
||||
<h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
|
||||
</h4>
|
||||
<p>The development of this package is part of, related to, or made
|
||||
possible by:</p>
|
||||
<p>The development of this package is part of, related to, or made possible by:</p>
|
||||
<div align="center">
|
||||
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a>
|
||||
<a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a>
|
||||
<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a>
|
||||
<a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a>
|
||||
<a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
|
||||
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
@ -412,33 +350,21 @@ possible by:</p>
|
||||
</h3>
|
||||
<p>This package can be used for:</p>
|
||||
<ul>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package
|
||||
contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in
|
||||
Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Interpreting raw MIC and disk diffusion values, based on the latest
|
||||
CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
|
||||
<li>Retrieving antimicrobial drug names, doses and forms of
|
||||
administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
|
||||
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
|
||||
<li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
|
||||
<li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant
|
||||
organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
|
||||
<li>Calculating (empirical) susceptibility of both mono therapy and
|
||||
combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Predicting future antimicrobial resistance using regression models
|
||||
(<a href="./articles/resistance_predict.html">tutorial</a>)</li>
|
||||
<li>Getting properties for any microorganism (like Gram stain, species,
|
||||
genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting properties for any antibiotic (like name, code of
|
||||
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
|
||||
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
|
||||
<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
|
||||
<li>Getting SNOMED codes of a microorganism, or getting properties of a
|
||||
microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting LOINC codes of an antibiotic, or getting properties of an
|
||||
antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
|
||||
translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
|
||||
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
|
||||
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
|
||||
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
|
||||
</ul>
|
||||
</div>
|
||||
@ -449,24 +375,17 @@ translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/d
|
||||
<h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a>
|
||||
</h4>
|
||||
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
|
||||
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R
|
||||
network (CRAN)</a>. Install this package in R from CRAN by using the
|
||||
command:</p>
|
||||
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click
|
||||
on the menu <em>Tools</em> > <em>Install Packages…</em> and then type
|
||||
in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be
|
||||
available in this latest release. To use all functions and data sets
|
||||
mentioned on this website, install the latest development version.</p>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> > <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
|
||||
</h4>
|
||||
<p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
|
||||
<p>The latest and unpublished development version can be installed from
|
||||
GitHub in two ways:</p>
|
||||
<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>
|
||||
<p>Manually, using:</p>
|
||||
@ -475,16 +394,11 @@ GitHub in two ways:</p>
|
||||
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe
|
||||
platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our
|
||||
R-universe address</a> to your list of repositories (‘repos’):</p>
|
||||
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
|
||||
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>After this, you can install and update this <code>AMR</code> package
|
||||
like any official release (e.g., using
|
||||
<code>install.packages("AMR")</code> or in RStudio via <em>Tools</em>
|
||||
> <em>Check for Package Updates…</em>).</p>
|
||||
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> > <em>Check for Package Updates…</em>).</p>
|
||||
</li>
|
||||
</ol>
|
||||
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p>
|
||||
@ -493,8 +407,7 @@ like any official release (e.g., using
|
||||
<div class="section level3">
|
||||
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
|
||||
</h3>
|
||||
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or
|
||||
click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
|
||||
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a>
|
||||
@ -502,181 +415,66 @@ click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How t
|
||||
<div class="section level4">
|
||||
<h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
|
||||
</h4>
|
||||
<p>This package contains the complete taxonomic tree of almost all
|
||||
~71,000 microorganisms from the authoritative and comprehensive
|
||||
Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>),
|
||||
supplemented by data from the List of Prokaryotic names with Standing in
|
||||
Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>).
