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(v0.7.1.9056) mo and ab subsetting

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dr. M.S. (Matthijs) Berends 2019-08-14 14:57:06 +02:00
parent 7108454ba5
commit 920212e815
46 changed files with 144 additions and 69 deletions
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6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.1.9055 Version: 0.7.1.9056
Date: 2019-08-13 Date: 2019-08-14
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
@ -11,6 +11,8 @@ Authors@R: c(
family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")), family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
person(role = c("aut", "ths"), person(role = c("aut", "ths"),
family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")), family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")),
person(role = c("aut", "ths"),
family = "Albers", given = c("Casper", "J."), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")),
person(role = c("aut", "ths"), person(role = c("aut", "ths"),
family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")), family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
person(role = "ctb", person(role = "ctb",

16
NAMESPACE
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@ -2,6 +2,12 @@
S3method("[",ab) S3method("[",ab)
S3method("[",mo) S3method("[",mo)
S3method("[<-",ab)
S3method("[<-",mo)
S3method("[[",ab)
S3method("[[",mo)
S3method("[[<-",ab)
S3method("[[<-",mo)
S3method(as.data.frame,ab) S3method(as.data.frame,ab)
S3method(as.data.frame,mo) S3method(as.data.frame,mo)
S3method(as.double,mic) S3method(as.double,mic)
@ -13,6 +19,8 @@ S3method(as.rsi,disk)
S3method(as.rsi,mic) S3method(as.rsi,mic)
S3method(barplot,mic) S3method(barplot,mic)
S3method(barplot,rsi) S3method(barplot,rsi)
S3method(c,ab)
S3method(c,mo)
S3method(droplevels,mic) S3method(droplevels,mic)
S3method(droplevels,rsi) S3method(droplevels,rsi)
S3method(freq,mo) S3method(freq,mo)
@ -172,6 +180,12 @@ export(skewness)
export(theme_rsi) export(theme_rsi)
exportMethods("[.ab") exportMethods("[.ab")
exportMethods("[.mo") exportMethods("[.mo")
exportMethods("[<-.ab")
exportMethods("[<-.mo")
exportMethods("[[.ab")
exportMethods("[[.mo")
exportMethods("[[<-.ab")
exportMethods("[[<-.mo")
exportMethods(as.data.frame.ab) exportMethods(as.data.frame.ab)
exportMethods(as.data.frame.mo) exportMethods(as.data.frame.mo)
exportMethods(as.double.mic) exportMethods(as.double.mic)
@ -179,6 +193,8 @@ exportMethods(as.integer.mic)
exportMethods(as.numeric.mic) exportMethods(as.numeric.mic)
exportMethods(barplot.mic) exportMethods(barplot.mic)
exportMethods(barplot.rsi) exportMethods(barplot.rsi)
exportMethods(c.ab)
exportMethods(c.mo)
exportMethods(droplevels.mic) exportMethods(droplevels.mic)
exportMethods(droplevels.rsi) exportMethods(droplevels.rsi)
exportMethods(freq.mo) exportMethods(freq.mo)

4
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9055 # AMR 0.7.1.9056
### Breaking ### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too. * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -73,7 +73,7 @@
* Classes `ab` and `mo` will now be preserved in any subsetting * Classes `ab` and `mo` will now be preserved in any subsetting
#### Other #### Other
* Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors * Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors
# AMR 0.7.1 # AMR 0.7.1

38
R/ab.R
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@ -282,10 +282,42 @@ as.data.frame.ab <- function (x, ...) {
#' @exportMethod [.ab #' @exportMethod [.ab
#' @export #' @export
#' @noRd #' @noRd
"[.ab" <- function (x, ...) { "[.ab" <- function(x, ...) {
# this function is needed to preserve the "ab" class for any subsetting, like df %>% filter(...)
y <- NextMethod() y <- NextMethod()
structure(y, class = "ab") attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.ab
#' @export
#' @noRd
"[<-.ab" <- function(value) {
y <- NextMethod()
attributes(y) <- attributes(value)
y
}
#' @exportMethod [[.ab
#' @export
#' @noRd
"[[.ab" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[<-.ab
#' @export
#' @noRd
"[[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(value)
y
}
#' @exportMethod c.ab
#' @export
#' @noRd
c.ab <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
} }
#' @importFrom pillar type_sum #' @importFrom pillar type_sum

