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How to
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2019-01-02 23:24:07 +01:00
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2018-12-23 21:26:21 +01:00
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<span class="fa fa-directions"></span>
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2019-01-02 23:24:07 +01:00
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Conduct AMR analysis
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</a>
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2019-02-11 10:27:10 +01:00
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2021-07-03 21:56:53 +02:00
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<span class="fa fa-dice"></span>
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2019-01-02 23:24:07 +01:00
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Predict antimicrobial resistance
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</a>
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2020-08-16 21:38:42 +02:00
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2020-09-03 12:31:48 +02:00
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Data sets for download / own use
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2020-08-16 21:38:42 +02:00
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</a>
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2020-03-07 21:48:21 +01:00
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2021-07-03 21:56:53 +02:00
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<span class="fa fa-compress"></span>
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2020-03-07 21:48:21 +01:00
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Conduct principal component analysis for AMR
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</a>
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2019-05-23 16:58:59 +02:00
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2019-05-23 16:58:59 +02:00
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Determine multi-drug resistance (MDR)
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</a>
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2019-01-29 00:06:50 +01:00
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2019-01-29 00:06:50 +01:00
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Work with WHONET data
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</a>
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</li>
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2019-02-14 15:18:17 +01:00
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2019-02-14 15:18:17 +01:00
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Import data from SPSS/SAS/Stata
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</a>
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</li>
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2019-01-02 23:24:07 +01:00
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2021-07-03 21:56:53 +02:00
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<span class="fa fa-exchange-alt"></span>
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2019-01-02 23:24:07 +01:00
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Apply EUCAST rules
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</a>
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</li>
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<li>
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2019-02-11 10:27:10 +01:00
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<a href="reference/mo_property.html">
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2021-07-03 21:56:53 +02:00
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<span class="fa fa-bug"></span>
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2019-01-02 23:24:07 +01:00
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Get properties of a microorganism
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</a>
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</li>
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<li>
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2019-05-10 16:44:59 +02:00
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<a href="reference/ab_property.html">
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2021-07-03 21:56:53 +02:00
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<span class="fa fa-capsules"></span>
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2019-01-02 23:24:07 +01:00
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Get properties of an antibiotic
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</a>
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</li>
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2019-01-11 20:37:23 +01:00
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<li>
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<a href="articles/benchmarks.html">
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2021-07-03 21:56:53 +02:00
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<span class="fa fa-shipping-fast"></span>
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2019-01-11 20:37:23 +01:00
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Other: benchmarks
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</a>
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</li>
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2019-01-02 23:24:07 +01:00
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</ul>
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2018-12-23 21:26:21 +01:00
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</li>
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<li>
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2020-07-28 18:39:57 +02:00
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<a href="reference/index.html">
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2021-07-03 21:56:53 +02:00
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<span class="fa fa-book-open"></span>
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2018-12-29 22:24:19 +01:00
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Manual
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</a>
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2018-12-23 21:26:21 +01:00
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2018-12-29 22:24:19 +01:00
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2018-12-29 22:24:19 +01:00
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Authors
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</a>
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2018-12-23 21:26:21 +01:00
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2018-12-29 22:24:19 +01:00
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<li>
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2020-07-28 18:39:57 +02:00
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2021-04-29 17:16:30 +02:00
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2018-12-23 21:26:21 +01:00
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2018-12-29 22:24:19 +01:00
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Changelog
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2018-12-23 21:26:21 +01:00
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</a>
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2019-01-02 23:24:07 +01:00
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</ul>
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<ul class="nav navbar-nav navbar-right">
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<li>
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2020-07-08 14:48:06 +02:00
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<a href="https://github.com/msberends/AMR">
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2021-04-29 17:16:30 +02:00
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<span class="fab fa-github"></span>
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2018-12-29 22:24:19 +01:00
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Source Code
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</a>
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2018-12-23 21:26:21 +01:00
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</div><!--/.nav-collapse -->
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</div><!--/.navbar -->
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2019-09-25 15:43:22 +02:00
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2018-12-23 21:26:21 +01:00
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</header>
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<div class="row">
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<div class="contents col-md-9">
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<div class="page-header">
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<h1>License</h1>
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</div>
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2019-08-07 15:37:39 +02:00
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<pre>GNU GENERAL PUBLIC LICENSE
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Version 2, June 1991
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2018-12-23 21:26:21 +01:00
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2019-08-07 15:37:39 +02:00
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Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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2018-12-23 21:26:21 +01:00
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2019-08-30 14:50:56 +02:00
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A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
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This R package, with package name 'AMR':
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- May be used for commercial purposes
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- May be used for private purposes
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- May NOT be used for patent purposes
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- May be modified, although:
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- Modifications MUST be released under the same license when distributing the package
|
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|
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- Changes made to the code MUST be documented
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|
- May be distributed, although:
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- Source code MUST be made available when the package is distributed
|
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- A copy of the license and copyright notice MUST be included with the package.