|
||||
This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished,
|
||||
which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be
|
||||
checked which version of the CoL is included in this package.</p>
|
||||
<p>This package contains the complete taxonomic tree of almost all ~71,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
|
||||
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
|
||||
</h4>
|
||||
<p>This package contains <strong>all ~570 antibiotic, antimycotic and
|
||||
antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC)
|
||||
codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the
|
||||
World Health Organization Collaborating Centre for Drug Statistics
|
||||
Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
|
||||
Community Register of the European Commission</a>.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial
|
||||
purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
<p>This package contains <strong>all ~570 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a>
|
||||
</h4>
|
||||
<p>We support WHONET and EARS-Net data. Exported files from WHONET can
|
||||
be imported into R and can be analysed easily using this package. For
|
||||
education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>
|
||||
with the exact same structure as a WHONET export file. Furthermore, this
|
||||
package also contains a <a href="./reference/antibiotics.html">data set
|
||||
antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows
|
||||
almost all WHONET abbreviations for microorganisms. When using WHONET
|
||||
data as input for analysis, all input parameters will be set
|
||||
automatically.</p>
|
||||
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work
|
||||
with WHONET data here</a>.</p>
|
||||
<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
|
||||
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a>
|
||||
</h4>
|
||||
<p>The <code>AMR</code> package basically does four important
|
||||
things:</p>
|
||||
<p>The <code>AMR</code> package basically does four important things:</p>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>
|
||||
<p>It <strong>cleanses existing data</strong> by providing new
|
||||
<em>classes</em> for microoganisms, antibiotics and antimicrobial
|
||||
results (both S/I/R and MIC). By installing this package, you teach R
|
||||
everything about microbiology that is needed for analysis. These
|
||||
functions all use intelligent rules to guess results that you would
|
||||
expect:</p>
|
||||
<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
|
||||
<ul>
|
||||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human
|
||||
readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em>
|
||||
is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S.
|
||||
aureus</em> is “B_STPHY_AURS”. The function takes almost any text as
|
||||
input that looks like the name or code of a microorganism like “E.
|
||||
coli”, “esco” or “esccol” and tries to find expected results using
|
||||
intelligent rules combined with the included Catalogue of Life data set.
|
||||
It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group
|
||||
<em>Staphylococci</em> into coagulase negative and positive (CoNS and
|
||||
CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can
|
||||
categorise <em>Streptococci</em> into Lancefield groups (like
|
||||
beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||||
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial
|
||||
IDs, these IDs are also human readable based on those used by EARS-Net.
|
||||
For example, the ID of amoxicillin is <code>AMX</code> and the ID of
|
||||
gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also
|
||||
uses intelligent rules to find results like accepting misspelling, trade
|
||||
names and abbrevations used in many laboratory systems. For instance,
|
||||
the values “Furabid”, “Furadantin”, “nitro” all return the ID of
|
||||
Nitrofurantoine. To accomplish this, the package contains a database
|
||||
with most LIS codes, official names, trade names, ATC codes, defined
|
||||
daily doses (DDD) and drug categories of antibiotics.</li>
|
||||
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on
|
||||
raw MIC values (in mg/L) or disk diffusion values (in mm), or transform
|
||||
existing values to valid antimicrobial results. It produces just S, I or
|
||||
R based on your input and warns about invalid values. Even values like
|
||||
“<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
|
||||
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a
|
||||
so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values
|
||||
as levels. A value like “<=0.002; S” (combined MIC/RSI) will result
|
||||
in “<=0.002”.</li>
|
||||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||||
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
|
||||
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
|
||||
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>enhances existing data</strong> and <strong>adds new
|
||||
data</strong> from data sets included in this package.</p>
|
||||
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
|
||||
<ul>
|
||||
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
|
||||
expert rules to isolates</a> (not the translation from MIC to R/SI
|
||||
values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
|
||||
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of
|
||||
every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using
|
||||
guidelines from the CLSI</a> (Clinical and Laboratory Standards
|
||||
Institute).
