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(v0.7.1.9068) gramstain to freq()

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v1.8.2
dr. M.S. (Matthijs) Berends 3 years ago
parent 34a82d091e
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  1. 6
      DESCRIPTION
  2. 136
      LICENSE
  3. 2
      NEWS.md
  4. 19
      R/freq.R
  5. 53
      README.md
  6. 138
      docs/LICENSE-text.html
  7. 2
      docs/articles/index.html
  8. 4
      docs/authors.html
  9. 13
      docs/extra.js
  10. 32
      docs/index.html
  11. 8
      docs/news/index.html
  12. 2
      docs/reference/index.html
  13. 27
      index.md
  14. 13
      pkgdown/extra.js
  15. 6
      tests/testthat/test-freq.R

6
DESCRIPTION
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@ -1,11 +1,11 @@
Package: AMR
Version: 0.7.1.9067
Date: 2019-08-28
Version: 0.7.1.9068
Date: 2019-08-30
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
family = "Berends", given = c("Matthijs", "S."), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")),
person(role = "aut",
person(role = c("aut", "ctb"),
family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")),
person(role = c("aut", "ths"),
family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),

136
LICENSE
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@ -6,71 +6,39 @@ Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
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.
A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
This R package, with package name 'AMR':
- May be used for commercial purposes
- May be used for private purposes
- May NOT be used for patent purposes
- May be modified, although:
- Modifications MUST be released under the same license when distributing the package
- Changes made to the code MUST be documented
- May be distributed, although:
- Source code MUST be made available when the package is distributed
- A copy of the license and copyright notice MUST be included with the package.
- Comes with a LIMITATION of liability
- Comes with NO warranty
END OF THE SUMMARY
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,
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,
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".
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
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).
@ -87,7 +55,7 @@ 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
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:
@ -111,11 +79,11 @@ above, provided that you also meet all of these conditions:
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
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
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
@ -131,7 +99,7 @@ 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,
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:
@ -153,10 +121,10 @@ Sections 1 and 2 above provided that you also do one of the following:
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
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
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
@ -169,27 +137,27 @@ 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
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
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
6. Each time you redistribute the Program (or any work based on the
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original licensor to copy, distribute or modify the Program subject to
these terms and conditions. You may not impose any further
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.
@ -197,11 +165,11 @@ 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
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
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
@ -216,7 +184,7 @@ 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
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
@ -231,39 +199,39 @@ 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
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
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
Each version is given a distinguishing version number. If the Program
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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
Software Foundation. If the Program does not specify a version number of
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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
to ask for permission. For software which is copyrighted by the Free
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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
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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
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
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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.
@ -272,9 +240,9 @@ 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
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PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
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

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9067
# AMR 0.7.1.9068
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:

19
R/freq.R
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@ -29,11 +29,22 @@ clean::freq
#' @export
#' @noRd
freq.mo <- function(x, ...) {
x_noNA <- x[!is.na(x)]
grams <- mo_gramstain(x_noNA, language = NULL)
freq.default(x = x, ...,
.add_header = list(families = n_distinct(mo_family(x, language = NULL)),
genera = n_distinct(mo_genus(x, language = NULL)),
species = n_distinct(paste(mo_genus(x, language = NULL),
mo_species(x, language = NULL)))))
.add_header = list(`Gram-negative` = paste0(format(sum(grams == "Gram-negative", na.rm = TRUE),
big.mark = ",",
decimal.mark = "."),
" (", percent(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), force_zero = TRUE),
" of total)"),
`Gram-positive` = paste0(format(sum(grams == "Gram-positive", na.rm = TRUE),
big.mark = ",",
decimal.mark = "."),
" (", percent(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), force_zero = TRUE),
" of total)"),
genera = n_distinct(mo_genus(x_noNA, language = NULL)),
species = n_distinct(paste(mo_genus(x_noNA, language = NULL),
mo_species(x_noNA, language = NULL)))))
}
#' @exportMethod freq.rsi

