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(v1.3.0.9002) intrinsic_resistant data set

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dr. M.S. (Matthijs) Berends 2020-08-14 13:36:10 +02:00
parent 7d16bec21f
commit 08d62bb5d5
111 changed files with 50487 additions and 525 deletions
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2
.github/workflows/check.yaml vendored
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@ -47,7 +47,7 @@ jobs:
# - {os: macOS-latest, r: 'oldrel'}
# - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: windows-latest, r: 'devel'}
- {os: macOS-latest, r: 'devel'}
# - {os: macOS-latest, r: 'devel'}
# - {os: ubuntu-16.04, r: '4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: windows-latest, r: '3.6'}
# - {os: ubuntu-16.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}

10
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.3.0.9001
Date: 2020-08-10
Version: 1.3.0.9002
Date: 2020-08-14
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@ -21,6 +21,8 @@ Authors@R: c(
family = "Hassing", given = c("Erwin", "E.", "A."), email = "e.hassing@certe.nl"),
person(role = "ctb",
family = "Hazenberg", given = c("Eric", "H.", "L.", "C.", "M."), email = "e.hazenberg@jbz.nl"),
person(role = "ctb",
family = "Knight", given = "Gwen", email = "gwen.knight@lshtm.ac.uk"),
person(role = "ctb",
family = "Lenglet", given = "Annick", email = "annick.lenglet@amsterdam.msf.org"),
person(role = "ctb",
@ -28,7 +30,9 @@ Authors@R: c(
person(role = "ctb",
family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"),
person(role = "ctb",
family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"))
family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"),
person(role = "ctb",
family = "Underwood", given = "Anthony", email = "au3@sanger.ac.uk"))
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods, like those defined by Leclercq et al. (2013)

23
NEWS.md
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@ -1,5 +1,18 @@
# AMR 1.3.0.9001
## <small>Last updated: 10 August 2020</small>
# AMR 1.3.0.9002
## <small>Last updated: 14 August 2020</small>
### New
* Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
Curious about which enterococci are actually intrinsic resistant to vancomycin?
```r
library(AMR)
library(dplyr)
intrinsic_resistant %>%
filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>%
pull(microorganism)
# [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
```
### Changed
* Support for using `dplyr`'s `across()` in `as.rsi()` to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.
@ -8,10 +21,12 @@
your_data %>% mutate_if(is.mic, as.rsi)
your_data %>% mutate_if(is.disk, as.rsi)
# since dplyr 1.0.0
your_data %>% mutate(across(where(is.mic), as.rsi))
# since dplyr 1.0.0
your_data %>% mutate(across(where(is.mic), as.rsi))
your_data %>% mutate(across(where(is.disk), as.rsi))
```
* Improved overall speed by tweaking joining functions
# AMR 1.3.0

38
R/aa_helper_functions.R
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@ -48,6 +48,37 @@ distinct.default <- function(.data, ..., .keep_all = FALSE) {
distinct.grouped_data <- function(.data, ..., .keep_all = FALSE) {
apply_grouped_function(.data, "distinct", ..., .keep_all = .keep_all)
}
# faster implementation of left_join than using base::merge() by poorman - we use base::match():
left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
if (is.null(by)) {
by <- intersect(names(x), names(y))[1L]
if (is.na(by)) {
stop_("no common column found for left_join()")
}
join_message(by)
} else if (!is.null(names(by))) {
by <- unname(c(names(by), by))
}
if (length(by) == 1) {
by <- rep(by, 2)
}
requires_suffix <- any(colnames(x) %in% colnames(y))
if (requires_suffix == TRUE) {
int_x <- colnames(x) %in% colnames(y) & colnames(x) != by[1]
int_y <- colnames(y) %in% colnames(x) & colnames(y) != by[2]
colnames(x)[int_x] <- paste0(colnames(x)[int_x], suffix[1L])
colnames(y)[int_y] <- paste0(colnames(y)[int_y], suffix[2L])
}
merged <- cbind(x,
y[match(x[, by[1], drop = TRUE],
y[, by[2], drop = TRUE]),
colnames(y)[!colnames(y) %in% colnames(x) & !colnames(y) == by[2]],
drop = FALSE])
rownames(merged) <- NULL
merged
}
filter_join_worker <- function(x, y, by = NULL, type = c("anti", "semi")) {
type <- match.arg(type, choices = c("anti", "semi"), several.ok = FALSE)
if (is.null(by)) {
@ -92,9 +123,10 @@ check_dataset_integrity <- function() {
"synonyms", "oral_ddd", "oral_units",
"iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
na.rm = TRUE)
}, error = function(e)
stop_('please use the command \'library("AMR")\' before using this function, to load the required reference data.', call = FALSE)
)
}, error = function(e) {
# package not yet loaded
require("AMR")
})
invisible(TRUE)
}

6
R/aa_helper_functions_dplyr.R
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@ -248,9 +248,9 @@ inner_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
join_worker(x = x, y = y, by = by, suffix = suffix, sort = FALSE)
}
left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
join_worker(x = x, y = y, by = by, suffix = suffix, all.x = TRUE)
}
# left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
# join_worker(x = x, y = y, by = by, suffix = suffix, all.x = TRUE)
# }
right_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
join_worker(x = x, y = y, by = by, suffix = suffix, all.y = TRUE)

19
R/ab.R
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@ -25,6 +25,7 @@
#' @inheritSection lifecycle Maturing lifecycle
#' @param x character vector to determine to antibiotic ID
#' @param flag_multiple_results logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
#' @param info logical to indicate whether a progress bar should be printed
#' @param ... arguments passed on to internal functions
#' @rdname as.ab
#' @inheritSection WHOCC WHOCC
@ -75,7 +76,7 @@
#' # they use as.ab() internally:
#' ab_name("J01FA01") # "Erythromycin"
#' ab_name("eryt") # "Erythromycin"
as.ab <- function(x, flag_multiple_results = TRUE, ...) {
as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
check_dataset_integrity()
@ -131,7 +132,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
}
if (initial_search == TRUE) {
progress <- progress_estimated(n = length(x), n_min = 25) # start if n >= 25
progress <- progress_estimated(n = length(x), n_min = ifelse(isTRUE(info), 25, length(x) + 1)) # start if n >= 25
on.exit(close(progress))
}
@ -158,6 +159,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
from_text <- character(0)
}
# exact name
found <- antibiotics[which(toupper(antibiotics$name) == x[i]), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
next
}
# exact AB code
found <- antibiotics[which(antibiotics$ab == x[i]), ]$ab
if (length(found) > 0) {
@ -179,13 +187,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
next
}
# exact name
found <- antibiotics[which(toupper(antibiotics$name) == x[i]), ]$ab
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# exact LOINC code
loinc_found <- unlist(lapply(antibiotics$loinc,
function(s) x[i] %in% s))

25
R/data.R
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@ -70,7 +70,7 @@
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <http://ec.europa.eu/health/documents/community-register/html/atc.htm>
#' @inheritSection WHOCC WHOCC
#' @inheritSection AMR Read more on our website!
