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(v1.2.0.9037) survey on website

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dr. M.S. (Matthijs) Berends 2020-07-28 18:39:57 +02:00
parent ab2b359e6b
commit 1b65d76cfb
140 changed files with 1309 additions and 941 deletions
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1
.github/workflows/codecovr.yaml vendored
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@ -22,7 +22,6 @@
on:
push:
branches:
- premaster
- master
pull_request:
branches:

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.2.0.9036
Date: 2020-07-22
Version: 1.2.0.9037
Date: 2020-07-28
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

12
NEWS.md
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@ -1,9 +1,9 @@
# AMR 1.2.0.9036
## <small>Last updated: 22 July 2020</small>
# AMR 1.2.0.9037
## <small>Last updated: 28 July 2020</small>
### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
* [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html) 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 Tidyverse selections, like `dplyr::select()` and `tidyr::pivot_longer()`:
* [Tidyverse selection helpers](https://tidyselect.r-lib.org/reference/language.html) 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 `dplyr::select()` and `tidyr::pivot_longer()`:
```r
library(dplyr)
@ -33,13 +33,17 @@
* The `as.ab()` function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.
* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
* All `*_join_microorganisms()` functions and `bug_drug_combinations()` now return the original data class (e.g. `tibble`s and `data.table`s)
* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`, and fixed a bug where not all different antimicrobial results were added as rows
* For functions `rsi_df()`, `proportion_df()` and `count_df()`:
* Fixed a bug for using grouped versions
* Fixed a bug where not all different antimicrobial results were added as rows
* Fixed a bug when only calculating counts (`count_df()`) when all antibiotics in the data set have only `NA`s
* Improved auto-determination for columns of types `<mo>` and `<Date>`
* Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
* Changed the summary for class `<rsi>`, to highlight the %SI vs. %R
* Improved error handling, giving more useful info when functions return an error
* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
* Speed improvement for `mdro()` and `filter_ab_class()`
* New option `arrows_textangled` for `ggplot_pca()` to indicate whether the text at the end of the arrows should be angled (defaults to `TRUE`, as it was in previous versions)
### Other
* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.

16
R/aa_helper_functions.R
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@ -72,6 +72,15 @@ addin_insert_like <- function() {
}
check_dataset_integrity <- function() {
# check if user overwrote our data sets in their global environment
data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
data_in_globalenv <- ls(envir = globalenv())
overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
stop_if(length(overwritten) > 0,
"the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
paste0("'", overwritten, "'", collapse = ", "),
".\nPlease rename your object before using this function.", call = FALSE)
# check if other packages did not overwrite our data sets
tryCatch({
check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
"class", "order", "family", "genus",
@ -86,13 +95,6 @@ check_dataset_integrity <- function() {
}, error = function(e)
stop_('please use the command \'library("AMR")\' before using this function, to load the required reference data.', call = FALSE)
)
data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
data_in_globalenv <- ls(envir = globalenv())
overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
stop_if(length(overwritten) > 0,
"the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
paste0("'", overwritten, "'", collapse = ", "),
".\nPlease rename your object before using this function.", call = FALSE)
invisible(TRUE)
}

21
R/amr.R
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@ -23,12 +23,14 @@
#'
#' Welcome to the `AMR` package.
#' @details
#' `AMR` is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.
#'
#' We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
#' `AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
#'
#' After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
#'
#' This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
#'
#' This package can be used for:
#' - Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the [Catalogue of Life](http://www.catalogueoflife.org)
#' - Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature
#' - Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
#' - Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
#' - Determining first isolates to be used for AMR analysis
@ -37,15 +39,16 @@
#' - Calculating (empirical) susceptibility of both mono therapy and combination therapies
#' - Predicting future antimicrobial resistance using regression models
#' - Getting properties for any microorganism (like Gram stain, species, genus or family)
#' - Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
#' - Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
#' - Plotting antimicrobial resistance
#' - Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
#' - Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
#' - Applying EUCAST expert rules
#' - Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code
#' - Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code
#' - Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
#' - Principal component analysis for AMR
#'
#' @section Read more on our website!:
#' On our website <https://msberends.github.io/AMR> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html).
#' On our website <https://msberends.github.io/AMR> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html). As we would like to better understand the backgrounds and needs of our users, please [participate in our survey](https://msberends.github.io/AMR/survey.html)!
#' @section Contact Us:
#' For suggestions, comments or questions, please contact us at:
#'

9
R/filter_ab_class.R
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@ -33,8 +33,7 @@
#' @seealso [antibiotic_class_selectors()] for the `select()` equivalent.
#' @export
#' @examples
#' \dontrun{
#' library(dplyr)
#' if (require(dplyr)) {
#'
#' # filter on isolates that have any result for any aminoglycoside
#' example_isolates %>% filter_ab_class("aminoglycoside")
@ -64,6 +63,12 @@
#' filter_aminoglycosides("R", "all") %>%
#' filter_fluoroquinolones("R", "all")
#' }
#'
#' \dontrun{
#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
#' example_isolates %>% filter_carbapenems("R", "all")
#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
#' }
filter_ab_class <- function(x,
ab_class,
result = NULL,

72
R/ggplot_pca.R
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@ -40,6 +40,7 @@
#' @param arrows_colour the colour of the arrow and their text
#' @param arrows_size the size (thickness) of the arrow lines
#' @param arrows_textsize the size of the text at the end of the arrows
#' @param arrows_textangled a logical whether the text at the end of the arrows should be angled
#' @param arrows_alpha the alpha (transparency) of the arrows and their text
#' @param base_textsize the text size for all plot elements except the labels and arrows
#' @param ... Parameters passed on to functions
@ -58,20 +59,25 @@
#' # `example_isolates` is a dataset available in the AMR package.
#' # See ?example_isolates.
#'
#' \dontrun{
#' # See ?pca for more info about Principal Component Analysis (PCA).