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- Comes with a LIMITATION of liability
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- Comes with NO warranty
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|
END OF THE SUMMARY
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2018-12-23 21:26:21 +01:00
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2019-08-07 15:37:39 +02:00
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GNU GENERAL PUBLIC LICENSE
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TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
2018-12-23 21:26:21 +01:00
|
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|
2019-08-07 15:37:39 +02:00
|
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0. This License applies to any program or other work which contains
|
2018-12-23 21:26:21 +01:00
|
|
|
a notice placed by the copyright holder saying it may be distributed
|
2019-08-30 14:50:56 +02:00
|
|
|
under the terms of this General Public License. The "Program", below,
|
2018-12-23 21:26:21 +01:00
|
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refers to any such program or work, and a "work based on the Program"
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means either the Program or any derivative work under copyright law:
|
2019-08-30 14:50:56 +02:00
|
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that is to say, a work containing the Program or a portion of it,
|
2018-12-23 21:26:21 +01:00
|
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either verbatim or with modifications and/or translated into another
|
2019-08-30 14:50:56 +02:00
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language. (Hereinafter, translation is included without limitation in
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the term "modification".) Each licensee is addressed as "you".
|
2018-12-23 21:26:21 +01:00
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Activities other than copying, distribution and modification are not
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2019-08-30 14:50:56 +02:00
|
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covered by this License; they are outside its scope. The act of
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2018-12-23 21:26:21 +01:00
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running the Program is not restricted, and the output from the Program
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is covered only if its contents constitute a work based on the
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Program (independent of having been made by running the Program).
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Whether that is true depends on what the Program does.
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2019-08-07 15:37:39 +02:00
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1. You may copy and distribute verbatim copies of the Program's
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2018-12-23 21:26:21 +01:00
|
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source code as you receive it, in any medium, provided that you
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conspicuously and appropriately publish on each copy an appropriate
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copyright notice and disclaimer of warranty; keep intact all the
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notices that refer to this License and to the absence of any warranty;
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and give any other recipients of the Program a copy of this License
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along with the Program.
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You may charge a fee for the physical act of transferring a copy, and
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you may at your option offer warranty protection in exchange for a fee.
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|
2019-08-30 14:50:56 +02:00
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2. You may modify your copy or copies of the Program or any portion
|
2018-12-23 21:26:21 +01:00
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|
of it, thus forming a work based on the Program, and copy and
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distribute such modifications or work under the terms of Section 1
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above, provided that you also meet all of these conditions:
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a) You must cause the modified files to carry prominent notices
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stating that you changed the files and the date of any change.
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b) You must cause any work that you distribute or publish, that in
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whole or in part contains or is derived from the Program or any
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part thereof, to be licensed as a whole at no charge to all third
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parties under the terms of this License.
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c) If the modified program normally reads commands interactively
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when run, you must cause it, when started running for such
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interactive use in the most ordinary way, to print or display an
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announcement including an appropriate copyright notice and a
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notice that there is no warranty (or else, saying that you provide
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a warranty) and that users may redistribute the program under
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these conditions, and telling the user how to view a copy of this
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License. (Exception: if the Program itself is interactive but
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does not normally print such an announcement, your work based on
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the Program is not required to print an announcement.)
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|
2019-08-30 14:50:56 +02:00
|
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These requirements apply to the modified work as a whole. If
|
2018-12-23 21:26:21 +01:00
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|
|
identifiable sections of that work are not derived from the Program,
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and can be reasonably considered independent and separate works in
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themselves, then this License, and its terms, do not apply to those
|
2019-08-30 14:50:56 +02:00
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|
sections when you distribute them as separate works. But when you
|
2018-12-23 21:26:21 +01:00
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|
|
distribute the same sections as part of a whole which is a work based
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on the Program, the distribution of the whole must be on the terms of
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this License, whose permissions for other licensees extend to the
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entire whole, and thus to each and every part regardless of who wrote it.
|
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Thus, it is not the intent of this section to claim rights or contest
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|
|
your rights to work written entirely by you; rather, the intent is to
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|
exercise the right to control the distribution of derivative or
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|
collective works based on the Program.
