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(v0.7.1.9056) mo and ab subsetting

new-mo-algorithm
parent
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  1. 6
      DESCRIPTION
  2. 16
      NAMESPACE
  3. 4
      NEWS.md
  4. 38
      R/ab.R
  5. 6
      R/first_isolate.R
  6. 4
      R/key_antibiotics.R
  7. 38
      R/mo.R
  8. 6
      _pkgdown.yml
  9. 4
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      docs/index.html
  23. 12
      docs/news/index.html
  24. 2
      docs/reference/as.mo.html
  25. 2
      docs/reference/catalogue_of_life.html
  26. 2
      docs/reference/catalogue_of_life_version.html
  27. 4
      docs/reference/first_isolate.html
  28. 4
      docs/reference/index.html
  29. 4
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  30. 2
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  31. 2
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  32. 2
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  33. 2
      docs/reference/mo_property.html
  34. 6
      index.md
  35. 4
      man/first_isolate.Rd
  36. 4
      man/key_antibiotics.Rd
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6
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9055
Date: 2019-08-13
Version: 0.7.1.9056
Date: 2019-08-14
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@ -11,6 +11,8 @@ Authors@R: c( @@ -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")),
person(role = c("aut", "ths"),
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"),
family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
person(role = "ctb",

16
NAMESPACE

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

4
NEWS.md

@ -1,4 +1,4 @@ @@ -1,4 +1,4 @@
# AMR 0.7.1.9055
# AMR 0.7.1.9056
### 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.
@ -73,7 +73,7 @@ @@ -73,7 +73,7 @@
* Classes `ab` and `mo` will now be preserved in any subsetting
#### 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

38
R/ab.R

@ -282,10 +282,42 @@ as.data.frame.ab <- function (x, ...) { @@ -282,10 +282,42 @@ as.data.frame.ab <- function (x, ...) {
#' @exportMethod [.ab
#' @export
#' @noRd
"[.ab" <- function (x, ...) {
# this function is needed to preserve the "ab" class for any subsetting, like df %>% filter(...)
"[.ab" <- function(x, ...) {
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

6
R/first_isolate.R

@ -79,8 +79,8 @@ @@ -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/}.
#' @inheritSection AMR Read more on our website!
#' @examples
#' # septic_patients is a dataset available in the AMR package. It is true, genuine data.
#' ?septic_patients
#' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
#' # See ?septic_patients.
#'
#' library(dplyr)
#' # Filter on first isolates:
@ -97,7 +97,7 @@ @@ -97,7 +97,7 @@
#' # or for first weighted isolates:
#' septic_patients %>%
#' filter_first_weighted_isolate()
#'
#'
#' # Now let's see if first isolates matter:
#' A <- septic_patients %>%
#' group_by(hospital_id) %>%

4
R/key_antibiotics.R

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

38
R/mo.R

@ -1723,10 +1723,42 @@ as.data.frame.mo <- function(x, ...) { @@ -1723,10 +1723,42 @@ as.data.frame.mo <- function(x, ...) {
#' @exportMethod [.mo
#' @export
#' @noRd
"[.mo" <- function (x, ...) {
# this function is needed to preserve the "mo" class for any subsetting, like df %>% filter(...)
"[.mo" <- function(x, ...) {
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

6
_pkgdown.yml

@ -172,12 +172,14 @@ authors: @@ -172,12 +172,14 @@ authors:
href: https://www.rug.nl/staff/m.s.berends/
Christian F. Luz:
href: https://www.rug.nl/staff/c.f.luz/
Corinna Glasner:
href: https://www.rug.nl/staff/c.glasner/
Alex W. Friedrich:
href: https://www.rug.nl/staff/a.w.friedrich/
Bhanu N. M. 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:
assets: "pkgdown/logos" # use logos in this folder

4
docs/LICENSE-text.html

@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</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">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>
</div>
@ -513,7 +513,7 @@ END OF TERMS AND CONDITIONS @@ -513,7 +513,7 @@ END OF TERMS AND CONDITIONS
<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 class="pkgdown">