53
README.md
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@ -4,26 +4,26 @@
<img src="man/figures/logo.png" align="right" height="120px" />
### Not a developer? Then please visit our website [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR) to read about this package.
**It contains documentation about all of the included functions and also a comprehensive tutorial about how to conduct AMR analysis.**
## Development source
*NOTE: the original source code is on GitLab (https://gitlab.com/msberends/AMR), so you can report a bug at https://gitlab.com/msberends/AMR/issues. There is a mirror repository on GitHub (https://github.com/msberends/AMR). As the mirror process is automated by GitLab, both repositories always contain the latest changes.*
*NOTE: the original source code is on GitLab (https://gitlab.com/msberends/AMR). There is a mirror repository on GitHub (https://github.com/msberends/AMR). As the mirror process is automated by GitLab, both repositories always contain the latest changes.*
This is the **development source** of `AMR`, a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
## Authors
Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.rstudio.com/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.rstudio.com/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.rstudio.com/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.rstudio.com/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.rstudio.com/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
Matthijs S. Berends<sup>1,2</sup>,
Christian F. Luz<sup>1</sup>,
Alex W. Friedrich1</sup>,
Bhanu N.M. Sinha<sup>1</sup>,
Casper J. Albers<sup>3</sup>,
Corinna Glasner<sup>1</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>
<sup>a</sup> Thesis dissertant<br>
<sup>b</sup> Thesis advisor
<sup>3</sup> Heymans Institute for Psychological Research, University of Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl)<br>
<a href="https://www.rug.nl"><img src="man/figures/logo_rug.png" height="60px"></a>
<a href="https://www.umcg.nl"><img src="man/figures/logo_umcg.png" height="60px"></a>
@ -32,40 +32,7 @@ Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https
<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_interreg.png" height="60px"></a>
## How to get this package
All stable versions of this package [are published on CRAN](https://CRAN.R-project.org/package=AMR), the official R network with a peer-reviewed submission process.
### Install from CRAN
[![CRAN_Badge](https://www.r-pkg.org/badges/version/AMR)](https://CRAN.R-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://CRAN.R-project.org/package=AMR)
(Note: Downloads measured only by cran.rstudio.com, this excludes e.g. the official [cran.r-project.org](https://cran.r-project.org/package=AMR))
- <img src="http://www.rstudio.com/favicon.ico" alt="RStudio favicon" height="20px"> Install using [RStudio](http://www.rstudio.com) (recommended):
- Click on `Tools` and then `Install Packages...`
- Type in `AMR` and press <kbd>Install</kbd>
- <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px"> Install in R directly:
- `install.packages("AMR")`
### Install from Zenodo
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1305355.svg)](https://doi.org/10.5281/zenodo.1305355)
This package was also published on Zenodo (stable releases only): https://doi.org/10.5281/zenodo.1305355
### Install from GitLab
This is the latest **development version**. Although it may contain bugfixes and even new functions compared to the latest released version on CRAN, it is also subject to change and may be unstable or behave unexpectedly. Always consider this a beta version. All below 'badges' should be green:
Development Test | Result | Reference
--- | :---: | ---
All functions checked on Linux | [![pipeline status](https://gitlab.com/msberends/AMR/badges/master/pipeline.svg)](https://gitlab.com/msberends/AMR/commits/master) | GitLab CI [[ref 1]](https://gitlab.com/msberends/AMR)
All functions checked on Windows | [![AppVeyor_Build](https://ci.appveyor.com/api/projects/status/gitlab/msberends/AMR?branch=master&svg=true)](https://ci.appveyor.com/project/msberends/amr-svxon) | Appveyor Systems Inc. [[ref 2]](https://ci.appveyor.com/project/msberends/amr-svxon)
Percentage of syntax lines checked | [![Code_Coverage](https://codecov.io/gl/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gl/msberends/AMR) [![Code_Coverage](https://gitlab.com/msberends/AMR/badges/master/coverage.svg)](https://codecov.io/gl/msberends/AMR) | Codecov LLC [[ref 3]](https://codecov.io/gl/msberends/AMR)
If so, try it with:
```r
install.packages("devtools")
devtools::install_gitlab("msberends/AMR")
```
Please see [our website](https://msberends.gitlab.io/AMR/#get-this-package).
## Copyright

