Browse Source

gitlab pages

new-mo-algorithm
parent
commit
92d2553dfe
  1. 1
      .Rbuildignore
  2. 4
      DESCRIPTION
  3. 2
      README.md
  4. 476
      pages/LICENSE-text.html
  5. 186
      pages/articles/AMR.html
  6. 1648
      pages/articles/freq.html
  7. 142
      pages/articles/index.html
  8. 162
      pages/authors.html
  9. 148
      pages/docsearch.css
  10. 85
      pages/docsearch.js
  11. 716
      pages/index.html
  12. 12
      pages/link.svg
  13. 143
      pages/news/index.html
  14. 236
      pages/pkgdown.css
  15. 115
      pages/pkgdown.js
  16. 7
      pages/pkgdown.yml
  17. 153
      pages/reference/AMR-deprecated.html
  18. 183
      pages/reference/AMR.html
  19. 201
      pages/reference/ab_property.html
  20. 213
      pages/reference/abname.html
  21. 179
      pages/reference/age.html
  22. BIN
      pages/reference/age_groups-1.png
  23. 234
      pages/reference/age_groups.html
  24. 190
      pages/reference/antibiotics.html
  25. 204
      pages/reference/as.atc.html
  26. BIN
      pages/reference/as.mic-1.png
  27. 202
      pages/reference/as.mic.html
  28. 306
      pages/reference/as.mo.html
  29. BIN
      pages/reference/as.rsi-1.png
  30. BIN
      pages/reference/as.rsi-2.png
  31. 20221
      pages/reference/as.rsi.html
  32. 235
      pages/reference/atc_property.html
  33. 289
      pages/reference/count.html
  34. 423
      pages/reference/eucast_rules.html
  35. BIN
      pages/reference/figures/clipboard_copy.png
  36. BIN
      pages/reference/figures/clipboard_paste.png
  37. BIN
      pages/reference/figures/clipboard_rsi.png
  38. BIN
      pages/reference/figures/combi_therapy_2.png
  39. BIN
      pages/reference/figures/combi_therapy_3.png
  40. BIN
      pages/reference/figures/itis_logo.jpg
  41. BIN
      pages/reference/figures/logo_amr.png
  42. 3547
      pages/reference/figures/logo_amr.svg
  43. BIN
      pages/reference/figures/logo_certe.png
  44. BIN
      pages/reference/figures/logo_eh1h.png
  45. BIN
      pages/reference/figures/logo_interreg.png
  46. BIN
      pages/reference/figures/logo_rug.png
  47. BIN
      pages/reference/figures/logo_umcg.png
  48. BIN
      pages/reference/figures/mic_example.png
  49. BIN
      pages/reference/figures/mono_therapy.png
  50. BIN
      pages/reference/figures/plus.png
  51. BIN
      pages/reference/figures/rsi_example1.png
  52. BIN
      pages/reference/figures/rsi_example2.png
  53. BIN
      pages/reference/figures/rsi_example3.png
  54. BIN
      pages/reference/figures/rsi_example4.png
  55. 20580
      pages/reference/first_isolate.html
  56. BIN
      pages/reference/freq-1.png
  57. BIN
      pages/reference/freq-2.png
  58. 910
      pages/reference/freq.html
  59. 309
      pages/reference/g.test.html
  60. 166
      pages/reference/get_locale.html
  61. BIN
      pages/reference/ggplot_rsi-1.png
  62. BIN
      pages/reference/ggplot_rsi-2.png
  63. BIN
      pages/reference/ggplot_rsi-3.png
  64. BIN
      pages/reference/ggplot_rsi-4.png
  65. BIN
      pages/reference/ggplot_rsi-5.png
  66. BIN
      pages/reference/ggplot_rsi-6.png
  67. BIN
      pages/reference/ggplot_rsi-7.png
  68. 333
      pages/reference/ggplot_rsi.html
  69. 386
      pages/reference/index.html
  70. 12922
      pages/reference/join.html
  71. 269
      pages/reference/key_antibiotics.html
  72. 182
      pages/reference/kurtosis.html
  73. 236
      pages/reference/like.html
  74. 10345
      pages/reference/mdro.html
  75. 168
      pages/reference/microorganisms.certe.html
  76. 197
      pages/reference/microorganisms.html
  77. 186
      pages/reference/microorganisms.old.html
  78. 168
      pages/reference/microorganisms.umcg.html
  79. 159
      pages/reference/mo_failures.html
  80. 329
      pages/reference/mo_property.html
  81. 159
      pages/reference/mo_renamed.html
  82. 173
      pages/reference/p.symbol.html
  83. 337
      pages/reference/portion.html
  84. 298
      pages/reference/read.4D.html
  85. 339
      pages/reference/resistance_predict.html
  86. 180
      pages/reference/rsi.html
  87. 233
      pages/reference/septic_patients.html
  88. 184
      pages/reference/skewness.html
  89. 165
      pages/reference/supplementary_data.html