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docs/articles/index.html

@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</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">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>
</div>
@ -243,7 +243,7 @@ @@ -243,7 +243,7 @@
<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 class="pkgdown">

8
docs/authors.html

@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</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">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>
</div>
@ -241,6 +241,10 @@ @@ -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>
</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>
<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>
@ -270,7 +274,7 @@ @@ -270,7 +274,7 @@
<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 class="pkgdown">

8
docs/extra.js

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

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11
docs/index.html

@ -42,7 +42,7 @@ @@ -42,7 +42,7 @@
</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">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>
</div>
@ -283,16 +283,12 @@ @@ -283,16 +283,12 @@
<div id="microbial-taxonomic-reference-data" class="section level4">
<h4 class="hasAnchor">
<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>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
</div>
<div id="antimicrobial-reference-data" class="section level4">
<h4 class="hasAnchor">
<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><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>
@ -300,7 +296,6 @@ @@ -300,7 +296,6 @@
<div id="whonet-ears-net" class="section level4">
<h4 class="hasAnchor">
<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>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
</div>
@ -394,6 +389,8 @@ @@ -394,6 +389,8 @@
<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>
<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>
<li><a href="authors.html">All authors...</a></li>
</ul>
@ -403,7 +400,7 @@ @@ -403,7 +400,7 @@
</div>
<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 class="pkgdown">

12
docs/news/index.html

@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</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">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>
</div>
@ -225,9 +225,9 @@ @@ -225,9 +225,9 @@
</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">
<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>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -323,7 +323,7 @@ @@ -323,7 +323,7 @@
<h4 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h4>
<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>
</div>
</div>
@ -1237,7 +1237,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a @@ -1237,7 +1237,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<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-0-7-0">0.7.0</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 @@ -1256,7 +1256,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<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 class="pkgdown">

2
docs/reference/as.mo.html

@ -442,7 +442,7 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod @@ -442,7 +442,7 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<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 class="pkgdown">

2
docs/reference/catalogue_of_life.html

@ -319,7 +319,7 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel @@ -319,7 +319,7 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
<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 class="pkgdown">

2
docs/reference/catalogue_of_life_version.html

@ -291,7 +291,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( @@ -291,7 +291,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 class="pkgdown">

4
docs/reference/first_isolate.html

@ -373,8 +373,8 @@ To conduct an analysis of antimicrobial resistance, you should only include the @@ -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>
<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='no'>septic_patients</span>
<span class='co'># `septic_patients` is a dataset available in the AMR package. It is true, genuine data.</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='co'># Filter on first isolates:</span>

4
docs/reference/index.html

@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</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">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>
</div>
@ -575,7 +575,7 @@ @@ -575,7 +575,7 @@
<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 class="pkgdown">

4
docs/reference/key_antibiotics.html

@ -337,8 +337,8 @@ @@ -337,8 +337,8 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<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='no'>septic_patients</span>
<span class='co'># `septic_patients` is a dataset available in the AMR package. It is true, genuine data.</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='co'># set key antibiotics to a new variable</span>

2
docs/reference/microorganisms.codes.html

@ -279,7 +279,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( @@ -279,7 +279,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 class="pkgdown">

2
docs/reference/microorganisms.html

@ -313,7 +313,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( @@ -313,7 +313,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 class="pkgdown">

2
docs/reference/microorganisms.old.html

@ -287,7 +287,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( @@ -287,7 +287,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 class="pkgdown">

2
docs/reference/mo_property.html

@ -460,7 +460,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( @@ -460,7 +460,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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 class="pkgdown">

6
index.md

@ -100,16 +100,12 @@ To find out how to conduct AMR analysis, please [continue reading here to get st @@ -100,16 +100,12 @@ To find out how to conduct AMR analysis, please [continue reading here to get st
#### 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.
Read more about which data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html).
#### 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).
**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). @@ -118,8 +114,6 @@ Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
#### 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.
Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).

4
man/first_isolate.Rd

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

4
man/key_antibiotics.Rd

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

8
pkgdown/extra.js

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

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