#' @seealso [microorganisms]
#' @seealso [microorganisms], [intrinsic_resistant]
"antibiotics"
#' @rdname antibiotics
@ -119,7 +119,7 @@
#'
#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> and <https://lpsn.dsmz.de> (check included version with [catalogue_of_life_version()]).
#' @inheritSection AMR Read more on our website!
#' @seealso [as.mo()], [mo_property()], [microorganisms.codes]
#' @seealso [as.mo()], [mo_property()], [microorganisms.codes], [intrinsic_resistant]
"microorganisms"
catalogue_of_life <- list(
@ -235,4 +235,25 @@ catalogue_of_life <- list(
#' - `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/master/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.
#' @inheritSection AMR Read more on our website!
#' @seealso [intrinsic_resistant]
"rsi_translation"
#' Data set with bacterial intrinsic resistance
#'
#' Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
#' @format A [`data.frame`] with `r format(nrow(intrinsic_resistant), big.mark = ",")` observations and `r ncol(intrinsic_resistant)` variables:
#' - `microorganism`\cr Name of the microorganism
#' - `antibiotic`\cr Name of the antibiotic drug
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
#'
#' This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
#' @inheritSection AMR Read more on our website!
#' @examples
#' if (require("dplyr")) {
#' intrinsic_resistant %>%
#' filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>%
#' pull(microorganism)
#' # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#' }
#' @seealso [intrinsic_resistant]
"intrinsic_resistant"

8
R/eucast_rules.R
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@ -668,7 +668,13 @@ eucast_rules <- function(x,
# Official EUCAST rules ---------------------------------------------------
eucast_notification_shown <- FALSE
eucast_rules_df <- eucast_rules_file # internal data file
if (!is.null(list(...)$eucast_rules_df)) {
# this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
eucast_rules_df <- list(...)$eucast_rules_df
} else {
# otherwise internal data file, created in data-raw/internals.R
eucast_rules_df <- eucast_rules_file
}
for (i in seq_len(nrow(eucast_rules_df))) {
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule"]

4
R/guess_ab_col.R
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@ -141,7 +141,7 @@ get_column_abx <- function(x,
x <- x[, x_columns, drop = FALSE] # without drop = TRUE, x will become a vector when x_columns is length 1
df_trans <- data.frame(colnames = colnames(x),
abcode = suppressWarnings(as.ab(colnames(x))))
abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)))
df_trans <- df_trans[!is.na(df_trans$abcode), ]
x <- as.character(df_trans$colnames)
names(x) <- df_trans$abcode
@ -150,7 +150,7 @@ get_column_abx <- function(x,
# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
dots <- list(...)
if (length(dots) > 0) {
newnames <- suppressWarnings(as.ab(names(dots)))
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (any(is.na(newnames))) {
warning("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
call. = FALSE, immediate. = TRUE)

2
R/lifecycle.R
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@ -28,7 +28,7 @@
#' @rdname lifecycle
#' @description Functions in this `AMR` package are categorised using [the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle](https://www.Tidyverse.org/lifecycle).
#'
#' \if{html}{\figure{lifecycle_Tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
#' This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions.
#' @section Experimental lifecycle:
#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}

16
R/mo.R
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@ -375,22 +375,20 @@ exec_as.mo <- function(x,
x <- data.frame(fullname_lower = tolower(x), stringsAsFactors = FALSE) %>%
left_join_MO_lookup(by = "fullname_lower") %>%
pull(property)
# x <- reference_data_to_use[data.table(fullname_lower = tolower(x)),
# on = "fullname_lower",
# ..property][[1]]
} else if (all(x %in% reference_data_to_use$fullname)) {
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
x <- data.frame(fullname = x, stringsAsFactors = FALSE) %>%
left_join_MO_lookup(by = "fullname") %>%
pull(property)
} else if (all(toupper(x) %in% microorganisms.codes$code)) {
# commonly used MO codes
x <- data.frame(code = toupper(x), stringsAsFactors = FALSE) %>%
left_join(microorganisms.codes, by = "code") %>%
left_join_MO_lookup(by = "mo") %>%
pull(property)
# y <- as.data.table(microorganisms.codes)[data.table(code = toupper(x)),
# on = "code", ]
#
# x <- reference_data_to_use[data.table(mo = y[["mo"]]),
# on = "mo",
# ..property][[1]]
} else if (!all(x %in% microorganisms[, property])) {

2
R/proportion.R
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@ -44,7 +44,7 @@
#'
#' The function [proportion_df()] takes any variable from `data` that has an [`rsi`] class (created with [as.rsi()]) and calculates the proportions R, I and S. It also supports grouped variables. The function [rsi_df()] works exactly like [proportion_df()], but adds the number of isolates.