6
R/first_isolate.R
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@ -79,8 +79,8 @@
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. #' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' # septic_patients is a dataset available in the AMR package. It is true, genuine data. #' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
#' ?septic_patients #' # See ?septic_patients.
#' #'
#' library(dplyr) #' library(dplyr)
#' # Filter on first isolates: #' # Filter on first isolates:
@ -97,7 +97,7 @@
#' # or for first weighted isolates: #' # or for first weighted isolates:
#' septic_patients %>% #' septic_patients %>%
#' filter_first_weighted_isolate() #' filter_first_weighted_isolate()
#' #'
#' # Now let's see if first isolates matter: #' # Now let's see if first isolates matter:
#' A <- septic_patients %>% #' A <- septic_patients %>%
#' group_by(hospital_id) %>% #' group_by(hospital_id) %>%

4
R/key_antibiotics.R
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@ -48,8 +48,8 @@
#' @seealso \code{\link{first_isolate}} #' @seealso \code{\link{first_isolate}}
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' # septic_patients is a dataset available in the AMR package #' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
#' ?septic_patients #' # See ?septic_patients.
#' #'
#' library(dplyr) #' library(dplyr)
#' # set key antibiotics to a new variable #' # set key antibiotics to a new variable

38
R/mo.R
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@ -1723,10 +1723,42 @@ as.data.frame.mo <- function(x, ...) {
#' @exportMethod [.mo #' @exportMethod [.mo
#' @export #' @export
#' @noRd #' @noRd
"[.mo" <- function (x, ...) { "[.mo" <- function(x, ...) {
# this function is needed to preserve the "mo" class for any subsetting, like df %>% filter(...)
y <- NextMethod() y <- NextMethod()
to_class_mo(y) attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.mo
#' @export
#' @noRd
"[<-.mo" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(value)
y
}
#' @exportMethod [[.mo
#' @export
#' @noRd
"[[.mo" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[<-.mo
#' @export
#' @noRd
"[[<-.mo" <- function(value) {
y <- NextMethod()
attributes(y) <- attributes(value)
y
}
#' @exportMethod c.mo
#' @export
#' @noRd
c.mo <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
} }
#' @rdname as.mo #' @rdname as.mo

6
_pkgdown.yml
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@ -172,12 +172,14 @@ authors:
href: https://www.rug.nl/staff/m.s.berends/ href: https://www.rug.nl/staff/m.s.berends/
Christian F. Luz: Christian F. Luz:
href: https://www.rug.nl/staff/c.f.luz/ href: https://www.rug.nl/staff/c.f.luz/
Corinna Glasner:
href: https://www.rug.nl/staff/c.glasner/
Alex W. Friedrich: Alex W. Friedrich:
href: https://www.rug.nl/staff/a.w.friedrich/ href: https://www.rug.nl/staff/a.w.friedrich/
Bhanu N. M. Sinha: Bhanu N. M. Sinha:
href: https://www.rug.nl/staff/b.sinha/ href: https://www.rug.nl/staff/b.sinha/
Casper J. Albers:
href: https://www.rug.nl/staff/c.j.albers/
Corinna Glasner:
href: https://www.rug.nl/staff/c.glasner/
template: template:
assets: "pkgdown/logos" # use logos in this folder assets: "pkgdown/logos" # use logos in this folder

4
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
</span> </span>
</div> </div>
@ -513,7 +513,7 @@ END OF TERMS AND CONDITIONS
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
</span> </span>
</div> </div>
@ -243,7 +243,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