#' library(dplyr)
#' pca_model <- example_isolates %>%
#' filter(mo_genus(mo) == "Staphylococcus") %>%
#' group_by(species = mo_shortname(mo)) %>%
#' summarise_if (is.rsi, resistance) %>%
#' pca(FLC, AMC, CXM, GEN, TOB, TMP, SXT, CIP, TEC, TCY, ERY)
#' if (require("dplyr")) {
#' pca_model <- example_isolates %>%
#' filter(mo_genus(mo) == "Staphylococcus") %>%
#' group_by(species = mo_shortname(mo)) %>%
#' summarise_if (is.rsi, resistance) %>%
#' pca(FLC, AMC, CXM, GEN, TOB, TMP, SXT, CIP, TEC, TCY, ERY)
#'
#' # old (base R)
#' biplot(pca_model)
#'
#' # old
#' biplot(pca_model)
#'
#' # new
#' ggplot_pca(pca_model)
#' # new
#' ggplot_pca(pca_model)
#'
#' if (require("ggplot2")) {
#' ggplot_pca(pca_model) +
#' scale_colour_viridis_d() +
#' labs(title = "Title here")
#' }
#' }
ggplot_pca <- function(x,
choices = 1:2,
@ -91,26 +97,28 @@ ggplot_pca <- function(x,
arrows_colour = "darkblue",
arrows_size = 0.5,
arrows_textsize = 3,
arrows_textangled = TRUE,
arrows_alpha = 0.75,
base_textsize = 10,
...) {
stop_ifnot_installed("ggplot2")
stop_ifnot(length(choices) == 2, "`choices` must be of length 2")
stop_ifnot(is.logical(scale), "`scale` must be TRUE or FALSE")
stop_ifnot(is.logical(pc.biplot), "`pc.biplot` must be TRUE or FALSE")
stop_ifnot(is.numeric(choices), "`choices` must be numeric")
stop_ifnot(is.numeric(labels_textsize), "`labels_textsize` must be numeric")
stop_ifnot(is.numeric(labels_text_placement), "`labels_text_placement` must be numeric")
stop_ifnot(is.logical(ellipse), "`ellipse` must be TRUE or FALSE")
stop_ifnot(is.numeric(ellipse_prob), "`ellipse_prob` must be numeric")
stop_ifnot(is.numeric(ellipse_size), "`ellipse_size` must be numeric")
stop_ifnot(is.numeric(ellipse_alpha), "`ellipse_alpha` must be numeric")
stop_ifnot(is.logical(arrows), "`arrows` must be TRUE or FALSE")
stop_ifnot(is.logical(arrows_textangled), "`arrows_textangled` must be TRUE or FALSE")
stop_ifnot(is.logical(ellipse), "`ellipse` must be TRUE or FALSE")
stop_ifnot(is.logical(pc.biplot), "`pc.biplot` must be TRUE or FALSE")
stop_ifnot(is.logical(scale), "`scale` must be TRUE or FALSE")
stop_ifnot(is.numeric(arrows_alpha), "`arrows_alpha` must be numeric")
stop_ifnot(is.numeric(arrows_size), "`arrows_size` must be numeric")
stop_ifnot(is.numeric(arrows_textsize), "`arrows_textsize` must be numeric")
stop_ifnot(is.numeric(arrows_alpha), "`arrows_alpha` must be numeric")
stop_ifnot(is.numeric(base_textsize), "`base_textsize` must be numeric")
stop_ifnot(is.numeric(choices), "`choices` must be numeric")
stop_ifnot(is.numeric(ellipse_alpha), "`ellipse_alpha` must be numeric")
stop_ifnot(is.numeric(ellipse_prob), "`ellipse_prob` must be numeric")
stop_ifnot(is.numeric(ellipse_size), "`ellipse_size` must be numeric")
stop_ifnot(is.numeric(labels_text_placement), "`labels_text_placement` must be numeric")
stop_ifnot(is.numeric(labels_textsize), "`labels_textsize` must be numeric")
calculations <- pca_calculations(pca_model = x,
groups = groups,
@ -206,12 +214,20 @@ ggplot_pca <- function(x,
type = "open"),
colour = arrows_colour,
size = arrows_size,
alpha = arrows_alpha) +
ggplot2::geom_text(data = df.v,
ggplot2::aes(label = varname, x = xvar, y = yvar, angle = angle, hjust = hjust),
colour = arrows_colour,
size = arrows_textsize,
alpha = arrows_alpha)
alpha = arrows_alpha)
if (arrows_textangled == TRUE) {
g <- g + ggplot2::geom_text(data = df.v,
ggplot2::aes(label = varname, x = xvar, y = yvar, angle = angle, hjust = hjust),
colour = arrows_colour,
size = arrows_textsize,
alpha = arrows_alpha)
} else {
g <- g + ggplot2::geom_text(data = df.v,
ggplot2::aes(label = varname, x = xvar, y = yvar, hjust = hjust),
colour = arrows_colour,
size = arrows_textsize,
alpha = arrows_alpha)
}
}
# Add caption label about total explained variance

2
R/rsi.R
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@ -37,7 +37,7 @@
#'
#' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline.
#'
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This **allows for easy implementation of these rules in laboratory information systems (LIS)**.
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**.
#'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'

2
R/rsi_calc.R
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@ -214,7 +214,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
out <- data.frame(antibiotic = character(0),
interpretation = character(0),
value = double(0),
isolates <- integer(0),
isolates = integer(0),
stringsAsFactors = FALSE)
if (data_has_groups) {
group_values <- unique(.data[, which(colnames(.data) %in% groups), drop = FALSE])

BIN
R/sysdata.rda
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Binary file not shown.

8
README.md
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@ -3,7 +3,13 @@
# `AMR` (for R)
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read about this package.
`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read more about this package.