1
.Rbuildignore

@ -8,3 +8,4 @@ appveyor.yml @@ -8,3 +8,4 @@ appveyor.yml
_noinclude
^cran-comments\.md$
git.sh
pages

4
DESCRIPTION

@ -16,7 +16,7 @@ Authors@R: c( @@ -16,7 +16,7 @@ Authors@R: c(
role = c("aut", "rev"),
comment = c(ORCID = "0000-0001-5809-5995")),
person(
given = c("Erwin", "E.A."),
given = c("Erwin", "E.", "A."),
family = "Hassing",
email = "e.hassing@certe.nl",
role = "ctb"),
@ -33,7 +33,7 @@ Authors@R: c( @@ -33,7 +33,7 @@ Authors@R: c(
role = "ths",
comment = c(ORCID = "0000-0003-4881-038X")),
person(
given = "Bhanu",
given = c("Bhanu", "N.", "M."),
family = "Sinha",
email = "b.sinha@umcg.nl",
role = "ths",

2
README.md

@ -13,7 +13,7 @@ Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https @@ -13,7 +13,7 @@ Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https
Erwin E.A. Hassing<sup>2</sup>,
Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
Bhanu Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
<sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)<br>
<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>

476
pages/LICENSE-text.html

@ -0,0 +1,476 @@ @@ -0,0 +1,476 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>License • AMR</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script>
<meta property="og:title" content="License" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-title-body">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9007</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="articles/AMR.html">Get started</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="articles/freq.html">Creating Frequency Tables</a>
</li>
</ul>
</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>License</h1>
</div>
<pre> GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc., &lt;http://fsf.org/&gt;
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Lesser General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must give the recipients all the rights that
you have. You must make sure that they, too, receive or can get the
source code. And you must show them these terms so they know their
rights.
We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain
that everyone understands that there is no warranty for this free
software. If the software is modified by someone else and passed on, we
want its recipients to know that what they have is not the original, so
that any problems introduced by others will not reflect on the original
authors' reputations.
Finally, any free program is threatened constantly by software
patents. We wish to avoid the danger that redistributors of a free
program will individually obtain patent licenses, in effect making the
program proprietary. To prevent this, we have made it clear that any
patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and
modification follow.
GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
under the terms of this General Public License. The "Program", below,
refers to any such program or work, and a "work based on the Program"
means either the Program or any derivative work under copyright law:
that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another
language. (Hereinafter, translation is included without limitation in
the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running the Program is not restricted, and the output from the Program
is covered only if its contents constitute a work based on the
Program (independent of having been made by running the Program).
Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate
copyright notice and disclaimer of warranty; keep intact all the
notices that refer to this License and to the absence of any warranty;
and give any other recipients of the Program a copy of this License
along with the Program.
You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion
of it, thus forming a work based on the Program, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
a warranty) and that users may redistribute the program under
these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but
does not normally print such an announcement, your work based on
the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Program,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Program, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Program.
In addition, mere aggregation of another work not based on the Program
with the Program (or with a work based on the Program) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may copy and distribute the Program (or a work based on it,
under Section 2) in object code or executable form under the terms of
Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of Sections
1 and 2 above on a medium customarily used for software interchange; or,
b) Accompany it with a written offer, valid for at least three
years, to give any third party, for a charge no more than your
cost of physically performing source distribution, a complete
machine-readable copy of the corresponding source code, to be
distributed under the terms of Sections 1 and 2 above on a medium
customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer
to distribute corresponding source code. (This alternative is
allowed only for noncommercial distribution and only if you
received the program in object code or executable form with such
an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for
making modifications to it. For an executable work, complete source
code means all the source code for all modules it contains, plus any
associated interface definition files, plus the scripts used to
control compilation and installation of the executable. However, as a
special exception, the source code distributed need not include
anything that is normally distributed (in either source or binary
form) with the major components (compiler, kernel, and so on) of the
operating system on which the executable runs, unless that component
itself accompanies the executable.
If distribution of executable or object code is made by offering
access to copy from a designated place, then offering equivalent
access to copy the source code from the same place counts as
distribution of the source code, even though third parties are not
compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program
except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense or distribute the Program is
void, and will automatically terminate your rights under this License.
However, parties who have received copies, or rights, from you under
this License will not have their licenses terminated so long as such
parties remain in full compliance.
5. You are not required to accept this License, since you have not
signed it. However, nothing else grants you permission to modify or
distribute the Program or its derivative works. These actions are
prohibited by law if you do not accept this License. Therefore, by
modifying or distributing the Program (or any work based on the
Program), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Program or works based on it.
6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the
original licensor to copy, distribute or modify the Program subject to
these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties to
this License.
7. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Program at all. For example, if a patent
license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under
any particular circumstance, the balance of the section is intended to
apply and the section as a whole is intended to apply in other
circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system, which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
countries not thus excluded. In such case, this License incorporates
the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program
specifies a version number of this License which applies to it and "any
later version", you have the option of following the terms and conditions
either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
this License, you may choose any version ever published by the Free Software
Foundation.
10. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the author
to ask for permission. For software which is copyrighted by the Free
Software Foundation, write to the Free Software Foundation; we sometimes
make exceptions for this. Our decision will be guided by the two goals
of preserving the free status of all derivatives of our free software and
of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
{description}
Copyright (C) {year} {fullname}
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
{signature of Ty Coon}, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.
</pre>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Matthijs S. Berends, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
</body>
</html>