#' @section Combination therapy:
#' When using more than one variable for `...` (= combination therapy)), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how [susceptibility()] works to calculate the %SI:
#' When using more than one variable for `...` (= combination therapy), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how [susceptibility()] works to calculate the %SI:
#'
#' ```
#' --------------------------------------------------------------------

4
R/zzz.R
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@ -30,13 +30,13 @@
}
.onAttach <- function(...) {
if (!interactive() || stats::runif(1) > 0.25 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
return()
}
packageStartupMessage("Thank you for using the AMR package! ",
"If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities:",
"\nhttps://msberends.github.io/AMR/survey.html",
"\n[ permanently turn this message off with: Sys.setenv(AMR_silentstart = TRUE) ]")
"\n[ prevent his notice with suppressPackageStartupMessages(library(AMR)) or use Sys.setenv(AMR_silentstart = TRUE) ]")
}
create_MO_lookup <- function() {

2
data-raw/internals.R
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@ -81,3 +81,5 @@ write.table(dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character),
"data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
write.table(dplyr::mutate_all(antivirals, as.character),
"data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)
write.table(intrinsic_resistant,
"data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE)

49463
data-raw/intrinsic_resistant.txt Normal file
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41
data-raw/reproduction_of_intrinsic_resistant.R Normal file
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@ -0,0 +1,41 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
library(AMR)
int_resis <- data.frame(microorganism = microorganisms$mo, stringsAsFactors = FALSE)
for (i in seq_len(nrow(antibiotics))) {
int_resis$new <- as.rsi("S")
colnames(int_resis)[ncol(int_resis)] <- antibiotics$name[i]
}
int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::eucast_rules_file, is.na(have_these_values)))
int_resis <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
tidyr::pivot_longer(-microorganism) %>%
filter(value == "R") %>%
select(microorganism, antibiotic = name)
int_resis$microorganism <- mo_name(int_resis$microorganism, language = NULL)
intrinsic_resistant <- as.data.frame(int_resis, stringsAsFactors = FALSE)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2)
rm(intrinsic_resistant)

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2
docs/404.html
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@ -81,7 +81,7 @@
</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="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

511
docs/articles/AMR.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -195,7 +195,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 10 August 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 14 August 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -226,21 +226,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-08-10</td>
<td align="center">2020-08-14</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">2020-08-10</td>
<td align="center">2020-08-14</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">2020-08-10</td>
<td align="center">2020-08-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -354,70 +354,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-08-12</td>
<td align="center">M9</td>
<td align="center">Hospital D</td>
<td align="center">2010-03-16</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</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>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-13</td>
<td align="center">W1</td>
<td align="center">2013-10-27</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-12-02</td>
<td align="center">L5</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</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="even">
<td align="center">2017-09-11</td>
<td align="center">O7</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</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>
</tr>
<tr class="odd">
<td align="center">2014-06-03</td>
<td align="center">K4</td>
<td align="center">2014-12-09</td>
<td align="center">F7</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">Escherichia coli</td>
<td align="center">R</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">2010-07-19</td>
<td align="center">W4</td>
<td align="center">2014-06-08</td>
<td align="center">S9</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="odd">
<td align="center">2015-01-01</td>
<td align="center">N10</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2015-11-12</td>
<td align="center">H6</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>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -452,16 +452,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,386</td>
<td align="right">51.93%</td>
<td align="right">10,386</td>
<td align="right">51.93%</td>
<td align="right">10,276</td>
<td align="right">51.38%</td>
<td align="right">10,276</td>
<td align="right">51.38%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,614</td>
<td align="right">48.07%</td>
<td align="right">9,724</td>
<td align="right">48.62%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -511,7 +511,7 @@ Longest: 1</p>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
<span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span>
</pre></div>
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb16"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">first</span> <span class="op">==</span> <span class="fl">TRUE</span>)
@ -525,7 +525,7 @@ Longest: 1</p>
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient A7, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient N8, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -541,10 +541,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-03</td>
<td align="center">A7</td>
<td align="center">2010-05-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -552,10 +552,10 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-04</td>
<td align="center">A7</td>
<td align="center">2010-07-03</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_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">S</td>
@ -563,52 +563,52 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">A7</td>
<td align="center">2010-07-31</td>
<td align="center">N8</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">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">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-15</td>
<td align="center">A7</td>
<td align="center">2010-09-13</td>
<td align="center">N8</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-28</td>
<td align="center">A7</td>
<td align="center">2010-09-15</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-03</td>
<td align="center">A7</td>
<td align="center">2010-10-16</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-14</td>
<td align="center">A7</td>
<td align="center">2010-10-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -618,30 +618,30 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-02-14</td>
<td align="center">A7</td>
<td align="center">2010-10-24</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-06</td>
<td align="center">A7</td>
<td align="center">2010-12-27</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-03-09</td>
<td align="center">A7</td>
<td align="center">2011-02-25</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -651,14 +651,13 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb18"><pre class="downlit">
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(keyab = <span class="fu"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(<span class="kw">.</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(first_weighted = <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">.</span>))
<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
<span class="co"># NOTE: more than one result was found for item 1: amoxicillin/clavulanic acid, azidocillin</span>
<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
<span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span>
@ -680,10 +679,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-03</td>
<td align="center">A7</td>
<td align="center">2010-05-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -692,10 +691,10 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-04</td>
<td align="center">A7</td>
<td align="center">2010-07-03</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_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">S</td>
@ -704,56 +703,56 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">A7</td>
<td align="center">2010-07-31</td>
<td align="center">N8</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">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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-15</td>
<td align="center">A7</td>
<td align="center">2010-09-13</td>