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).*

14
_pkgdown.yml
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@ -70,20 +70,20 @@ navbar:
href: "articles/benchmarks.html"
- text: "Manual"
icon: "fa-book-open"
href: "reference/"
href: "reference/index.html"
- text: "Authors"
icon: "fa-users"
href: "authors.html"
- text: "Changelog"
icon: "far fa-newspaper"
href: "news/"
href: "news/index.html"
right:
- text: "Source Code"
icon: "fab fa-github"
href: "https://github.com/msberends/AMR"
- text: "Licence"
icon: "fa-book"
href: "LICENSE-text.html"
- text: "Survey"
icon: "fa-clipboard-list"
href: "survey.html"
reference:
- title: "Cleaning your data"
@ -156,7 +156,7 @@ reference:
- "`catalogue_of_life_version`"
- "`WHOCC`"
- "`lifecycle`"
- title: Other functions
- title: "Other functions"
desc: >
These functions are mostly for internal use, but some of
them may also be suitable for your analysis. Especially the
@ -164,7 +164,7 @@ reference:
contents:
- "`get_locale`"
- "`like`"
- title: Deprecated functions
- title: "Deprecated functions"
desc: >
These functions are deprecated, meaning that they will still
work but show a warning with every use and will be removed

6
data-raw/create_survey_page.R Normal file
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@ -0,0 +1,6 @@
license_text <- readLines("docs/LICENSE-text.html")
license_text <- paste(license_text, collapse = "|||")
license_text <- gsub("licen(s|c)e", "Survey", license_text, ignore.case = TRUE)
license_text <- gsub("<pre>.*</pre>", '<p>If no form is showing below, please <a href="https://forms.office.com/Pages/ResponsePage.aspx?id=-SJRM_TUZ02i_M1twg3ecDlnO1BBtdxGi-GnYu7DKfdUNTFLQ0xVSUlRVVlXTlVTNjZFMjdRUVpCSy4u" target="_blank">click here to open it</a>.</p><iframe width="100%" height= "500px" src= "https://forms.office.com/Pages/ResponsePage.aspx?id=-SJRM_TUZ02i_M1twg3ecDlnO1BBtdxGi-GnYu7DKfdUNTFLQ0xVSUlRVVlXTlVTNjZFMjdRUVpCSy4u&embed=true" frameborder= "0" marginwidth= "0" marginheight= "0" style= "border: none; max-width:100%; max-height:100vh" allowfullscreen webkitallowfullscreen mozallowfullscreen msallowfullscreen> </iframe>', license_text)
writeLines(unlist(strsplit(license_text, "|||", fixed = TRUE)), "docs/survey.html")

2
data-raw/eucast_rules.tsv
View File

@ -177,7 +177,7 @@ genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G) PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
family is Enterobacteriaceae TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods Expert Rules
order is Enterobacterales TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) Expert Rules
genus like .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus like .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus like .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules

Can't render this file because it contains an unexpected character in line 6 and column 96.

12
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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -176,7 +176,7 @@
</ul>
</li>
<li>
<a href="reference/">
<a href="reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -190,7 +190,7 @@
</a>
</li>
<li>
<a href="news/">
<a href="news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -206,10 +206,10 @@
</a>
</li>
<li>
<a href="LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>

12
docs/LICENSE-text.html
View File

@ -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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -176,7 +176,7 @@
</ul>
</li>
<li>
<a href="reference/">
<a href="reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -190,7 +190,7 @@
</a>
</li>
<li>
<a href="news/">
<a href="news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -206,10 +206,10 @@
</a>
</li>
<li>
<a href="LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>

580
docs/articles/AMR.html
View File

@ -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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 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 09 July 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 24 July 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">2020-07-09</td>
<td align="center">2020-07-24</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">2020-07-09</td>
<td align="center">2020-07-24</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">2020-07-09</td>
<td align="center">2020-07-24</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -336,68 +336,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-01-30</td>
<td align="center">Y5</td>
<td align="center">2014-06-04</td>
<td align="center">V5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-09-20</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-13</td>
<td align="center">Y1</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-07-21</td>
<td align="center">U10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-03-14</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-04-22</td>
<td align="center">O8</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-11-14</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">2017-05-14</td>
<td align="center">Q6</td>
<td align="center">Hospital C</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">2017-03-12</td>
<td align="center">O3</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-12-27</td>
<td align="center">P8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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">F</td>
</tr>
<tr class="even">
<td align="center">2013-11-30</td>
<td align="center">B10</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
@ -432,18 +432,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,300</td>
<td align="right">51.5%</td>
<td align="right">10,487</td>
<td align="right">52.44%</td>
<td align="right">10,487</td>
<td align="right">52.44%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,700</td>
<td align="right">48.5%</td>
<td align="right">9,513</td>
<td align="right">47.57%</td>
<td align="right">20,000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -481,7 +481,7 @@ Longest: 1</p>
<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></pre></body></html></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"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">first</span> <span class="kw">==</span> <span class="fl">TRUE</span>)</pre></body></html></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -491,7 +491,7 @@ 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 Y2, 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 J1, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -507,19 +507,19 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-16</td>
<td align="center">Y2</td>
<td align="center">2010-04-08</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-08-04</td>
<td align="center">Y2</td>
<td align="center">2010-06-01</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -529,21 +529,21 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-10-06</td>
<td align="center">Y2</td>
<td align="center">2010-06-21</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-11</td>
<td align="center">Y2</td>
<td align="center">2010-07-08</td>
<td align="center">J1</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>
@ -551,30 +551,30 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-11-23</td>
<td align="center">Y2</td>
<td align="center">2011-01-29</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-01</td>
<td align="center">Y2</td>
<td align="center">2011-02-23</td>
<td align="center">J1</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">R</td>
<td align="center">TRUE</td>
<td align="center">S</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">2011-04-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-23</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -584,19 +584,19 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-28</td>
<td align="center">J1</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">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-05</td>
<td align="center">Y2</td>
<td align="center">2011-03-13</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -606,14 +606,14 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-25</td>
<td align="center">Y2</td>