186
pages/articles/AMR.html

@ -0,0 +1,186 @@ @@ -0,0 +1,186 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Introduction to the AMR package • AMR</title>
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to the AMR package">
<meta property="og:description" content="">
<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9007</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../articles/AMR.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/freq.html">Creating Frequency Tables</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right"></ul>
</div>
<!--/.nav-collapse -->
</div>
<!--/.container -->
</div>
<!--/.navbar -->
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1>Introduction to the AMR package</h1>
<h4 class="author">Matthijs S. Berends</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
</div>
<p>This R package was intended <strong>to make microbial epidemiology easier</strong>. Most functions contain extensive help pages to get started.</p>
<p>The <code>AMR</code> package basically does four important things:</p>
<ol style="list-style-type: decimal">
<li>It <strong>cleanses existing data</strong>, by transforming it to reproducible and profound <em>classes</em>, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:</li>
</ol>
<ul>
<li>Use <code>as.mo</code> to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” and “esccol”. Even <code><a href="../reference/as.mo.html">as.mo("MRSA")</a></code> will return the ID of <em>S. aureus</em>. Moreover, it can group all coagulase negative and positive <em>Staphylococci</em>, and can transform <em>Streptococci</em> into Lancefield groups. To find bacteria based on your input, it uses Artificial Intelligence to look up values in the included ITIS data, consisting of more than 18,000 microorganisms.</li>
<li>Use <code>as.rsi</code> to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
<li>Use <code>as.mic</code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
<li>Use <code>as.atc</code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.</li>
</ul>
<ol start="2" style="list-style-type: decimal">
<li>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</li>
</ol>
<ul>
<li>Use <code>EUCAST_rules</code> to apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a>.</li>
<li>Use <code>first_isolate</code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
<ul>
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
</ul>
</li>
<li>Use <code>MDRO</code> (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.</li>
<li>The data set <code>microorganisms</code> contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code>mo_genus</code>, <code>mo_family</code>, <code>mo_gramstain</code> or even <code>mo_phylum</code>. As they use <code>as.mo</code> internally, they also use artificial intelligence. For example, <code><a href="../reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="../reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, French, Italian, Spanish and Portuguese. These functions can be used to add new variables to your data.</li>
<li>The data set <code>antibiotics</code> contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like <code>ab_name</code> and <code>ab_tradenames</code> to look up values. The <code>ab_*</code> functions use <code>as.atc</code> internally so they support AI to guess your expected result. For example, <code><a href="../reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="../reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="../reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
</ul>
<ol start="3" style="list-style-type: decimal">
<li>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</li>
</ol>
<ul>
<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> functions. All these functions can be used <a href="https://dplyr.tidyverse.org/#usage">with the <code>dplyr</code> package</a> (e.g. in conjunction with <a href="https://dplyr.tidyverse.org/reference/summarise.html"><code>summarise</code></a>)</li>
<li>Plot AMR results with <code>geom_rsi</code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code>resistance_predict</code> function</li>
<li>Conduct descriptive statistics to enhance base R: calculate kurtosis, skewness and create frequency tables</li>
</ul>
<ol start="4" style="list-style-type: decimal">
<li>It <strong>teaches the user</strong> how to use all the above actions.</li>
</ol>
<ul>
<li>The package contains extensive help pages with many examples.</li>
<li>It also contains an example data set called <code>septic_patients</code>. This data set contains:
<ul>
<li>2,000 blood culture isolates from anonymised septic patients between 2001 and 2017 in the Northern Netherlands</li>