8
docs/authors.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
</span> </span>
</div> </div>
@ -241,6 +241,10 @@
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a> <p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p> </p>
</li> </li>
<li>
<p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
<li> <li>
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a> <p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p> </p>
@ -270,7 +274,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

8
docs/extra.js
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@ -77,16 +77,14 @@ $( document ).ready(function() {
// doctoral titles of authors // doctoral titles of authors
function doct_tit(x) { function doct_tit(x) {
if (typeof(x) != "undefined") { if (typeof(x) != "undefined") {
x = x.replace("Corinna", "Dr Corinna");
x = x.replace("Alex", "Prof Dr Alex"); x = x.replace("Alex", "Prof Dr Alex");
x = x.replace("Bhanu", "Prof Dr Bhanu"); x = x.replace("Bhanu", "Prof Dr Bhanu");
x = x.replace("Corinna", "Dr Corinna");
x = x.replace("Casper", "Prof Dr Casper");
x = x.replace("Bart", "Dr Bart"); x = x.replace("Bart", "Dr Bart");
x = x.replace("Dennis", "Dr Dennis"); x = x.replace("Dennis", "Dr Dennis");
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor"); x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
x = x.replace(/Authors/g, "aut_plural"); x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
x = x.replace(/Author, maintainer[.]?/g, "");
x = x.replace(/Author[.]?/g, "");
x = x.replace(/aut_plural/g, "Authors");
} }
return(x); return(x);
} }

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11
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
</span> </span>
</div> </div>
@ -283,16 +283,12 @@
<div id="microbial-taxonomic-reference-data" class="section level4"> <div id="microbial-taxonomic-reference-data" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4> <a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
<p><img src="reference/figures/logo_col.png"></p>
<p>This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>). With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p> <p>This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>). With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p> <p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
</div> </div>
<div id="antimicrobial-reference-data" class="section level4"> <div id="antimicrobial-reference-data" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</h4> <a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</h4>
<div>
<img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p>
</div>
<p>This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p> <p>This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p> <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p> <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
@ -300,7 +296,6 @@
<div id="whonet-ears-net" class="section level4"> <div id="whonet-ears-net" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#whonet-ears-net" class="anchor"></a>WHONET / EARS-Net</h4> <a href="#whonet-ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
<p><img src="./whonet.png"></p>
<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p> <p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p> <p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
</div> </div>
@ -394,6 +389,8 @@
<li> <li>
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li> <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li> <li>
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li> <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li><a href="authors.html">All authors...</a></li> <li><a href="authors.html">All authors...</a></li>
</ul> </ul>
@ -403,7 +400,7 @@
</div> </div>
<footer><div class="copyright"> <footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p> <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
</div> </div>
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9055" class="section level1"> <div id="amr-0-7-1-9056" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9055" class="anchor"></a>AMR 0.7.1.9055<small> Unreleased </small> <a href="#amr-0-7-1-9056" class="anchor"></a>AMR 0.7.1.9056<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -323,7 +323,7 @@
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h4> <a href="#other" class="anchor"></a>Other</h4>
<ul> <ul>
<li>Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors</li> <li>Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors</li>
</ul> </ul>
</div> </div>
</div> </div>
@ -1237,7 +1237,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9055">0.7.1.9055</a></li> <li><a href="#amr-0-7-1-9056">0.7.1.9056</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>
@ -1256,7 +1256,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

2
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@ -442,7 +442,7 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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@ -319,7 +319,7 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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@ -291,7 +291,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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@ -373,8 +373,8 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span> <pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a dataset available in the AMR package. It is true, genuine data.</span> <span class='co'># `septic_patients` is a dataset available in the AMR package. It is true, genuine data.</span>
?<span class='no'>septic_patients</span> <span class='co'># See ?septic_patients.</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># Filter on first isolates:</span> <span class='co'># Filter on first isolates:</span>