<td align="center">N8</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">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-28</td>
<td align="center">A7</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-15</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-03</td>
<td align="center">A7</td>
<td align="center">2010-10-16</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-11-14</td>
<td align="center">A7</td>
<td align="center">2010-10-17</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -764,49 +763,49 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-02-14</td>
<td align="center">A7</td>
<td align="center">2010-10-24</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-06</td>
<td align="center">A7</td>
<td align="center">2010-12-27</td>
<td align="center">N8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-03-09</td>
<td align="center">A7</td>
<td align="center">2011-02-25</td>
<td align="center">N8</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 9 isolates are flagged. In total, 79.0% of all isolates are marked ‘first weighted’ - 50.5% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 1, now 9 isolates are flagged. In total, 78.0% of all isolates are marked ‘first weighted’ - 49.7% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb19"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()
</pre></div>
<p>So we end up with 15,794 isolates for analysis.</p>
<p>So we end up with 15,607 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data_1st</span> <span class="op">%&gt;%</span>
@ -852,15 +851,15 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2014-08-12</td>
<td align="center">M9</td>
<td align="center">Hospital D</td>
<td align="center">2010-03-16</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</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>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
@ -868,27 +867,11 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2013-03-13</td>
<td align="center">W1</td>
<td align="center">2013-10-27</td>
<td align="center">G3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</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="left">3</td>
<td align="center">2015-12-02</td>
<td align="center">L5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
@ -898,11 +881,43 @@ Longest: 1</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2014-12-09</td>
<td align="center">F7</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_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>
<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="left">4</td>
<td align="center">2017-09-11</td>
<td align="center">O7</td>
<td align="center">2014-06-08</td>
<td align="center">S9</td>
<td align="center">Hospital B</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="odd">
<td align="left">5</td>
<td align="center">2015-01-01</td>
<td align="center">N10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -914,36 +929,20 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2014-06-03</td>
<td align="center">K4</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">S</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="left">7</td>
<td align="center">2011-02-14</td>
<td align="center">B9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2014-08-04</td>
<td align="center">O9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</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>
<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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -969,8 +968,8 @@ Longest: 1</p>
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,794<br>
Available: 15,794 (100%, NA: 0 = 0%)<br>
Length: 15,607<br>
Available: 15,607 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -987,33 +986,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,828</td>
<td align="right">49.56%</td>
<td align="right">7,828</td>
<td align="right">49.56%</td>
<td align="right">7,836</td>
<td align="right">50.21%</td>
<td align="right">7,836</td>
<td align="right">50.21%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,925</td>
<td align="right">24.85%</td>
<td align="right">11,753</td>
<td align="right">74.41%</td>
<td align="right">3,899</td>
<td align="right">24.98%</td>
<td align="right">11,735</td>
<td align="right">75.19%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,399</td>
<td align="right">15.19%</td>
<td align="right">14,152</td>
<td align="right">89.60%</td>
<td align="right">2,337</td>
<td align="right">14.97%</td>
<td align="right">14,072</td>
<td align="right">90.16%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,642</td>
<td align="right">10.40%</td>
<td align="right">15,794</td>
<td align="right">1,535</td>
<td align="right">9.84%</td>
<td align="right">15,607</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1042,50 +1041,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3722</td>
<td align="center">247</td>
<td align="center">3859</td>
<td align="center">7828</td>
<td align="center">3854</td>
<td align="center">265</td>
<td align="center">3717</td>
<td align="center">7836</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6127</td>
<td align="center">293</td>
<td align="center">1408</td>
<td align="center">7828</td>
<td align="center">6244</td>
<td align="center">287</td>
<td align="center">1305</td>
<td align="center">7836</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5959</td>
<td align="center">5880</td>
<td align="center">0</td>
<td align="center">1869</td>
<td align="center">7828</td>
<td align="center">1956</td>
<td align="center">7836</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7073</td>
<td align="center">7050</td>
<td align="center">0</td>
<td align="center">755</td>
<td align="center">7828</td>
<td align="center">786</td>
<td align="center">7836</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">1642</td>
<td align="center">1642</td>
<td align="center">1535</td>
<td align="center">1535</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1304</td>
<td align="center">58</td>
<td align="center">280</td>
<td align="center">1642</td>
<td align="center">1199</td>
<td align="center">50</td>
<td align="center">286</td>
<td align="center">1535</td>
</tr>
</tbody>
</table>
@ -1110,34 +1109,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5959</td>
<td align="center">5880</td>
<td align="center">0</td>
<td align="center">1869</td>
<td align="center">7828</td>
<td align="center">1956</td>
<td align="center">7836</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1237</td>
<td align="center">1166</td>
<td align="center">0</td>
<td align="center">405</td>
<td align="center">1642</td>
<td align="center">369</td>
<td align="center">1535</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">3006</td>
<td align="center">2942</td>
<td align="center">0</td>
<td align="center">919</td>
<td align="center">3925</td>
<td align="center">957</td>
<td align="center">3899</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1801</td>
<td align="center">1799</td>
<td align="center">0</td>
<td align="center">598</td>
<td align="center">2399</td>
<td align="center">538</td>
<td align="center">2337</td>
</tr>
</tbody>
</table>
@ -1150,7 +1149,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb28"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>)
<span class="co"># [1] 0.5372293</span>
<span class="co"># [1] 0.5233549</span>
</pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb29"><pre class="downlit">
@ -1167,19 +1166,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5349377</td>
<td align="center">0.5238399</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5382268</td>
<td align="center">0.5201802</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5455691</td>
<td align="center">0.5259455</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5325387</td>
<td align="center">0.5264182</td>
</tr>
</tbody>
</table>
@ -1200,23 +1199,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5349377</td>
<td align="center">4737</td>
<td align="center">0.5238399</td>
<td align="center">4698</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5382268</td>
<td align="center">5572</td>
<td align="center">0.5201802</td>
<td align="center">5550</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5455691</td>
<td align="center">2381</td>
<td align="center">0.5259455</td>
<td align="center">2274</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5325387</td>
<td align="center">3104</td>
<td align="center">0.5264182</td>
<td align="center">3085</td>
</tr>
</tbody>
</table>
@ -1239,27 +1238,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8201329</td>
<td align="center">0.9035514</td>
<td align="center">0.9853091</td>
<td align="center">0.8334609</td>
<td align="center">0.8996937</td>
<td align="center">0.9857070</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8294762</td>
<td align="center">0.9025579</td>
<td align="center">0.9829476</td>
<td align="center">0.8136808</td>
<td align="center">0.8983713</td>
<td align="center">0.9798046</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8219108</td>