|
||||
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
|
||||
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
|
||||
<ul>
|
||||
<li>You can also identify first <em>weighted</em> isolates of every
|
||||
patient, an adjusted version of the CLSI guideline. This takes into
|
||||
account key antibiotics of every strain and compares them.</li>
|
||||
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are
|
||||
multi-drug resistant organisms (MDRO). It supports a variety of
|
||||
international guidelines, such as the MDR-paper by Magiorakos <em>et
|
||||
al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID
|
||||
21793988</a>), the exceptional phenotype definitions of EUCAST and the
|
||||
WHO guideline on multi-drug resistant TB. It also supports the national
|
||||
guidelines of the Netherlands and Germany.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set
|
||||
microorganisms</a> contains the complete taxonomic tree of ~70,000
|
||||
microorganisms. Furthermore, some colloquial names and all Gram stains
|
||||
are available, which enables resistance analysis of e.g. different
|
||||
antibiotics per Gram stain. The package also contains functions to look
|
||||
up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>,
|
||||
<code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even
|
||||
<code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any
|
||||
SNOMED CT code associated with a microorganism. As all these function
|
||||
use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent
|
||||
rules for determination. For example, <code>mo_genus("MRSA")</code> and
|
||||
<code>mo_genus("S. aureus")</code> will both return
|
||||
<code>"Staphylococcus"</code>. They also come with support for German,
|
||||
Danish, Dutch, Spanish, Italian, French and Portuguese. These functions
|
||||
can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a>
|
||||
contains ~450 antimicrobial drugs with their EARS-Net code, ATC code,
|
||||
PubChem compound ID, LOINC code, official name, common LIS codes and
|
||||
DDDs of both oral and parenteral administration. It also contains all
|
||||
(thousands of) trade names found in PubChem. Use functions like
|
||||
<code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>,
|
||||
<code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up
|
||||
values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code>
|
||||
internally so they support the same intelligent rules to guess the most
|
||||
probable result. For example, <code>ab_name("Fluclox")</code>,
|
||||
<code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code>
|
||||
will all return <code>"Flucloxacillin"</code>. These functions can again
|
||||
be used to add new variables to your data.</li>
|
||||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code>mo_genus("MRSA")</code> and <code>mo_genus("S. aureus")</code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code>ab_name("Fluclox")</code>, <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>analyses the data</strong> with convenient functions
|
||||
that use well-known methods.</p>
|
||||
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
|
||||
<ul>
|
||||
<li>Calculate the microbial susceptibility or resistance (and even
|
||||
co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and
|
||||
<code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the
|
||||
<code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>,
|
||||
<code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and
|
||||
<code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of
|
||||
isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>,
|
||||
<code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions.
|
||||
All these functions can be used with the <code>dplyr</code> package
|
||||
(e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
|
||||
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for
|
||||
the <code>ggplot2</code> package</li>
|
||||
<li>Predict antimicrobial resistance for the nextcoming years using
|
||||
logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code>
|
||||
function</li>
|
||||
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
|
||||
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
|
||||
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>It <strong>teaches the user</strong> how to use all the above
|
||||
actions.</p>
|
||||
<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
|
||||
<ul>
|
||||
<li>Aside from this website with many tutorials, the package itself
|
||||
contains extensive help pages with many examples for all functions.</li>
|
||||
<li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
|
||||
<li>The package also contains example data sets:
|
||||
<ul>
|
||||
<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code>
|
||||
data set</a>. This data set contains 2,000 microbial isolates with their
|
||||
full antibiograms. It reflects reality and can be used to practice AMR
|
||||
data analysis.</li>
|
||||
<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data
|
||||
set</a>. This data set only contains fake data, but with the exact same
|
||||
structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
|
||||
<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> data set</a>. This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.</li>
|
||||
<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data set</a>. This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
@ -687,9 +485,7 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
|
||||
<div class="section level3">
|
||||
<h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
|
||||
</h3>
|
||||
<p>This R package is free, open-source software and licensed under the
|
||||
<a href="./LICENSE-text.html">GNU General Public License v2.0
|
||||
(GPL-2)</a>. In a nutshell, this means that this package:</p>
|
||||
<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
|
||||
<ul>
|
||||
<li><p>May be used for commercial purposes</p></li>
|
||||
<li><p>May be used for private purposes</p></li>
|
||||
@ -697,18 +493,15 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
|
||||
<li>
|
||||
<p>May be modified, although:</p>
|
||||
<ul>
|
||||
<li>Modifications <strong>must</strong> be released under the same
|
||||
license when distributing the package</li>
|
||||
<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
|
||||
<li>Changes made to the code <strong>must</strong> be documented</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>May be distributed, although:</p>
|
||||
<ul>
|
||||
<li>Source code <strong>must</strong> be made available when the package
|
||||
is distributed</li>
|
||||
<li>A copy of the license and copyright notice <strong>must</strong> be
|
||||
included with the package.</li>
|
||||
<li>Source code <strong>must</strong> be made available when the package is distributed</li>
|
||||
<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><p>Comes with a LIMITATION of liability</p></li>
|
||||
@ -764,14 +557,12 @@ included with the package.</li>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