138
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
</span>
</div>
@ -232,71 +232,39 @@ Copyright (C) 1989, 1991 Free Software Foundation, Inc., &lt;http://fsf.org/&gt;
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.
A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
This R package, with package name 'AMR':
- May be used for commercial purposes
- May be used for private purposes
- May NOT be used for patent purposes
- May be modified, although:
- Modifications MUST be released under the same license when distributing the package
- Changes made to the code MUST be documented
- May be distributed, although:
- Source code MUST be made available when the package is distributed
- A copy of the license and copyright notice MUST be included with the package.
- Comes with a LIMITATION of liability
- Comes with NO warranty
END OF THE SUMMARY
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,
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,
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".
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
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).
@ -313,7 +281,7 @@ 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
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:
@ -337,11 +305,11 @@ above, provided that you also meet all of these conditions:
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
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
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
@ -357,7 +325,7 @@ 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,
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:
@ -379,10 +347,10 @@ Sections 1 and 2 above provided that you also do one of the following:
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
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
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
@ -395,27 +363,27 @@ 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
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
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
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
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.
@ -423,11 +391,11 @@ 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
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
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
@ -442,7 +410,7 @@ 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
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
@ -457,39 +425,39 @@ 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
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
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
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
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
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
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
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
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.
@ -498,9 +466,9 @@ 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
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

2
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
</span>
</div>

4
docs/authors.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
</span>
</div>
@ -230,7 +230,7 @@
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author. <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><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <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>

13
docs/extra.js
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@ -77,14 +77,17 @@ $( document ).ready(function() {
// doctoral titles of authors
function doct_tit(x) {
if (typeof(x) != "undefined") {
x = x.replace("Alex", "Prof Dr Alex");
x = x.replace("Bhanu", "Prof Dr Bhanu");
// authors
x = x.replace(/Author, maintainer/g, "Main developer");
x = x.replace(/Author, contributor/g, "Main contributor");
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
x = x.replace("Alex", "Prof. Dr Alex");
x = x.replace("Bhanu", "Prof. Dr Bhanu");
x = x.replace("Casper", "Prof. Dr Casper");
x = x.replace("Corinna", "Dr Corinna");
x = x.replace("Casper", "Prof Dr Casper");
// others
x = x.replace("Bart", "Dr Bart");
x = x.replace("Dennis", "Dr Dennis");
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
}
return(x);
}

32
docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
</span>
</div>
@ -194,7 +194,7 @@
<a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. Since its first public release in early 2018, this package has been downloaded over 20,000 times from more than 40 countries <small>(source: <a href="https://cran-logs.rstudio.com">CRAN logs, 2019</a>)</small>.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 microorganisms</strong></a> (distinct microbial species) and <a href="./reference/antibiotics.html"><strong>~450 antibiotics</strong></a> by name and code, and knows all about valid RSI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software; you can freely use and distribute it for both personal and commercial (but <strong>not</strong> patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full license <a href="./LICENSE-text.html">here</a>.</p>
<p>We created this package for both routine analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
<p><strong>Used to SPSS?</strong> Read our <a href="./articles/SPSS.html">tutorial on how to import data from SPSS, SAS or Stata</a>.</p>
<div id="partners" class="section level4">
<h4 class="hasAnchor">
@ -356,6 +356,32 @@
</ol>
</div>
</div>
<div id="copyright" class="section level3">
<h3 class="hasAnchor">
<a href="#copyright" class="anchor"></a>Copyright</h3>
<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
<ul>
<li><p>May be used for commercial purposes</p></li>
<li><p>May be used for private purposes</p></li>
<li><p>May <strong>not</strong> be used for patent purposes</p></li>
<li>
<p>May be modified, although:</p>
<ul>
<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
<li>Changes made to the code <strong>must</strong> be documented</li>
</ul>
</li>
<li>
<p>May be distributed, although:</p>
<ul>
<li>Source code <strong>must</strong> be made available when the package is distributed</li>
<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
</ul>
</li>
<li><p>Comes with a LIMITATION of liability</p></li>
<li><p>Comes with NO warranty</p></li>
</ul>
</div>
</div>
</div>
@ -383,7 +409,7 @@
<li>
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <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> </li>
<li>
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author </small> <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> </li>
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <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> </li>
<li>
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <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> </li>
<li>