<td align="center">0.9141401</td>
<td align="center">0.9844586</td>
<td align="center">0.8304694</td>
<td align="center">0.9253655</td>
<td align="center">0.9894845</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5414756</td>
<td align="center">0.5537013</td>
<td align="center">0.0000000</td>
<td align="center">0.5414756</td>
<td align="center">0.5537013</td>
</tr>
</tbody>
</table>

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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

60
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -315,19 +315,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 R R R R I I</span>
<span class="co"># 2 S S S R S R</span>
<span class="co"># 3 S I S S S S</span>
<span class="co"># 4 S I S R R R</span>
<span class="co"># 5 S S R S S R</span>
<span class="co"># 6 S R S R R R</span>
<span class="co"># 1 R R R R R S</span>
<span class="co"># 2 S R S I I S</span>
<span class="co"># 3 R R R S S S</span>
<span class="co"># 4 S I S R I S</span>
<span class="co"># 5 S R R R S R</span>
<span class="co"># 6 S S R S S R</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 S</span>
<span class="co"># 4 S</span>
<span class="co"># 2 I</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 6 R</span>
<span class="co"># 6 I</span>
</pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
@ -363,40 +363,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3229</td>
<td align="right">64.58%</td>
<td align="right">3241</td>
<td align="right">64.82%</td>
<td align="right">3241</td>
<td align="right">64.82%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">674</td>
<td align="right">13.48%</td>
<td align="right">3903</td>
<td align="right">78.06%</td>
<td align="right">642</td>
<td align="right">12.84%</td>
<td align="right">3883</td>
<td align="right">77.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">616</td>
<td align="right">12.32%</td>
<td align="right">4519</td>
<td align="right">90.38%</td>
<td align="right">595</td>
<td align="right">11.90%</td>
<td align="right">4478</td>
<td align="right">89.56%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">285</td>
<td align="right">5.70%</td>
<td align="right">4804</td>
<td align="right">96.08%</td>
<td align="right">311</td>
<td align="right">6.22%</td>
<td align="right">4789</td>
<td align="right">95.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">196</td>
<td align="right">3.92%</td>
<td align="right">211</td>
<td align="right">4.22%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
<div class="hidden name"><code>PCA.Rmd</code></div>

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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>

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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="hidden name"><code>WHONET.Rmd</code></div>

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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -224,21 +224,21 @@
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">2</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") 11.0 14 21 15 16 51 10</span>
<span class="co"># as.mo("stau") 170.0 170 190 190 210 240 10</span>
<span class="co"># as.mo("STAU") 160.0 170 180 180 200 210 10</span>
<span class="co"># as.mo("staaur") 11.0 13 19 14 18 48 10</span>
<span class="co"># as.mo("STAAUR") 11.0 13 22 17 37 40 10</span>
<span class="co"># as.mo("S. aureus") 15.0 15 24 17 26 56 10</span>
<span class="co"># as.mo("S aureus") 12.0 13 21 16 23 49 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 9.8 13 21 14 15 65 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 960.0 960 1100 980 1100 1400 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 440.0 450 480 470 480 570 10</span>
<span class="co"># as.mo("MRSA") 12.0 14 22 15 17 86 10</span>
<span class="co"># as.mo("VISA") 15.0 18 25 19 40 42 10</span>
<span class="co"># as.mo("VRSA") 14.0 15 30 22 44 69 10</span>
<span class="co"># as.mo(22242419) 130.0 150 160 170 180 190 10</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 9.1 11.0 21 11 13 77 10</span>
<span class="co"># as.mo("stau") 180.0 180.0 190 180 190 210 10</span>
<span class="co"># as.mo("STAU") 170.0 170.0 190 180 210 210 10</span>
<span class="co"># as.mo("staaur") 8.7 12.0 18 12 14 47 10</span>
<span class="co"># as.mo("STAAUR") 9.9 10.0 12 12 12 13 10</span>
<span class="co"># as.mo("S. aureus") 13.0 15.0 29 28 43 47 10</span>
<span class="co"># as.mo("S aureus") 12.0 16.0 25 17 40 52 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 9.1 9.7 14 11 11 44 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 920.0 960.0 990 980 1000 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 430.0 440.0 460 460 460 510 10</span>
<span class="co"># as.mo("MRSA") 9.1 11.0 16 12 12 37 10</span>
<span class="co"># as.mo("VISA") 15.0 17.0 23 18 20 47 10</span>
<span class="co"># as.mo("VRSA") 15.0 17.0 27 19 44 50 10</span>
<span class="co"># as.mo(22242419) 140.0 140.0 150 150 160 170 10</span>
</pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></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 100 milliseconds, this is only 10 input values per second.</p>
@ -252,12 +252,12 @@
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">M.semesiae</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 186.900 192.90 204.70 199.10 207.70 251.20</span>
<span class="co"># as.mo("METSEM") 175.500 199.70 215.20 218.20 232.00 240.40</span>
<span class="co"># as.mo("M. semesiae") 11.500 13.29 16.47 13.85 16.84 36.90</span>
<span class="co"># as.mo("M. semesiae") 11.690 11.94 16.81 14.40 15.75 42.76</span>
<span class="co"># as.mo("Methanosarcina semesiae") 9.688 10.28 14.55 11.99 13.72 39.41</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 193.600 200.200 209.30 202.800 218.00 238.20</span>
<span class="co"># as.mo("METSEM") 186.500 193.500 208.40 202.600 228.90 244.80</span>
<span class="co"># as.mo("M. semesiae") 12.280 13.090 18.86 14.430 15.48 59.40</span>
<span class="co"># as.mo("M. semesiae") 14.060 14.520 20.98 16.420 17.56 46.18</span>
<span class="co"># as.mo("Methanosarcina semesiae") 8.065 9.203 12.65 9.715 10.65 39.96</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -299,9 +299,9 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</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) 1840 1870 1950 1940 1980 2140 10</span>
<span class="co"># mo_name(x) 1920 1940 2010 1990 2060 2120 10</span>
</pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.94 seconds. You only lose time on your unique input values.</p>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.99 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -315,11 +315,11 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.17 8.49 9.32 9.32 9.90 10.90 10</span>
<span class="co"># B 10.90 11.80 16.30 13.20 14.70 45.60 10</span>
<span class="co"># C 1.06 1.22 1.32 1.28 1.44 1.57 10</span>
<span class="co"># A 5.90 6.16 6.93 7.24 7.43 7.89 10</span>
<span class="co"># B 11.40 12.00 16.20 13.20 14.20 45.20 10</span>
<span class="co"># C 1.05 1.07 1.18 1.13 1.28 1.40 10</span>
</pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0013 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>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0011 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="cb6"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
@ -333,14 +333,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.020 1.030 1.11 1.060 1.22 1.33 10</span>
<span class="co"># B 0.982 1.010 1.10 1.040 1.21 1.38 10</span>
<span class="co"># C 0.992 1.020 1.13 1.040 1.24 1.58 10</span>
<span class="co"># D 0.987 1.000 1.07 1.030 1.08 1.29 10</span>
<span class="co"># E 0.978 0.982 1.02 0.999 1.03 1.15 10</span>
<span class="co"># F 0.975 0.992 1.05 1.000 1.03 1.26 10</span>
<span class="co"># G 0.976 0.983 1.02 0.994 1.03 1.22 10</span>
<span class="co"># H 0.977 1.010 1.11 1.090 1.21 1.28 10</span>
<span class="co"># A 0.976 0.993 1.13 1.07 1.29 1.34 10</span>
<span class="co"># B 1.000 1.060 1.13 1.07 1.15 1.40 10</span>
<span class="co"># C 0.927 1.030 1.08 1.06 1.11 1.35 10</span>
<span class="co"># D 0.896 0.983 1.11 1.08 1.27 1.41 10</span>
<span class="co"># E 0.866 1.020 1.10 1.07 1.23 1.37 10</span>
<span class="co"># F 0.967 0.993 1.16 1.05 1.32 1.61 10</span>
<span class="co"># G 0.855 1.020 1.07 1.07 1.17 1.31 10</span>
<span class="co"># H 0.966 1.010 1.12 1.06 1.19 1.36 10</span>
</pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></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 ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
@ -368,14 +368,14 @@
times = <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 12.40 14.34 17.88 14.89 15.48 55.22 100</span>
<span class="co"># de 13.17 14.30 17.90 15.84 16.66 56.60 100</span>
<span class="co"># nl 17.14 19.86 24.99 20.78 21.70 64.66 100</span>
<span class="co"># es 13.43 15.29 17.65 15.93 16.59 54.38 100</span>
<span class="co"># it 13.33 14.83 18.35 15.68 16.36 57.61 100</span>
<span class="co"># fr 13.40 15.43 18.66 16.01 16.59 54.35 100</span>