<li>Results of 40 antibiotics (each antibiotic in its own column) with a total of 38,414 antimicrobial results</li>
<li>Real and genuine data</li>
</ul>
</li>
</ul>
<div id="itis" class="section level3">
<h3 class="hasAnchor">
<a href="#itis" class="anchor"></a>ITIS</h3>
<p>This package contains the <strong>complete microbial taxonomic data</strong> (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href="https://www.itis.gov" class="uri">https://www.itis.gov</a>).</p>
<p>All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists.</p>
<p><strong>Get a note when a species was renamed</strong></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mo_property.html">mo_shortname</a></span>(<span class="st">"Chlamydia psittaci"</span>)
<span class="co"># Note: 'Chlamydia psittaci' (Page, 1968) was renamed 'Chlamydophila psittaci' (Everett et al., 1999)</span>
<span class="co"># [1] "C. psittaci"</span></code></pre></div>
<p><strong>Get any property from the entire taxonomic tree for all included species</strong></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] "Gammaproteobacteria"</span>
<span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] "Enterobacteriaceae"</span>
<span class="kw"><a href="../reference/mo_property.html">mo_ref</a></span>(<span class="st">"E. coli"</span>)
<span class="co"># [1] "Castellani and Chalmers, 1919"</span></code></pre></div>
<p><strong>Do not get mistaken - the package only includes microorganisms</strong></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"C. elegans"</span>)
<span class="co"># [1] "Cyanobacteria" # Bacteria?!</span>
<span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"C. elegans"</span>)
<span class="co"># [1] "Chroococcus limneticus elegans" # Because a microorganism was found </span></code></pre></div>
<hr>
<p>AMR, (c) 2018, <a href="https://gitlab.com/msberends/AMR" class="uri">https://gitlab.com/msberends/AMR</a></p>
<p>Licensed under the <a href="https://github.com/msberends/AMR/blob/master/LICENSE">GNU General Public License v2.0</a>.</p>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
</div>
</div>
<footer><div class="copyright">
<p>Developed by Matthijs S. Berends, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
</body>
</html>

1648
pages/articles/freq.html

File diff suppressed because it is too large Load Diff

142
pages/articles/index.html

@ -0,0 +1,142 @@ @@ -0,0 +1,142 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Articles • AMR</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Articles" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-article-index">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9007</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../articles/AMR.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/freq.html">Creating Frequency Tables</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Articles</h1>
</div>
<div class="section ">
<h3>All vignettes</h3>
<p class="section-desc"></p>
<ul>
<li><a href="AMR.html">Introduction to the AMR package</a></li>
<li><a href="freq.html">Creating Frequency Tables</a></li>
</ul>
</div>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Matthijs S. Berends, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
</body>
</html>

162
pages/authors.html

@ -0,0 +1,162 @@ @@ -0,0 +1,162 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Authors • AMR</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script>
<meta property="og:title" content="Authors" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-authors">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9007</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="articles/AMR.html">Get started</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="articles/freq.html">Creating Frequency Tables</a>
</li>
</ul>
</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>Authors</h1>
</div>
<ul class="list-unstyled">
<li>
<p><strong>Matthijs S. Berends</strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' 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>Christian F. Luz</strong>. Author, reviewer. <a href='https://orcid.org/0000-0001-5809-5995' 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>Erwin E. A. Hassing</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Corinna Glasner</strong>. 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>
</li>
<li>
<p><strong>Alex W. Friedrich</strong>. Thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' 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>Bhanu N. M. Sinha</strong>. 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>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Matthijs S. Berends, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
</body>
</html>