<td align="center">2011-05-14</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
@ -644,20 +644,20 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-03-16</td>
<td align="center">Y2</td>
<td align="center">2010-04-08</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-08-04</td>
<td align="center">Y2</td>
<td align="center">2010-06-01</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -668,56 +668,44 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-10-06</td>
<td align="center">Y2</td>
<td align="center">2010-06-21</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-11</td>
<td align="center">Y2</td>
<td align="center">2010-07-08</td>
<td align="center">J1</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>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-11-23</td>
<td align="center">Y2</td>
<td align="center">2011-01-29</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-01</td>
<td align="center">Y2</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">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-04-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-23</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -726,22 +714,34 @@ Longest: 1</p>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-02-23</td>
<td align="center">J1</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="even">
<td align="center">8</td>
<td align="center">2011-05-27</td>
<td align="center">Y2</td>
<td align="center">2011-02-28</td>
<td align="center">J1</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">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-07-05</td>
<td align="center">Y2</td>
<td align="center">2011-03-13</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -752,23 +752,23 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-09-25</td>
<td align="center">Y2</td>
<td align="center">2011-05-14</td>
<td align="center">J1</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 10 isolates are flagged. In total, 78.3% of all isolates are marked ‘first weighted’ - 49.8% 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 2, now 7 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.2% 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"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</pre></body></html></div>
<p>So we end up with 15,664 isolates for analysis.</p>
<p>So we end up with 15,719 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">first</span>, <span class="no">keyab</span>))</pre></body></html></div>
@ -776,6 +776,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">data_1st</span>)</pre></body></html></div>
<table class="table">
<colgroup>
<col width="2%">
<col width="8%">
<col width="8%">
<col width="8%">
@ -791,6 +792,7 @@ Longest: 1</p>
<col width="11%">
</colgroup>
<thead><tr class="header">
<th align="left"></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -807,24 +809,10 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-01-30</td>
<td align="center">Y5</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</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="even">
<td align="center">2010-11-13</td>
<td align="center">Y1</td>
<td align="center">Hospital D</td>
<td align="left">1</td>
<td align="center">2014-06-04</td>
<td align="center">V5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -836,66 +824,86 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2017-05-14</td>
<td align="center">Q6</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-07-21</td>
<td align="center">U10</td>
<td align="left">4</td>
<td align="center">2017-03-12</td>
<td align="center">O3</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2017-12-27</td>
<td align="center">P8</td>
<td align="center">Hospital B</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">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">6</td>
<td align="center">2013-11-30</td>
<td align="center">B10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2011-06-14</td>
<td align="center">A2</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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="center">2013-03-14</td>
<td align="center">Q1</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2013-04-22</td>
<td align="center">O8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-11-14</td>
<td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -915,8 +923,8 @@ Longest: 1</p>
<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>, <span class="no">species</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,664<br>
Available: 15,664 (100%, NA: 0 = 0%)<br>
Length: 15,719<br>
Available: 15,719 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -933,33 +941,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,860</td>
<td align="right">50.18%</td>
<td align="right">7,860</td>
<td align="right">50.18%</td>
<td align="right">7,902</td>
<td align="right">50.27%</td>
<td align="right">7,902</td>
<td align="right">50.27%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,867</td>
<td align="right">24.69%</td>
<td align="right">11,727</td>
<td align="right">74.87%</td>
<td align="right">3,926</td>
<td align="right">24.98%</td>
<td align="right">11,828</td>
<td align="right">75.25%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,386</td>
<td align="right">15.23%</td>
<td align="right">14,113</td>
<td align="right">90.10%</td>
<td align="right">2,350</td>
<td align="right">14.95%</td>
<td align="right">14,178</td>
<td align="right">90.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,551</td>
<td align="right">9.90%</td>
<td align="right">15,664</td>
<td align="right">1,541</td>
<td align="right">9.80%</td>
<td align="right">15,719</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -986,50 +994,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3765</td>
<td align="center">268</td>
<td align="center">3827</td>
<td align="center">7860</td>
<td align="center">3775</td>
<td align="center">258</td>
<td align="center">3869</td>
<td align="center">7902</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6198</td>
<td align="center">6238</td>
<td align="center">319</td>
<td align="center">1343</td>
<td align="center">7860</td>
<td align="center">1345</td>
<td align="center">7902</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5971</td>
<td align="center">6031</td>
<td align="center">0</td>
<td align="center">1889</td>
<td align="center">7860</td>
<td align="center">1871</td>
<td align="center">7902</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7088</td>
<td align="center">7105</td>
<td align="center">0</td>
<td align="center">772</td>
<td align="center">7860</td>
<td align="center">797</td>
<td align="center">7902</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">1551</td>
<td align="center">1551</td>
<td align="center">1541</td>
<td align="center">1541</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1209</td>
<td align="center">72</td>
<td align="center">270</td>
<td align="center">1551</td>
<td align="center">1230</td>
<td align="center">43</td>
<td align="center">268</td>
<td align="center">1541</td>
</tr>
</tbody>
</table>
@ -1052,34 +1060,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5971</td>
<td align="center">6031</td>
<td align="center">0</td>
<td align="center">1889</td>
<td align="center">7860</td>
<td align="center">1871</td>
<td align="center">7902</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1192</td>
<td align="center">1174</td>
<td align="center">0</td>
<td align="center">359</td>
<td align="center">1551</td>
<td align="center">367</td>
<td align="center">1541</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">2946</td>
<td align="center">2993</td>
<td align="center">0</td>
<td align="center">921</td>
<td align="center">3867</td>
<td align="center">933</td>
<td align="center">3926</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1813</td>
<td align="center">1807</td>
<td align="center">0</td>
<td align="center">573</td>
<td align="center">2386</td>
<td align="center">543</td>
<td align="center">2350</td>
</tr>
</tbody>
</table>
@ -1091,7 +1099,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</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"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>)