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In addition, mere aggregation of another work not based on the Program
|
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|
with the Program (or with a work based on the Program) on a volume of
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a storage or distribution medium does not bring the other work under
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|
the scope of this License.
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|
2019-08-30 14:50:56 +02:00
|
|
|
3. You may copy and distribute the Program (or a work based on it,
|
2018-12-23 21:26:21 +01:00
|
|
|
under Section 2) in object code or executable form under the terms of
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Sections 1 and 2 above provided that you also do one of the following:
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a) Accompany it with the complete corresponding machine-readable
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|
source code, which must be distributed under the terms of Sections
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1 and 2 above on a medium customarily used for software interchange; or,
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b) Accompany it with a written offer, valid for at least three
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|
years, to give any third party, for a charge no more than your
|
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|
|
cost of physically performing source distribution, a complete
|
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|
|
machine-readable copy of the corresponding source code, to be
|
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|
distributed under the terms of Sections 1 and 2 above on a medium
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|
customarily used for software interchange; or,
|
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|
c) Accompany it with the information you received as to the offer
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|
|
to distribute corresponding source code. (This alternative is
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|
|
allowed only for noncommercial distribution and only if you
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|
|
received the program in object code or executable form with such
|
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|
an offer, in accord with Subsection b above.)
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|
The source code for a work means the preferred form of the work for
|
2019-08-30 14:50:56 +02:00
|
|
|
making modifications to it. For an executable work, complete source
|
2018-12-23 21:26:21 +01:00
|
|
|
code means all the source code for all modules it contains, plus any
|
|
|
|
|
associated interface definition files, plus the scripts used to
|
2019-08-30 14:50:56 +02:00
|
|
|
control compilation and installation of the executable. However, as a
|
2018-12-23 21:26:21 +01:00
|
|
|
special exception, the source code distributed need not include
|
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|
|
anything that is normally distributed (in either source or binary
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|
|
form) with the major components (compiler, kernel, and so on) of the
|
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|
|
operating system on which the executable runs, unless that component
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|
itself accompanies the executable.
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|
If distribution of executable or object code is made by offering
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|
access to copy from a designated place, then offering equivalent
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|
access to copy the source code from the same place counts as
|
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|
|
distribution of the source code, even though third parties are not
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|
|
compelled to copy the source along with the object code.
|
|
|
|
|
|
2019-08-30 14:50:56 +02:00
|
|
|
4. You may not copy, modify, sublicense, or distribute the Program
|
|
|
|
|
except as expressly provided under this License. Any attempt
|
2018-12-23 21:26:21 +01:00
|
|
|
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.
|
|
|
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|
|
2019-08-30 14:50:56 +02:00
|
|
|
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
|
2018-12-23 21:26:21 +01:00
|
|
|
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.
|
|
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|
|
|
2019-08-30 14:50:56 +02:00
|
|
|
6. Each time you redistribute the Program (or any work based on the
|
2018-12-23 21:26:21 +01:00
|
|
|
Program), the recipient automatically receives a license from the
|
|
|
|
|
original licensor to copy, distribute or modify the Program subject to
|
2019-08-30 14:50:56 +02:00
|
|
|
these terms and conditions. You may not impose any further
|
2018-12-23 21:26:21 +01:00
|
|
|
restrictions on the recipients' exercise of the rights granted herein.
|
|
|
|
|
You are not responsible for enforcing compliance by third parties to
|
|
|
|
|
this License.
|
|
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
7. If, as a consequence of a court judgment or allegation of patent
|
2018-12-23 21:26:21 +01:00
|
|
|
infringement or for any other reason (not limited to patent issues),
|
|
|
|
|
conditions are imposed on you (whether by court order, agreement or
|
2019-08-30 14:50:56 +02:00
|
|
|
otherwise) that contradict the conditions of this License, they do not
|
|
|
|
|
excuse you from the conditions of this License. If you cannot
|
2018-12-23 21:26:21 +01:00
|
|
|
distribute so as to satisfy simultaneously your obligations under this
|
|
|
|
|
License and any other pertinent obligations, then as a consequence you
|
2019-08-30 14:50:56 +02:00
|
|
|
may not distribute the Program at all. For example, if a patent
|
2018-12-23 21:26:21 +01:00
|
|
|
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.