148
pages/docsearch.css

File diff suppressed because one or more lines are too long

85
pages/docsearch.js

@ -0,0 +1,85 @@ @@ -0,0 +1,85 @@
$(function() {
// register a handler to move the focus to the search bar
// upon pressing shift + "/" (i.e. "?")
$(document).on('keydown', function(e) {
if (e.shiftKey && e.keyCode == 191) {
e.preventDefault();
$("#search-input").focus();
}
});
$(document).ready(function() {
// do keyword highlighting
/* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
var mark = function() {
var referrer = document.URL ;
var paramKey = "q" ;
if (referrer.indexOf("?") !== -1) {
var qs = referrer.substr(referrer.indexOf('?') + 1);
var qs_noanchor = qs.split('#')[0];
var qsa = qs_noanchor.split('&');
var keyword = "";
for (var i = 0; i < qsa.length; i++) {
var currentParam = qsa[i].split('=');
if (currentParam.length !== 2) {
continue;
}
if (currentParam[0] == paramKey) {
keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
}
}
if (keyword !== "") {
$(".contents").unmark({
done: function() {
$(".contents").mark(keyword);
}
});
}
}
};
mark();
});
});
/* Search term highlighting ------------------------------*/
function matchedWords(hit) {
var words = [];
var hierarchy = hit._highlightResult.hierarchy;
// loop to fetch from lvl0, lvl1, etc.
for (var idx in hierarchy) {
words = words.concat(hierarchy[idx].matchedWords);
}
var content = hit._highlightResult.content;
if (content) {
words = words.concat(content.matchedWords);
}
// return unique words
var words_uniq = [...new Set(words)];
return words_uniq;
}
function updateHitURL(hit) {
var words = matchedWords(hit);
var url = "";
if (hit.anchor) {
url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
} else {
url = hit.url + '?q=' + escape(words.join(" "));
}
return url;
}