<span class="co"># [1] 0.5335802</span></pre></body></html></div>
<span class="co"># [1] 0.5350213</span></pre></body></html></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"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital</span>) <span class="kw">%&gt;%</span>
@ -1105,19 +1113,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5286835</td>
<td align="center">0.5308117</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5301545</td>
<td align="center">0.5304522</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5366460</td>
<td align="center">0.5364381</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5447207</td>
<td align="center">0.5479751</td>
</tr>
</tbody>
</table>
@ -1136,23 +1144,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5286835</td>
<td align="center">4846</td>
<td align="center">0.5308117</td>
<td align="center">4706</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5301545</td>
<td align="center">5306</td>
<td align="center">0.5304522</td>
<td align="center">5484</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5366460</td>
<td align="center">2415</td>
<td align="center">0.5364381</td>
<td align="center">2319</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5447207</td>
<td align="center">3097</td>
<td align="center">0.5479751</td>
<td align="center">3210</td>
</tr>
</tbody>
</table>
@ -1173,27 +1181,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8291349</td>
<td align="center">0.9017812</td>
<td align="center">0.9870229</td>
<td align="center">0.8297899</td>
<td align="center">0.8991395</td>
<td align="center">0.9851936</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8259188</td>
<td align="center">0.8994197</td>
<td align="center">0.9890393</td>
<td align="center">0.8260870</td>
<td align="center">0.8994160</td>
<td align="center">0.9883193</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8233773</td>
<td align="center">0.9229377</td>
<td align="center">0.9847427</td>
<td align="center">0.8352012</td>
<td align="center">0.9238411</td>
<td align="center">0.9852267</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5481978</td>
<td align="center">0.5425532</td>
<td align="center">0.0000000</td>
<td align="center">0.5481978</td>
<td align="center">0.5425532</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 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
docs/articles/MDR.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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -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">09 July 2020</h4>
<h4 class="date">24 July 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>
@ -306,19 +306,19 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S R R S S I</span>
<span class="co"># 2 S R S S S S</span>
<span class="co"># 3 S S S S S S</span>
<span class="co"># 4 S R S S S R</span>
<span class="co"># 5 R S S S R R</span>
<span class="co"># 6 S R I R R S</span>
<span class="co"># 1 R S S R R R</span>
<span class="co"># 2 R R R R I S</span>
<span class="co"># 3 S S S S R S</span>
<span class="co"># 4 S S R S S S</span>
<span class="co"># 5 R S R R I S</span>
<span class="co"># 6 R S R I S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 R</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span></pre></body></html></div>
<span class="co"># 6 R</span></pre></body></html></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="no">my_TB_data</span>, <span class="kw">guideline</span> <span class="kw">=</span> <span class="st">"TB"</span>)</pre></body></html></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -347,32 +347,32 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3300</td>
<td align="right">66.00%</td>
<td align="right">3300</td>
<td align="right">66.00%</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
<td align="right">3196</td>
<td align="right">63.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">636</td>
<td align="right">12.72%</td>
<td align="right">3936</td>
<td align="right">78.72%</td>
<td align="right">694</td>
<td align="right">13.88%</td>
<td align="right">3890</td>
<td align="right">77.80%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">561</td>
<td align="right">11.22%</td>
<td align="right">4497</td>
<td align="right">89.94%</td>
<td align="right">606</td>
<td align="right">12.12%</td>
<td align="right">4496</td>
<td align="right">89.92%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">310</td>
<td align="right">6.20%</td>
<td align="right">311</td>
<td align="right">6.22%</td>
<td align="right">4807</td>
<td align="right">96.14%</td>
</tr>

14
docs/articles/PCA.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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
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<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
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<a href="../news/">
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<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -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">09 July 2020</h4>
<h4 class="date">24 July 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>

14
docs/articles/SPSS.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
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<a href="../news/">
<a href="../news/index.html">
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Changelog
@ -164,10 +164,10 @@
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<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -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">09 July 2020</h4>
<h4 class="date">24 July 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>

14
docs/articles/WHONET.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">1.2.0.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -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">12 July 2020</h4>
<h4 class="date">24 July 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>

100
docs/articles/benchmarks.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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -148,7 +148,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -164,10 +164,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 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>
@ -221,21 +221,21 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <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") 9.9 14 22 15 36 48 10</span>
<span class="co"># as.mo("stau") 160.0 160 180 170 210 210 10</span>
<span class="co"># as.mo("STAU") 160.0 160 180 170 200 210 10</span>
<span class="co"># as.mo("staaur") 9.5 13 14 14 16 17 10</span>
<span class="co"># as.mo("STAAUR") 9.7 11 13 13 15 19 10</span>
<span class="co"># as.mo("S. aureus") 12.0 13 17 15 18 35 10</span>
<span class="co"># as.mo("S aureus") 11.0 16 26 19 42 43 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 8.7 11 19 13 14 55 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 890.0 910 930 920 950 1000 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 420.0 430 450 440 470 510 10</span>
<span class="co"># as.mo("MRSA") 9.8 10 13 12 14 19 10</span>
<span class="co"># as.mo("VISA") 12.0 14 33 18 43 120 10</span>
<span class="co"># as.mo("VRSA") 12.0 15 24 17 37 48 10</span>
<span class="co"># as.mo(22242419) 140.0 150 150 150 150 180 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 11 13 16 14 15 38 10</span>
<span class="co"># as.mo("stau") 170 170 180 180 190 200 10</span>
<span class="co"># as.mo("STAU") 160 170 190 190 200 210 10</span>
<span class="co"># as.mo("staaur") 12 13 15 14 15 20 10</span>
<span class="co"># as.mo("STAAUR") 13 14 17 15 15 38 10</span>
<span class="co"># as.mo("S. aureus") 13 14 23 17 36 42 10</span>
<span class="co"># as.mo("S aureus") 14 15 31 25 43 82 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 11 11 17 12 14 42 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 920 940 960 950 970 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 420 440 460 460 460 500 10</span>
<span class="co"># as.mo("MRSA") 13 14 20 14 16 43 10</span>
<span class="co"># as.mo("VISA") 15 15 28 27 40 42 10</span>
<span class="co"># as.mo("VRSA") 13 15 18 15 17 45 10</span>