2493
docs/news/index.html
2493
docs/news/index.html
File diff suppressed because it is too large
Load Diff
@ -1,4 +1,4 @@
|
||||
pandoc: 2.17.1.1
|
||||
pandoc: 2.9.2.1
|
||||
pkgdown: 2.0.2
|
||||
pkgdown_sha: ~
|
||||
articles:
|
||||
@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2022-03-14T15:38Z
|
||||
last_built: 2022-03-27T07:33Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -184,13 +184,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -221,13 +221,11 @@ The Netherlands
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -195,13 +195,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -215,13 +215,11 @@
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -275,13 +275,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
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||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -344,13 +344,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -226,13 +226,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -250,13 +250,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -256,7 +256,7 @@
|
||||
<p>The <code>ab_class()</code> function can be used to filter/select on a manually defined antibiotic class. It searches for results in the <a href="antibiotics.html">antibiotics</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
|
||||
<p>The <code>ab_selector()</code> function can be used to internally filter the <a href="antibiotics.html">antibiotics</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p>
|
||||
<p>The <code>administrable_per_os()</code> and <code>administrable_iv()</code> functions also rely on the <a href="antibiotics.html">antibiotics</a> data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the <a href="antibiotics.html">antibiotics</a> data set.</p>
|
||||
<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
|
||||
<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
|
||||
</div>
|
||||
<div id="full-list-of-supported-antibiotic-classes">
|
||||
<h2>Full list of supported (antibiotic) classes</h2>
|
||||
@ -430,13 +430,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -259,13 +259,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -280,13 +280,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -239,13 +239,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
File diff suppressed because one or more lines are too long
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -377,13 +377,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -225,13 +225,13 @@
|
||||
<dt>ab</dt>
|
||||
<dd><p>any (vector of) text that can be coerced to a valid antimicrobial code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
|
||||
<dt>guideline</dt>
|
||||
<dd><p>defaults to the latest included EUCAST guideline, see <em>Details</em> for all options</p></dd>
|
||||
<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="rsi_translation.html">rsi_translation</a> data set), supports EUCAST (2011-2022) and CLSI (2011-2022), see <em>Details</em></p></dd>
|
||||
<dt>uti</dt>
|
||||
<dd><p>(Urinary Tract Infection) A vector with <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, this can also be a column containing <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
|
||||
<dt>conserve_capped_values</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that MIC values starting with <code>">"</code> (but not <code>">="</code>) must always return "R" , and that MIC values starting with <code>"<"</code> (but not <code>"<="</code>) must always return "S"</p></dd>
|
||||
<dt>add_intrinsic_resistance</dt>
|
||||
<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p></dd>
|
||||
<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p></dd>
|
||||
<dt>reference_data</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="rsi_translation.html">rsi_translation</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="rsi_translation.html">rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd>
|
||||
<dt>col_mo</dt>
|
||||
@ -263,8 +263,8 @@
|
||||
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
|
||||
|
||||
|
||||
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).</p>
|
||||
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2021"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
|
||||
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022).</p>
|
||||
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2022"</code> or <code>"CLSI 2022"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
|
||||
</div>
|
||||
|
||||
<div class="section">
|
||||
@ -278,7 +278,7 @@
|
||||
<h3 id="machine-readable-interpretation-guidelines">Machine-Readable Interpretation Guidelines<a class="anchor" aria-label="anchor" href="#machine-readable-interpretation-guidelines"></a></h3>
|
||||
|
||||
|
||||
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 20,318 rows and 11 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/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 20,369 rows and 11 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>
|
||||
</div>
|
||||
|
||||
<div class="section">
|
||||
@ -289,7 +289,7 @@
|
||||
<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> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
|
||||
</div>
|
||||
|
||||
<p><code>NA_rsi_</code> is a missing value of the new <code><rsi></code> class.</p>
|
||||
<p><code>NA_rsi_</code> is a missing value of the new <code><rsi></code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
|
||||
</div>
|
||||
<div id="interpretation-of-r-and-s-i">
|
||||
<h2>Interpretation of R and S/I</h2>
|
||||
@ -408,7 +408,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.rsi.eligible</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># note: from dplyr 1.0.0 on, this will be: </span>
|
||||
<span class="co"># since dplyr 1.0.0, this can also be: </span>
|
||||
<span class="co"># example_isolates %>%</span>
|
||||
<span class="co"># mutate(across(where(is.rsi.eligible), as.rsi))</span>
|
||||
<span class="op">}</span>
|
||||
@ -423,13 +423,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -257,13 +257,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -216,13 +216,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -265,13 +265,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -235,13 +235,11 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -200,13 +200,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -31,7 +31,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -358,13 +358,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -301,13 +301,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -202,13 +202,11 @@
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -31,7 +31,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -334,13 +334,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9007</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -199,13 +199,11 @@
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||||
Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||||
2.0.2.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user