716
pages/index.html

<
@ -0,0 +1,716 @@ @@ -0,0 +1,716 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Antimicrobial Resistance Analysis • AMR</title>
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script><meta property="og:title" content="Antimicrobial Resistance Analysis">
<meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods.">
<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-home">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9007</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="articles/AMR.html">Get started</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="articles/freq.html">Creating Frequency Tables</a>
</li>
</ul>
</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right"></ul>
</div>
<!--/.nav-collapse -->
</div>
<!--/.container -->
</div>
<!--/.navbar -->
</header><div class="row">
<div class="contents col-md-9">
<div id="amr" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#amr" class="anchor"></a><code>AMR</code> <img src="reference/figures/logo_amr.png" align="right" height="120px">
</h1></div>
<div id="an-r-package-to-simplify-the-analysis-and-prediction-of-antimicrobial-resistance-amr-and-to-work-with-antibiotic-properties-by-using-evidence-based-methods-" class="section level3">
<h3 class="hasAnchor">
<a href="#an-r-package-to-simplify-the-analysis-and-prediction-of-antimicrobial-resistance-amr-and-to-work-with-antibiotic-properties-by-using-evidence-based-methods-" class="anchor"></a>An <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with antibiotic properties by using evidence-based methods.</h3>
<p>This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a> and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the <a href="https://www.umcg.nl">University Medical Center Groningen (UMCG)</a>.</p>
<p> Get it with <code><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages("AMR")</a></code> or see below for other possibilities.</p>
<p> Read the <a href="https://gitlab.com/msberends/AMR/blob/master/NEWS.md">changelog here</a>.</p>
</div>
<div id="authors" class="section level2">
<h2 class="hasAnchor">
<a href="#authors" class="anchor"></a>Authors</h2>
<p>Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>, Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,a</sup>, Erwin E.A. Hassing<sup>2</sup>, Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>, Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>, Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup></p>
<p><sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - <a href="http://www.rug.nl">rug.nl</a> <a href="http://www.umcg.nl">umcg.nl</a><br><sup>2</sup> Certe Medical Diagnostics &amp; Advice, Groningen, the Netherlands - <a href="http://www.certe.nl">certe.nl</a><br><sup>a</sup> R package author and thesis dissertant<br><sup>b</sup> Thesis advisor</p>
<p><a href="https://www.rug.nl"><img src="reference/figures/logo_rug.png" height="60px"></a> <a href="https://www.umcg.nl"><img src="reference/figures/logo_umcg.png" height="60px"></a> <a href="https://www.certe.nl"><img src="reference/figures/logo_certe.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="reference/figures/logo_eh1h.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="reference/figures/logo_interreg.png" height="60px"></a></p>
</div>
<div id="contents" class="section level2">
<h2 class="hasAnchor">
<a href="#contents" class="anchor"></a>Contents</h2>
<ul>
<li><a href="#why-this-package">Why this package?</a></li>
<li><a href="#itis">ITIS</a></li>
<li><a href="#how-to-get-it">How to get it?</a></li>
<li><a href="#install-from-cran">Install from CRAN</a></li>
<li><a href="#install-from-zenodo">Install from Zenodo</a></li>
<li><a href="#install-from-gitlab">Install from GitLab</a></li>
<li><a href="#how-to-use-it">How to use it?</a></li>
<li><a href="#new-classes">New classes</a></li>
<li><a href="#overwriteforce-resistance-based-on-eucast-rules">Overwrite/force resistance based on EUCAST rules</a></li>
<li><a href="#other-microbial-epidemiological-functions">Other (microbial) epidemiological functions</a></li>
<li><a href="#frequency-tables">Frequency tables</a></li>
<li><a href="#data-sets-included-in-package">Data sets included in package</a></li>
<li><a href="#benchmarks">Benchmarks</a></li>
<li><a href="#copyright">Copyright</a></li>
</ul>
</div>
<div id="why-this-package" class="section level2">
<h2 class="hasAnchor">
<a href="#why-this-package" class="anchor"></a>Why this package?</h2>
<p>This R package was intended <strong>to make microbial epidemiology easier</strong>. Most functions contain extensive help pages to get started.</p>
<p>The <code>AMR</code> package basically does four important things:</p>
<ol>
<li>It <strong>cleanses existing data</strong>, by transforming it to reproducible and profound <em>classes</em>, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:</li>
</ol>
<ul>
<li>Use <code>as.mo</code> to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” and “esccol”. Even <code><a href="reference/as.mo.html">as.mo("MRSA")</a></code> will return the ID of <em>S. aureus</em>. Moreover, it can group all coagulase negative and positive <em>Staphylococci</em>, and can transform <em>Streptococci</em> into Lancefield groups. To find bacteria based on your input, it uses Artificial Intelligence to look up values in the included ITIS data, consisting of more than 18,000 microorganisms. It is <em>very</em> fast, see <a href="#benchmarks">Benchmarks</a>.</li>
<li>Use <code>as.rsi</code> to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
<li>Use <code>as.mic</code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
<li>Use <code>as.atc</code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.</li>
</ul>
<ol>
<li>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</li>
</ol>
<ul>
<li>Use <code>EUCAST_rules</code> to apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a>.</li>
<li>Use <code>first_isolate</code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
<ul>
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
</ul>
</li>
<li>Use <code>MDRO</code> (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.</li>
<li>The data set <code>microorganisms</code> contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code>mo_genus</code>, <code>mo_family</code>, <code>mo_gramstain</code> or even <code>mo_phylum</code>. As they use <code>as.mo</code> internally, they also use artificial intelligence. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
<li>The data set <code>antibiotics</code> contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like <code>ab_name</code> and <code>ab_tradenames</code> to look up values. The <code>ab_*</code> functions use <code>as.atc</code> internally so they support AI to guess your expected result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
</ul>
<ol>
<li>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</li>
</ol>
<ul>
<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> functions. All these functions can be used <a href="https://dplyr.tidyverse.org/#usage">with the <code>dplyr</code> package</a> (e.g. in conjunction with <a href="https://dplyr.tidyverse.org/reference/summarise.html"><code>summarise</code></a>)</li>
<li>Plot AMR results with <code>geom_rsi</code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code>resistance_predict</code> function</li>
<li>Conduct descriptive statistics to enhance base R: calculate kurtosis, skewness and create frequency tables</li>
</ul>
<ol>
<li>It <strong>teaches the user</strong> how to use all the above actions.</li>
</ol>
<ul>
<li>The package contains extensive help pages with many examples.</li>
<li>It also contains an example data set called <code>septic_patients</code>. This data set contains:
<ul>