<span class="co"># as.mo(22242419) 130 140 150 150 170 180 10</span></pre></body></html></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>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
@ -247,12 +247,12 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <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") 169.600 189.900 199.30 199.70 211.00 223.90</span>
<span class="co"># as.mo("METSEM") 170.000 186.900 197.40 191.80 210.70 232.30</span>
<span class="co"># as.mo("M. semesiae") 11.330 11.620 12.37 12.21 13.20 13.78</span>
<span class="co"># as.mo("M. semesiae") 11.410 12.090 15.74 12.48 13.55 43.19</span>
<span class="co"># as.mo("Methanosarcina semesiae") 8.592 8.906 12.89 9.31 11.54 41.08</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 180.20 190.40 199.00 199.10 204.40 218.80</span>
<span class="co"># as.mo("METSEM") 190.00 191.50 203.30 193.70 221.00 236.30</span>
<span class="co"># as.mo("M. semesiae") 11.60 12.58 15.84 13.42 14.40 37.45</span>
<span class="co"># as.mo("M. semesiae") 12.14 12.59 19.44 14.19 14.78 43.90</span>
<span class="co"># as.mo("Methanosarcina semesiae") 10.65 10.78 16.81 12.13 14.08 37.01</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -292,8 +292,8 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <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) 1610 1650 1680 1670 1710 1780 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.67 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 1840 1850 1910 1900 1950 2020 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.9 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -306,10 +306,10 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <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 8.15 8.69 9.63 9.05 10.40 12.40 10</span>
<span class="co"># B 11.30 12.70 17.50 13.40 14.80 54.30 10</span>
<span class="co"># C 1.04 1.17 1.28 1.28 1.38 1.59 10</span></pre></body></html></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>
<span class="co"># A 8.08 8.52 8.94 8.57 9.49 10.50 10</span>
<span class="co"># B 10.40 10.70 14.60 11.00 11.70 45.70 10</span>
<span class="co"># C 1.04 1.10 1.19 1.15 1.29 1.46 10</span></pre></body></html></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0012 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"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
@ -321,15 +321,15 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <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 0.852 0.977 1.040 0.990 1.040 1.29 10</span>
<span class="co"># B 0.802 0.933 1.070 0.994 1.160 1.65 10</span>
<span class="co"># C 0.804 0.983 1.060 1.000 1.210 1.32 10</span>
<span class="co"># D 0.783 0.855 0.996 0.989 1.030 1.36 10</span>
<span class="co"># E 0.820 0.962 1.020 0.982 1.070 1.27 10</span>
<span class="co"># F 0.770 0.785 0.937 0.953 0.996 1.30 10</span>
<span class="co"># G 0.963 0.981 1.140 1.160 1.250 1.38 10</span>
<span class="co"># H 0.778 0.842 0.985 0.977 0.995 1.30 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.862 1.030 1.070 1.060 1.08 1.33 10</span>
<span class="co"># B 0.837 1.020 1.010 1.030 1.05 1.13 10</span>
<span class="co"># C 0.836 0.936 0.993 1.020 1.03 1.17 10</span>
<span class="co"># D 0.838 0.947 1.030 1.050 1.10 1.31 10</span>
<span class="co"># E 0.807 0.906 0.994 1.010 1.03 1.28 10</span>
<span class="co"># F 0.804 0.920 1.060 1.040 1.11 1.54 10</span>
<span class="co"># G 0.805 0.906 1.000 1.030 1.07 1.25 10</span>
<span class="co"># H 0.792 0.805 0.949 0.941 1.04 1.29 10</span></pre></body></html></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>
<div id="results-in-other-languages" class="section level3">
@ -356,13 +356,13 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <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 12.84 13.10 18.11 14.63 15.54 58.10 100</span>
<span class="co"># de 13.58 14.02 18.05 14.61 16.58 69.21 100</span>
<span class="co"># nl 17.07 17.89 22.36 18.97 20.85 68.70 100</span>
<span class="co"># es 13.63 14.20 20.75 15.82 16.79 73.94 100</span>
<span class="co"># it 13.64 13.95 16.95 15.40 16.57 50.96 100</span>
<span class="co"># fr 13.74 14.12 19.84 15.81 16.62 61.13 100</span>
<span class="co"># pt 13.58 14.02 19.00 14.90 16.49 53.41 100</span></pre></body></html></div>
<span class="co"># en 12.09 12.45 16.18 12.63 13.57 48.69 100</span>
<span class="co"># de 13.01 13.51 16.67 13.82 15.26 48.22 100</span>
<span class="co"># nl 16.88 17.25 19.13 17.54 18.36 51.99 100</span>
<span class="co"># es 13.13 13.42 18.26 13.69 14.59 53.66 100</span>
<span class="co"># it 13.01 13.35 17.33 13.71 15.16 50.65 100</span>
<span class="co"># fr 13.13 13.40 16.31 13.64 13.88 49.44 100</span>
<span class="co"># pt 13.17 13.38 15.10 13.54 13.94 49.61 100</span></pre></body></html></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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docs/articles/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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -176,7 +176,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -190,7 +190,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -206,10 +206,10 @@
</a>
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<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
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</li>
</ul>

14
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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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -134,7 +134,7 @@
</ul>
</li>
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<span class="fa fa-book-open"></span>
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@ -148,7 +148,7 @@
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@ -164,10 +164,10 @@
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</ul>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4>
<h4 class="date">24 July 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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<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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
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@ -176,7 +176,7 @@
</ul>
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@ -190,7 +190,7 @@
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@ -206,10 +206,10 @@
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li p {
margin-top: 10.5px;
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margin: 0;
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/* slightly smaller blockquote */
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font-size: 98%;
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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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
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@ -138,7 +138,7 @@
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@ -152,7 +152,7 @@
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@ -168,10 +168,10 @@
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@ -191,8 +191,8 @@
<a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
</h1></div>
<blockquote>
<p><strong>METHODS PAPER PREPRINTED</strong><br>
A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/810622). Please click <a href="https://doi.org/10.1101/810622">here for the paper on bioRxiv’s publishers page</a>.</p>
<p><em>July 2020</em><br><span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> <strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br>
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!</p>
</blockquote>
<div id="what-is-amr-for-r" class="section level3">
<h3 class="hasAnchor">
@ -200,10 +200,10 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<p><em>(To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p>
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
<div class="main-content">
<p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in more than 100 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(source: <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in more than 100 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from more than 100 countries. Click the map to enlarge and to also see the names of the countries.