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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
</span> </span>
</div> </div>
@ -575,7 +575,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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@ -337,8 +337,8 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span> <pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a dataset available in the AMR package</span> <span class='co'># `septic_patients` is a dataset available in the AMR package. It is true, genuine data.</span>
?<span class='no'>septic_patients</span> <span class='co'># See ?septic_patients.</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># set key antibiotics to a new variable</span> <span class='co'># set key antibiotics to a new variable</span>

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@ -279,7 +279,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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@ -313,7 +313,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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@ -287,7 +287,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

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@ -460,7 +460,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

6
index.md
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@ -100,16 +100,12 @@ To find out how to conduct AMR analysis, please [continue reading here to get st
#### Microbial (taxonomic) reference data #### Microbial (taxonomic) reference data
<img src="man/figures/logo_col.png">
This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, [www.catalogueoflife.org](http://www.catalogueoflife.org)). With `catalogue_of_life_version()` can be checked which version of the CoL is included in this package. This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, [www.catalogueoflife.org](http://www.catalogueoflife.org)). With `catalogue_of_life_version()` can be checked which version of the CoL is included in this package.
Read more about which data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html). Read more about which data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html).
#### Antimicrobial reference data #### Antimicrobial reference data
<div><img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p></div>
This package contains **all ~450 antimicrobial drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm). This package contains **all ~450 antimicrobial drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm).
**NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://www.whocc.no/copyright_disclaimer/.** **NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://www.whocc.no/copyright_disclaimer/.**
@ -118,8 +114,6 @@ Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
#### WHONET / EARS-Net #### WHONET / EARS-Net
<img src="./whonet.png">
We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an [example data set `WHONET`](./reference/WHONET.html) with the exact same structure as a WHONET export file. Furthermore, this package also contains a [data set `antibiotics`](./reference/antibiotics.html) with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically. We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an [example data set `WHONET`](./reference/WHONET.html) with the exact same structure as a WHONET export file. Furthermore, this package also contains a [data set `antibiotics`](./reference/antibiotics.html) with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.
Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html). Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).

4
man/first_isolate.Rd
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@ -106,8 +106,8 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\examples{ \examples{
# septic_patients is a dataset available in the AMR package. It is true, genuine data. # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
?septic_patients # See ?septic_patients.
library(dplyr) library(dplyr)
# Filter on first isolates: # Filter on first isolates:

4
man/key_antibiotics.Rd
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@ -82,8 +82,8 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\examples{ \examples{
# septic_patients is a dataset available in the AMR package # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
?septic_patients # See ?septic_patients.
library(dplyr) library(dplyr)
# set key antibiotics to a new variable # set key antibiotics to a new variable

8
pkgdown/extra.js
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@ -77,16 +77,14 @@ $( document ).ready(function() {
// doctoral titles of authors // doctoral titles of authors
function doct_tit(x) { function doct_tit(x) {
if (typeof(x) != "undefined") { if (typeof(x) != "undefined") {
x = x.replace("Corinna", "Dr Corinna");
x = x.replace("Alex", "Prof Dr Alex"); x = x.replace("Alex", "Prof Dr Alex");
x = x.replace("Bhanu", "Prof Dr Bhanu"); x = x.replace("Bhanu", "Prof Dr Bhanu");
x = x.replace("Corinna", "Dr Corinna");
x = x.replace("Casper", "Prof Dr Casper");
x = x.replace("Bart", "Dr Bart"); x = x.replace("Bart", "Dr Bart");
x = x.replace("Dennis", "Dr Dennis"); x = x.replace("Dennis", "Dr Dennis");
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor"); x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
x = x.replace(/Authors/g, "aut_plural"); x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
x = x.replace(/Author, maintainer[.]?/g, "");
x = x.replace(/Author[.]?/g, "");
x = x.replace(/aut_plural/g, "Authors");
} }
return(x); return(x);
} }

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