<span class="co"># pt 13.47 15.33 18.93 16.15 16.84 57.28 100</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 13.09 14.02 18.36 14.59 16.22 61.92 100</span>
<span class="co"># de 14.00 14.83 18.06 15.48 16.85 56.01 100</span>
<span class="co"># nl 17.71 18.99 24.79 20.09 22.22 58.50 100</span>
<span class="co"># es 13.99 15.02 20.94 15.88 16.70 141.90 100</span>
<span class="co"># it 13.68 14.97 19.02 15.52 16.72 50.26 100</span>
<span class="co"># fr 13.96 15.05 20.63 15.72 17.14 52.71 100</span>
<span class="co"># pt 14.13 14.86 19.81 15.69 17.46 53.89 100</span>
</pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

4
docs/articles/resistance_predict.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd"><code>vignettes/resistance_predict.Rmd</code></a></small>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>

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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Welcome to the AMR package</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<div class="hidden name"><code>welcome_to_AMR.Rmd</code></div>
@ -195,7 +195,7 @@
<p><strong>READ ALL VIGNETTES <a href="https://msberends.github.io/AMR/articles/">ON OUR WEBSITE</a></strong></p>
<p><strong>READ ALL VIGNETTES <a href="https://msberends.github.io/AMR/articles/">ON OUR WEBSITE</a>.</strong></p>
<div id="welcome-to-the-amr-package" class="section level1">
<h1 class="hasAnchor">
<a href="#welcome-to-the-amr-package" class="anchor"></a>Welcome to the AMR package</h1>

10
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -280,6 +280,10 @@
<p><strong>Eric H. L. C. M. Hazenberg</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Gwen Knight</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Annick Lenglet</strong>. Contributor.
</p>
@ -296,6 +300,10 @@
<p><strong>Dennis Souverein</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Anthony Underwood</strong>. Contributor.
</p>
</li>
</ul>
</div>

1
docs/extra.js
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@ -85,6 +85,7 @@ $(document).ready(function() {
x = x.replace("Dennis", "Dr. Dennis");
x = x.replace("Judith", "Dr. Judith");
x = x.replace("Gwen", "Dr. Gwen");
x = x.replace("Anthony", "Dr. Anthony");
}
return(x);
}

2
docs/index.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

161
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -229,30 +229,49 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309001" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9001">
<a href="#amr-1309001" class="anchor"></a>AMR 1.3.0.9001<small> Unreleased </small>
<div id="amr-1309002" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9002">
<a href="#amr-1309002" class="anchor"></a>AMR 1.3.0.9002<small> Unreleased </small>
</h1>
<div id="last-updated-10-august-2020" class="section level2">
<div id="last-updated-14-august-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-10-august-2020" class="anchor"></a><small>Last updated: 10 August 2020</small>
<a href="#last-updated-14-august-2020" class="anchor"></a><small>Last updated: 14 August 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>
<p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">intrinsic_resistant</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="kw">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(<span class="kw">microorganism</span>)
<span class="co"># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span>
</pre></div>
</li>
</ul>
</div>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.</p>
<div class="sourceCode" id="cb1"><pre class="downlit">
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="co"># until dplyr 1.0.0</span>
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.mic</span>, <span class="kw">as.rsi</span>)
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.disk</span>, <span class="kw">as.rsi</span>)
<span class="co"># since dplyr 1.0.0</span>
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.mic</span>), <span class="kw">as.rsi</span>))
<span class="co"># since dplyr 1.0.0</span>
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.mic</span>), <span class="kw">as.rsi</span>))
<span class="kw">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.disk</span>), <span class="kw">as.rsi</span>))
</pre></div>
</li>
<li><p>Improved overall speed by tweaking joining functions</p></li>
</ul>
</div>
</div>
@ -261,14 +280,14 @@
<h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small>
</h1>
<div id="new" class="section level3">
<div id="new-1" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<a href="#new-1" class="anchor"></a>New</h3>
<ul>
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb2"><pre class="downlit">
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
@ -408,9 +427,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="1.1.0">
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small>
</h1>
<div id="new-1" class="section level3">
<div id="new-2" class="section level3">
<h3 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h3>
<a href="#new-2" class="anchor"></a>New</h3>
<ul>
<li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
@ -457,7 +476,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb3"><pre class="downlit">
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="kw">yourdata</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="st">"E. coli"</span>)
@ -476,9 +495,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
</h1>
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
<div id="new-2" class="section level3">
<div id="new-3" class="section level3">
<h3 class="hasAnchor">
<a href="#new-2" class="anchor"></a>New</h3>
<a href="#new-3" class="anchor"></a>New</h3>
<ul>
<li>Support for the newest <a href="http://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
@ -486,7 +505,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
<div class="sourceCode" id="cb4"><pre class="downlit">
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
<span class="co">#&gt; [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)
@ -497,7 +516,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<div class="sourceCode" id="cb6"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
<span class="co">#&gt; [1] 115329001 3092008 113961008</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>)
@ -562,11 +581,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
<div class="sourceCode" id="cb7"><pre class="downlit">
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="kw">...</span>
</pre></div>
<p>then please adjust this to:</p>
<div class="sourceCode" id="cb7"><pre class="downlit">
<div class="sourceCode" id="cb8"><pre class="downlit">
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacterales"</span>) <span class="kw">...</span>
</pre></div>
</li>
@ -574,13 +593,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="new-3" class="section level3">
<div id="new-4" class="section level3">
<h3 class="hasAnchor">
<a href="#new-3" class="anchor"></a>New</h3>
<a href="#new-4" class="anchor"></a>New</h3>
<ul>
<li>
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
<div class="sourceCode" id="cb8"><pre class="downlit">
<div class="sourceCode" id="cb9"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(bug = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span>
@ -609,7 +628,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
<li>
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
<div class="sourceCode" id="cb9"><pre class="downlit">
<div class="sourceCode" id="cb10"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
<span class="st">"staphylokok aureuz"</span>))
<span class="co">#&gt; Warning: </span>
@ -668,14 +687,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
<div class="sourceCode" id="cb10"><pre class="downlit">
<div class="sourceCode" id="cb11"><pre class="downlit">
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">...</span>, include_unknown = <span class="fl">TRUE</span>)
</pre></div>
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
</li>
<li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
<div class="sourceCode" id="cb11"><pre class="downlit">
<div class="sourceCode" id="cb12"><pre class="downlit">
<span class="co"># how it works in base R:</span>
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
<span class="kw">x</span>[<span class="fl">1</span>] <span class="op">&lt;-</span> <span class="st">"B"</span>
@ -694,13 +713,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
<div id="new-4" class="section level3">
<div id="new-5" class="section level3">
<h3 class="hasAnchor">
<a href="#new-4" class="anchor"></a>New</h3>
<a href="#new-5" class="anchor"></a>New</h3>
<ul>
<li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<div class="sourceCode" id="cb12"><pre class="downlit">
<div class="sourceCode" id="cb13"><pre class="downlit">
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>)
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, ]
@ -723,13 +742,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
</pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<div class="sourceCode" id="cb13"><pre class="downlit">
<div class="sourceCode" id="cb14"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="kw">x</span>, combine_IR = <span class="fl">FALSE</span>)
</pre></div>
</li>
<li>
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
<div class="sourceCode" id="cb14"><pre class="downlit">
<div class="sourceCode" id="cb15"><pre class="downlit">
<span class="co"># --------------------------------------------------------------------</span>
<span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span>
<span class="co"># ----------------------- -----------------------</span>
@ -751,7 +770,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
<div class="sourceCode" id="cb15"><pre class="downlit">
<div class="sourceCode" id="cb16"><pre class="downlit">
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
<span class="kw">example_isolates</span> <span class="op">%&gt;%</span>
@ -828,13 +847,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.7.1">
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
</h1>
<div id="new-5" class="section level4">
<div id="new-6" class="section level4">
<h4 class="hasAnchor">
<a href="#new-5" class="anchor"></a>New</h4>
<a href="#new-6" class="anchor"></a>New</h4>
<ul>
<li>
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb16"><pre class="downlit">
<div class="sourceCode" id="cb17"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">AMX</span>, <span class="kw">CIP</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>()
@ -861,7 +880,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
</ul>
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb17"><pre class="downlit">
<div class="sourceCode" id="cb18"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
<span class="co"># B_ESCHR_COL</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
@ -913,9 +932,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.7.0">
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
</h1>
<div id="new-6" class="section level4">
<div id="new-7" class="section level4">
<h4 class="hasAnchor">
<a href="#new-6" class="anchor"></a>New</h4>
<a href="#new-7" class="anchor"></a>New</h4>
<ul>
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
@ -966,7 +985,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>when all values are unique it now shows a message instead of a warning</p></li>
<li>
<p>support for boxplots:</p>
<div class="sourceCode" id="cb18"><pre class="downlit">
<div class="sourceCode" id="cb19"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
@ -1030,9 +1049,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
</ul>
<div id="new-7" class="section level4">
<div id="new-8" class="section level4">
<h4 class="hasAnchor">
<a href="#new-7" class="anchor"></a>New</h4>
<a href="#new-8" class="anchor"></a>New</h4>
<ul>
<li><p><strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</p></li>
<li>
@ -1061,7 +1080,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<div class="sourceCode" id="cb19"><pre class="downlit">
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
@ -1075,7 +1094,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()
</pre></div>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<div class="sourceCode" id="cb20"><pre class="downlit">
<div class="sourceCode" id="cb21"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>)
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>, scope = <span class="st">"all"</span>)
@ -1084,7 +1103,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb21"><pre class="downlit">
<div class="sourceCode" id="cb22"><pre class="downlit">
<span class="kw">ab_property</span> <span class="op">-&gt;</span> <span class="fu">atc_property</span>()
<span class="kw">ab_name</span> <span class="op">-&gt;</span> <span class="fu">atc_name</span>()
<span class="kw">ab_official</span> <span class="op">-&gt;</span> <span class="fu">atc_official</span>()
@ -1105,7 +1124,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</p></li>
<li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/graphics/plot.default.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb22"><pre class="downlit">
<div class="sourceCode" id="cb23"><pre class="downlit">
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">septic_patients</span>, col_ab = <span class="st">"amox"</span>)
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span>(<span class="kw">x</span>)
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">x</span>)
@ -1113,13 +1132,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb23"><pre class="downlit">
<div class="sourceCode" id="cb24"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">...</span>)
<span class="co"># or</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)
</pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb24"><pre class="downlit">
<div class="sourceCode" id="cb25"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(only_firsts = <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">only_firsts</span> <span class="op">==</span> <span class="fl">TRUE</span>) <span class="op">%&gt;%</span>
@ -1152,7 +1171,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<div class="sourceCode" id="cb25"><pre class="downlit">
<div class="sourceCode" id="cb26"><pre class="downlit">
<span class="co"># mo_fullname() uses as.mo() internally</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)
@ -1164,7 +1183,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
<div class="sourceCode" id="cb26"><pre class="downlit">
<div class="sourceCode" id="cb27"><pre class="downlit">
<span class="co"># equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">TRUE</span>)
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">2</span>)
@ -1179,7 +1198,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb27"><pre class="downlit">
<div class="sourceCode" id="cb28"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, language = <span class="st">"es"</span>)
<span class="co"># Warning: </span>
<span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
@ -1229,7 +1248,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb28"><pre class="downlit">
<div class="sourceCode" id="cb29"><pre class="downlit">
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<span class="co"># OLD WAY</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
@ -1276,9 +1295,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.5.0">
<a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
</h1>
<div id="new-8" class="section level4">
<div id="new-9" class="section level4">
<h4 class="hasAnchor">
<a href="#new-8" class="anchor"></a>New</h4>
<a href="#new-9" class="anchor"></a>New</h4>
<ul>
<li>Repository moved to GitLab</li>
<li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
@ -1313,7 +1332,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb29"><pre class="downlit">
<div class="sourceCode" id="cb30"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span>
@ -1330,7 +1349,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb30"><pre class="downlit">
<div class="sourceCode" id="cb31"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
@ -1338,7 +1357,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb31"><pre class="downlit">
<div class="sourceCode" id="cb32"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">count</span>, <span class="op">-</span><span class="kw">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span>
@ -1400,9 +1419,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.4.0">
<a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
</h1>
<div id="new-9" class="section level4">
<div id="new-10" class="section level4">
<h4 class="hasAnchor">
<a href="#new-9" class="anchor"></a>New</h4>
<a href="#new-10" class="anchor"></a>New</h4>
<ul>
<li><p>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</p></li>
<li>
@ -1418,7 +1437,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb32"><pre class="downlit">
<div class="sourceCode" id="cb33"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] "Gram negative"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, language = <span class="st">"de"</span>) <span class="co"># German</span>
@ -1429,7 +1448,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co"># [1] "Streptococcus grupo A"</span>
</pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb33"><pre class="downlit">
<div class="sourceCode" id="cb34"><pre class="downlit">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
<span class="co"># [1] "Gram negative"</span>
@ -1444,7 +1463,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
<div class="sourceCode" id="cb34"><pre class="downlit">
<div class="sourceCode" id="cb35"><pre class="downlit">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] B_ESCHR_COL</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)
@ -1453,7 +1472,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co"># [1] B_STRPTC_GRA</span>
</pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb35"><pre class="downlit">
<div class="sourceCode" id="cb36"><pre class="downlit">