</p>
<br><br>
</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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -176,7 +176,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -190,7 +190,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -206,10 +206,10 @@
</a>
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<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
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Survey
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</ul>
@ -229,13 +229,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209036" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9036">
<a href="#amr-1209036" class="anchor"></a>AMR 1.2.0.9036<small> Unreleased </small>
<div id="amr-1209037" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9037">
<a href="#amr-1209037" class="anchor"></a>AMR 1.2.0.9037<small> Unreleased </small>
</h1>
<div id="last-updated-22-july-2020" class="section level2">
<div id="last-updated-28-july-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-22-july-2020" class="anchor"></a><small>Last updated: 22 July 2020</small>
<a href="#last-updated-28-july-2020" class="anchor"></a><small>Last updated: 28 July 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -243,7 +243,7 @@
<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 selections</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 Tidyverse selections, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
@ -285,13 +285,21 @@
</li>
<li><p>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</p></li>
<li><p>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</p></li>
<li><p>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>, and fixed a bug where not all different antimicrobial results were added as rows</p></li>
<li>
<p>For functions <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>:</p>
<ul>
<li>Fixed a bug for using grouped versions</li>
<li>Fixed a bug where not all different antimicrobial results were added as rows</li>
<li>Fixed a bug when only calculating counts (<code><a href="../reference/count.html">count_df()</a></code>) when all antibiotics in the data set have only <code>NA</code>s</li>
</ul>
</li>
<li><p>Improved auto-determination for columns of types <code>&lt;mo&gt;</code> and <code>&lt;Date&gt;</code></p></li>
<li><p>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</p></li>
<li><p>Changed the summary for class <code>&lt;rsi&gt;</code>, to highlight the %SI vs. %R</p></li>
<li><p>Improved error handling, giving more useful info when functions return an error</p></li>
<li><p>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</p></li>
<li><p>Speed improvement for <code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code></p></li>
<li><p>New option <code>arrows_textangled</code> for <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> to indicate whether the text at the end of the arrows should be angled (defaults to <code>TRUE</code>, as it was in previous versions)</p></li>
</ul>
</div>
<div id="other" class="section level3">

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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-22T10:28Z
last_built: 2020-07-28T16:39Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -258,7 +258,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
</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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -239,10 +239,11 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><code>AMR</code> is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.</p>
<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p><code>AMR</code> is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href='http://www.catalogueoflife.org'>Catalogue of Life</a></p></li>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>
<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
<li><p>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</p></li>
<li><p>Determining first isolates to be used for AMR analysis</p></li>
@ -251,10 +252,11 @@
<li><p>Calculating (empirical) susceptibility of both mono therapy and combination therapies</p></li>
<li><p>Predicting future antimicrobial resistance using regression models</p></li>
<li><p>Getting properties for any microorganism (like Gram stain, species, genus or family)</p></li>
<li><p>Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)</p></li>
<li><p>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</p></li>
<li><p>Plotting antimicrobial resistance</p></li>
<li><p>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code</p></li>
<li><p>Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code</p></li>
<li><p>Applying EUCAST expert rules</p></li>
<li><p>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code</p></li>
<li><p>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code</p></li>
<li><p>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</p></li>
<li><p>Principal component analysis for AMR</p></li>
</ul>
@ -263,7 +265,7 @@
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>

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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -250,7 +250,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -273,7 +273,7 @@
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -304,7 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -330,7 +330,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -272,7 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>

14
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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -281,7 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>

12
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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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>

14
docs/reference/antibiotics.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -314,7 +314,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>

14
docs/reference/as.ab.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -296,7 +296,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'>

14
docs/reference/as.disk.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

14
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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">1.2.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
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<a href="../LICENSE-text.html">
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<a href="../survey.html">
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Licence
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</ul>
@ -378,7 +378,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a> for the <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that is being used to determine ID's.</p>

16
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
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<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
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Licence
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</a>
</li>
</ul>
@ -308,7 +308,7 @@
<p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
<p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -336,7 +336,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -178,7 +178,7 @@ This function requires an internet connection." />
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -192,7 +192,7 @@ This function requires an internet connection." />
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -208,10 +208,10 @@ This function requires an internet connection." />
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -312,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -267,7 +267,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>availability</span>(<span class='no'>example_isolates</span>)

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
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<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -333,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
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<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -263,7 +263,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -255,7 +255,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -178,7 +178,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -192,7 +192,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</a>
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Changelog
@ -208,10 +208,10 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</a>
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<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -360,7 +360,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</p></div>

14
docs/reference/eucast_rules.html
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -178,7 +178,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -192,7 +192,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -208,10 +208,10 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -403,7 +403,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -257,7 +257,7 @@
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

14
docs/reference/example_isolates_unclean.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -252,7 +252,7 @@
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

21
docs/reference/filter_ab_class.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">1.2.0.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -303,8 +303,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='antibiotic_class_selectors.html'>antibiotic_class_selectors()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>dplyr</span>)) {
<span class='co'># filter on isolates that have any result for any aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
@ -333,6 +332,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
}
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_carbapenems</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span>(), ~<span class='no'>.</span> <span class='kw'>==</span> <span class='st'>"R"</span>))
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

14
docs/reference/first_isolate.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
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<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -393,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics()</a></code></p></div>

14
docs/reference/g.test.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -334,7 +334,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

46
docs/reference/ggplot_pca.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -254,6 +254,7 @@
<span class='kw'>arrows_colour</span> <span class='kw'>=</span> <span class='st'>"darkblue"</span>,
<span class='kw'>arrows_size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>arrows_textsize</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>arrows_textangled</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>arrows_alpha</span> <span class='kw'>=</span> <span class='fl'>0.75</span>,
<span class='kw'>base_textsize</span> <span class='kw'>=</span> <span class='fl'>10</span>,
<span class='no'>...</span>
@ -343,6 +344,10 @@
<th>arrows_textsize</th>
<td><p>the size of the text at the end of the arrows</p></td>
</tr>
<tr>
<th>arrows_textangled</th>
<td><p>a logical whether the text at the end of the arrows should be angled</p></td>
</tr>
<tr>
<th>arrows_alpha</th>
<td><p>the alpha (transparency) of the arrows and their text</p></td>
@ -370,7 +375,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The colours for labels and points can be changed by adding another scale layer for colour, like <code>scale_colour_viridis_d()</code> or <code>scale_colour_brewer()</code>.</p>
<p>The colours for labels and points can be changed by adding another scale layer for colour, like <code><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d()</a></code> or <code><a href='https://ggplot2.tidyverse.org/reference/scale_brewer.html'>scale_colour_brewer()</a></code>.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
@ -382,20 +387,25 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>pca_model</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='pca.html'>pca</a></span>(<span class='no'>FLC</span>, <span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>, <span class='no'>CIP</span>, <span class='no'>TEC</span>, <span class='no'>TCY</span>, <span class='no'>ERY</span>)
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='no'>pca_model</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='pca.html'>pca</a></span>(<span class='no'>FLC</span>, <span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>, <span class='no'>CIP</span>, <span class='no'>TEC</span>, <span class='no'>TCY</span>, <span class='no'>ERY</span>)
<span class='co'># old</span>
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_model</span>)
<span class='co'># old (base R)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_model</span>)