8
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
</span>
</div>
@ -225,9 +225,9 @@
</div>
<div id="amr-0-7-1-9067" class="section level1">
<div id="amr-0-7-1-9068" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9067" class="anchor"></a>AMR 0.7.1.9067<small> Unreleased </small>
<a href="#amr-0-7-1-9068" class="anchor"></a>AMR 0.7.1.9068<small> Unreleased </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -1258,7 +1258,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9067">0.7.1.9067</a></li>
<li><a href="#amr-0-7-1-9068">0.7.1.9068</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9068</span>
</span>
</div>

27
index.md
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@ -10,8 +10,7 @@
After installing this package, R knows [**~70,000 microorganisms**](./reference/microorganisms.html) (distinct microbial species) and [**~450 antibiotics**](./reference/antibiotics.html) by name and code, and knows all about valid RSI and MIC values. It supports any data format, including WHONET/EARS-Net data.
We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
This R package is [actively maintained](./news) and is free software; you can freely use and distribute it for both personal and commercial (but **not** patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full license [here](./LICENSE-text.html).
We created this package for both routine analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
**Used to SPSS?** Read our [tutorial on how to import data from SPSS, SAS or Stata](./articles/SPSS.html).
@ -153,3 +152,27 @@ The `AMR` package basically does four important things:
* Results of 40 antibiotics (each antibiotic in its own column) with a total ~40,000 antimicrobial results
* Real and genuine data
* The [`WHONET` data set](./reference/WHONET.html). This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET [on its tutorial page](./articles/WHONET.html).
### Copyright
This R package is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](./LICENSE-text.html). In a nutshell, this means that this package:
- May be used for commercial purposes
- May be used for private purposes
- May **not** be used for patent purposes
- May be modified, although:
- Modifications **must** be released under the same license when distributing the package
- Changes made to the code **must** be documented
- May be distributed, although:
- Source code **must** be made available when the package is distributed
- A copy of the license and copyright notice **must** be included with the package.
- Comes with a LIMITATION of liability
- Comes with NO warranty

13
pkgdown/extra.js
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@ -77,14 +77,17 @@ $( document ).ready(function() {
// doctoral titles of authors
function doct_tit(x) {
if (typeof(x) != "undefined") {
x = x.replace("Alex", "Prof Dr Alex");
x = x.replace("Bhanu", "Prof Dr Bhanu");
// authors
x = x.replace(/Author, maintainer/g, "Main developer");
x = x.replace(/Author, contributor/g, "Main contributor");
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
x = x.replace("Alex", "Prof. Dr Alex");
x = x.replace("Bhanu", "Prof. Dr Bhanu");
x = x.replace("Casper", "Prof. Dr Casper");
x = x.replace("Corinna", "Dr Corinna");
x = x.replace("Casper", "Prof Dr Casper");
// others
x = x.replace("Bart", "Dr Bart");
x = x.replace("Dennis", "Dr Dennis");
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
}
return(x);
}

6
tests/testthat/test-freq.R
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@ -25,9 +25,13 @@ test_that("frequency table works", {
library(clean)
# mo
expect_true(is.freq(freq(example_isolates$mo)))
# for this to work, the output of mo_gramstain() is to be expected as follows:
expect_equal(mo_gramstain("B_ESCHR_COL"), "Gram-negative")
expect_equal(mo_gramstain("B_STPHY_AUR"), "Gram-positive")
# rsi
expect_true(is.freq(freq(example_isolates$AMX)))
library(dplyr)
expect_true(is.freq(example_isolates %>% freq(mo)))
expect_true(is.freq(example_isolates %>% freq(AMX)))
})

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