<span class="kw">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
<span class="kw">microbenchmark</span>::<span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">thousands_of_E_colis</span>), unit = <span class="st">"s"</span>)
<span class="co"># Unit: seconds</span>
@ -1487,7 +1506,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb36"><pre class="downlit">
<div class="sourceCode" id="cb37"><pre class="downlit">
<span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
<span class="co"># [1] "Mupirocin"</span>
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
@ -1504,7 +1523,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb37"><pre class="downlit">
<div class="sourceCode" id="cb38"><pre class="downlit">
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>) <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
<span class="co"># which is the same as:</span>
<span class="kw">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>)
@ -1524,12 +1543,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb38"><pre class="downlit">
<div class="sourceCode" id="cb39"><pre class="downlit">
<span class="kw">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="kw">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">age</span>, <span class="kw">gender</span>), ncol = <span class="fl">2</span>))
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_matrix</span>)
</pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb39"><pre class="downlit">
<div class="sourceCode" id="cb40"><pre class="downlit">
<span class="kw">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(age = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">age</span>, gender = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">gender</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>)
<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
@ -1549,9 +1568,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.3.0">
<a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
</h1>
<div id="new-10" class="section level4">
<div id="new-11" class="section level4">
<h4 class="hasAnchor">
<a href="#new-10" class="anchor"></a>New</h4>
<a href="#new-11" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@ -1686,9 +1705,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="0.2.0">
<a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
</h1>
<div id="new-11" class="section level4">
<div id="new-12" class="section level4">
<h4 class="hasAnchor">
<a href="#new-11" class="anchor"></a>New</h4>
<a href="#new-12" class="anchor"></a>New</h4>
<ul>
<li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>

2
docs/pkgdown.yml
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@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-08-10T10:37Z
last_built: 2020-08-14T11:29Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
docs/reference/AMR-deprecated.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/AMR.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/WHOCC.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/WHONET.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/ab_from_text.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/ab_property.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/age.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/age_groups.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/antibiotic_class_selectors.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -317,7 +317,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a>, <a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -235,7 +235,7 @@
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
</div>
<pre class="usage"><span class='fu'>as.ab</span>(<span class='kw'>x</span>, flag_multiple_results = <span class='fl'>TRUE</span>, <span class='kw'>...</span>)
<pre class="usage"><span class='fu'>as.ab</span>(<span class='kw'>x</span>, flag_multiple_results = <span class='fl'>TRUE</span>, info = <span class='fl'>TRUE</span>, <span class='kw'>...</span>)
<span class='fu'>is.ab</span>(<span class='kw'>x</span>)</pre>
@ -250,6 +250,10 @@
<th>flag_multiple_results</th>
<td><p>logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.</p></td>
</tr>
<tr>
<th>info</th>
<td><p>logical to indicate whether a progress bar should be printed</p></td>
</tr>
<tr>
<th>...</th>
<td><p>arguments passed on to internal functions</p></td>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
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@ -83,7 +83,7 @@ This function requires an internet connection." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
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</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

4
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@ -83,7 +83,7 @@ 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="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -330,7 +330,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as

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@ -83,7 +83,7 @@ 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="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
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2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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@ -82,7 +82,7 @@
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<span class="navbar-brand">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
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2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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<h1>Data set with bacterial intrinsic resistance</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>intrinsic_resistant.Rd</code></div>
</div>
<div class="ref-description">
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
</div>
<pre class="usage"><span class='kw'>intrinsic_resistant</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 49,462 observations and 2 variables:</p><ul>
<li><p><code>microorganism</code><br /> Name of the microorganism</p></li>
<li><p><code>antibiotic</code><br /> Name of the antibiotic drug</p></li>
</ul>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
<p>This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>intrinsic_resistant</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='kw'>intrinsic_resistant</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>antibiotic</span> <span class='op'>==</span> <span class='st'>"Vancomycin"</span>, <span class='kw'>microorganism</span> <span class='op'>%like%</span> <span class='st'>"Enterococcus"</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/pull.html'>pull</a></span>(<span class='kw'>microorganism</span>)
<span class='co'># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
}</pre>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

4
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@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -235,7 +235,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
<div class="ref-description">
<p>Functions in this <code>AMR</code> package are categorised using <a href='https://www.Tidyverse.org/lifecycle'>the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle</a>.</p>
<p><img src='figures/lifecycle_Tidyverse.svg' height=200px style=margin-bottom:5px /> <br />
<p><img src='figures/lifecycle_tidyverse.svg' height=200px style=margin-bottom:5px /> <br />
This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions.</p>
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
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2
docs/reference/mdro.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

4
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -302,7 +302,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a></p></div>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a>, <a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/mo_property.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
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@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/p_symbol.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
docs/reference/pca.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

4
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@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -328,7 +328,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as

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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

5
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -261,6 +261,9 @@
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>
</div>
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@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>

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@ -93,6 +93,9 @@
<url>
<loc>https://msberends.github.io/AMR/reference/guess_ab_col.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR/reference/intrinsic_resistant.html</loc>
</url>
<url>
<loc>https://msberends.github.io/AMR/reference/join.html</loc>
</url>

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