<span class='co'># new </span>
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)
<span class='co'># new </span>
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>)) {
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span>() +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Title here"</span>)
}
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -409,7 +409,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {

14
docs/reference/guess_ab_col.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">1.2.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -270,7 +270,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"S"</span>,

12
docs/reference/index.html
View File

@ -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">1.2.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -176,7 +176,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -190,7 +190,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -206,10 +206,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>

14
docs/reference/join.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -283,7 +283,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))

14
docs/reference/key_antibiotics.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -379,7 +379,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>

14
docs/reference/kurtosis.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -269,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='skewness.html'>skewness()</a></code></p></div>

12
docs/reference/lifecycle.html
View File

@ -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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -179,7 +179,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -193,7 +193,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -209,10 +209,10 @@ This page contains a section for every lifecycle (with text borrowed from the af
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>

14
docs/reference/like.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -285,7 +285,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>base::grep()</a></code></p></div>

14
docs/reference/mdro.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
</a>
</li>
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Licence
Survey
</a>
</li>
</ul>
@ -437,7 +437,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {

14
docs/reference/microorganisms.codes.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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
<li>
<a href="../news/">
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Changelog
@ -207,10 +207,10 @@
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Licence
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@ -256,7 +256,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <a href='microorganisms.html'>microorganisms</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">1.2.0.9035</span>
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</span>
</div>
@ -177,7 +177,7 @@
</ul>
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@ -191,7 +191,7 @@
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@ -207,10 +207,10 @@
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@ -299,7 +299,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<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>

14
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@ -82,7 +82,7 @@
</button>
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<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">1.2.0.9032</span>
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</span>
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@ -177,7 +177,7 @@
</ul>
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@ -191,7 +191,7 @@
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@ -207,10 +207,10 @@
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@ -262,7 +262,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<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.html'>microorganisms</a></p></div>

14
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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">1.2.0.9032</span>
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@ -177,7 +177,7 @@
</ul>
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@ -191,7 +191,7 @@
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@ -207,10 +207,10 @@
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@ -361,7 +361,7 @@ 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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -178,7 +178,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</ul>
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@ -192,7 +192,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -316,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
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@ -191,7 +191,7 @@
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@ -207,10 +207,10 @@
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@ -263,7 +263,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
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@ -177,7 +177,7 @@
</ul>
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@ -191,7 +191,7 @@
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@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
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@ -178,7 +178,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</ul>
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@ -192,7 +192,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -208,10 +208,10 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -379,7 +379,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='count.html'>count()</a></code> to count resistant and susceptible isolates.</p></div>

14
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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">1.2.0.9032</span>
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@ -177,7 +177,7 @@
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@ -381,7 +381,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>The <code><a href='proportion.html'>proportion()</a></code> functions to calculate resistance</p>

14
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@ -82,7 +82,7 @@
</button>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
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@ -177,7 +177,7 @@
</ul>
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@ -260,7 +260,7 @@
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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</span>
</div>
@ -178,7 +178,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -192,7 +192,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</a>
</li>
<li>
<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -208,10 +208,10 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</a>
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<a href="../LICENSE-text.html">
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<a href="../survey.html">
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Licence
Survey
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@ -271,7 +271,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<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>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='kurtosis.html'>kurtosis()</a></code></p></div>

14
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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">1.2.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
</span>
</div>
@ -177,7 +177,7 @@
</ul>
</li>
<li>
<a href="../reference/">
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
@ -191,7 +191,7 @@
</a>
</li>
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<a href="../news/">
<a href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
@ -207,10 +207,10 @@
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<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
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Survey
</a>
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</ul>
@ -256,7 +256,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># The 'language' parameter of below functions</span>

262
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@ -0,0 +1,262 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
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2
git_premaster.sh
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@ -122,6 +122,8 @@ echo "•••••••••••••••••"
echo "• Installing..."
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))"
# add the survey
Rscript -e "source('data-raw/create_survey_page.R')"
echo
echo "•••••••••••••••••••••••••"
echo "• List of changed files •"

11
index.md
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@ -1,7 +1,8 @@
# `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
> **METHODS PAPER PREPRINTED**
> A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/810622). Please click [here for the paper on bioRxiv's publishers page](https://doi.org/10.1101/810622).
> *July 2020*<br>
> <span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> **PLEASE TAKE PART IN OUR SURVEY!**
> Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. **If you have a minute, please [anonymously fill in this short questionnaire](./survey.html)**. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!
### What is `AMR` (for R)?
@ -11,13 +12,13 @@
After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
<div class="main-content">
<div class="main-content">
<p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
<strong>Used in more than 100 countries</strong><br>
Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(source: <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.</p><br><br>
Since its first public release in early 2018, this package has been downloaded from more than 100 countries. Click the map to enlarge and to also see the names of the countries.</p><br><br>
</div>
#### Partners

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@ -33,7 +33,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\keyword{internal}

17
man/AMR.Rd
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@ -7,13 +7,15 @@
Welcome to the \code{AMR} package.
}
\details{
\code{AMR} is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.
\code{AMR} is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This package can be used for:
\itemize{
\item Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the \href{http://www.catalogueoflife.org}{Catalogue of Life}
\item Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature
\item Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
\item Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
\item Determining first isolates to be used for AMR analysis
@ -22,17 +24,18 @@ This package can be used for:
\item Calculating (empirical) susceptibility of both mono therapy and combination therapies
\item Predicting future antimicrobial resistance using regression models
\item Getting properties for any microorganism (like Gram stain, species, genus or family)
\item Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
\item Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
\item Plotting antimicrobial resistance
\item Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
\item Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
\item Applying EUCAST expert rules
\item Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code
\item Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code
\item Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
\item Principal component analysis for AMR
}
}
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\section{Contact Us}{

2
man/WHOCC.Rd
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@ -20,7 +20,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{

2
man/WHONET.Rd
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@ -43,7 +43,7 @@ This example data set has the exact same structure as an export file from WHONET
}
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\keyword{datasets}

2
man/ab_from_text.Rd
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@ -62,7 +62,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unly
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{

2
man/ab_property.Rd
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@ -95,7 +95,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{

2
man/age.Rd
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@ -31,7 +31,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{

2
man/age_groups.Rd
View File

@ -43,7 +43,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{

2
man/antibiotics.Rd
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@ -89,7 +89,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\seealso{

2
man/as.ab.Rd
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@ -65,7 +65,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{

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