|
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|
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
|
2019-08-30 14:50:56 +02:00
|
|
|
implemented by public license practices. Many people have made
|
2018-12-23 21:26:21 +01:00
|
|
|
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
|
|
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|
|
to distribute software through any other system and a licensee cannot
|
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|
impose that choice.
|
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|
|
This section is intended to make thoroughly clear what is believed to
|
|
|
|
|
be a consequence of the rest of this License.
|
|
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
8. If the distribution and/or use of the Program is restricted in
|
2018-12-23 21:26:21 +01:00
|
|
|
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
|
2019-08-30 14:50:56 +02:00
|
|
|
countries not thus excluded. In such case, this License incorporates
|
2018-12-23 21:26:21 +01:00
|
|
|
the limitation as if written in the body of this License.
|
|
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
9. The Free Software Foundation may publish revised and/or new versions
|
2019-08-30 14:50:56 +02:00
|
|
|
of the General Public License from time to time. Such new versions will
|
2018-12-23 21:26:21 +01:00
|
|
|
be similar in spirit to the present version, but may differ in detail to
|
|
|
|
|
address new problems or concerns.
|
|
|
|
|
|
2019-08-30 14:50:56 +02:00
|
|
|
Each version is given a distinguishing version number. If the Program
|
2018-12-23 21:26:21 +01:00
|
|
|
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
|
2019-08-30 14:50:56 +02:00
|
|
|
Software Foundation. If the Program does not specify a version number of
|
2018-12-23 21:26:21 +01:00
|
|
|
this License, you may choose any version ever published by the Free Software
|
|
|
|
|
Foundation.
|
|
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
10. If you wish to incorporate parts of the Program into other free
|
2018-12-23 21:26:21 +01:00
|
|
|
programs whose distribution conditions are different, write to the author
|
2019-08-30 14:50:56 +02:00
|
|
|
to ask for permission. For software which is copyrighted by the Free
|
2018-12-23 21:26:21 +01:00
|
|
|
Software Foundation, write to the Free Software Foundation; we sometimes
|
2019-08-30 14:50:56 +02:00
|
|
|
make exceptions for this. Our decision will be guided by the two goals
|
2018-12-23 21:26:21 +01:00
|
|
|
of preserving the free status of all derivatives of our free software and
|
|
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|
|
of promoting the sharing and reuse of software generally.
|
|
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
NO WARRANTY
|
2018-12-23 21:26:21 +01:00
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
|
2019-08-30 14:50:56 +02:00
|
|
|
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
|
2018-12-23 21:26:21 +01:00
|
|
|
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
|
2019-08-30 14:50:56 +02:00
|
|
|
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
|
|
|
|
|
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
2018-12-23 21:26:21 +01:00
|
|
|
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
|
|
|
|
REPAIR OR CORRECTION.
|
|
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
2018-12-23 21:26:21 +01:00
|
|
|
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
|
2019-08-30 14:50:56 +02:00
|
|
|
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
|
2018-12-23 21:26:21 +01:00
|
|
|
POSSIBILITY OF SUCH DAMAGES.
|
|
|
|
|
|
2019-08-07 15:37:39 +02:00
|
|
|
END OF TERMS AND CONDITIONS
|
2018-12-23 21:26:21 +01:00
|
|
|
</pre>
|
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|
</div>
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|
2020-04-13 21:09:56 +02:00
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|
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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|
<nav id="toc" data-toggle="toc" class="sticky-top">
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<h2 data-toc-skip>Contents</h2>
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</nav>
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</div>
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|
2018-12-23 21:26:21 +01:00
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</div>
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2019-09-25 15:43:22 +02:00
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2018-12-23 21:26:21 +01:00
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|
<footer>
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<div class="copyright">
|
2021-09-29 12:12:35 +02:00
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
2018-12-23 21:26:21 +01:00
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</div>
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<div class="pkgdown">
|
2021-07-23 21:42:11 +02:00
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|
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
|
2018-12-23 21:26:21 +01:00
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</div>
|
2019-09-25 15:43:22 +02:00
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|
2018-12-23 21:26:21 +01:00
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</footer>
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</div>
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2019-09-25 15:43:22 +02:00
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2021-07-23 21:42:11 +02:00
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2018-12-23 21:26:21 +01:00
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</body>
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</html>
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2019-09-25 15:43:22 +02:00
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