mirror of https://github.com/msberends/AMR.git
(v0.7.1.9068) gramstain to freq()
This commit is contained in:
parent
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Package: AMR
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Version: 0.7.1.9067
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Date: 2019-08-28
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Version: 0.7.1.9068
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Date: 2019-08-30
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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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")),
|
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person(role = c("aut", "ths"),
|
||||
family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
|
||||
|
|
|
|||
82
LICENSE
82
LICENSE
|
|
@ -6,55 +6,23 @@ 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
|
||||
A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
|
||||
|
||||
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.
|
||||
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
|
||||
|
||||
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.
|
||||
END OF THE SUMMARY
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||||
|
||||
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
|
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distribute copies of the software, or if you modify it.
|
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|
||||
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
|
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source code. And you must show them these terms so they know their
|
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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
|
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program will individually obtain patent licenses, in effect making the
|
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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.
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||||
|
||||
The precise terms and conditions for copying, distribution and
|
||||
modification follow.
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||||
|
||||
GNU GENERAL PUBLIC LICENSE
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||||
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
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||||
|
|
@ -64,10 +32,10 @@ a notice placed by the copyright holder saying it may be distributed
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|||
under the terms of this General Public License. The "Program", below,
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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:
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that is to say, a work containing the Program or a portion of it,
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that is to say, a work containing the Program or a portion of it,
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either verbatim or with modifications and/or translated into another
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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".
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the term "modification".) Each licensee is addressed as "you".
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Activities other than copying, distribution and modification are not
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covered by this License; they are outside its scope. The act of
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@ -87,7 +55,7 @@ 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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2. You may modify your copy or copies of the Program or any portion
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2. You may modify your copy or copies of the Program or any portion
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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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@ -131,7 +99,7 @@ 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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3. You may copy and distribute the Program (or a work based on it,
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3. You may copy and distribute the Program (or a work based on it,
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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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@ -169,7 +137,7 @@ 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.
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4. You may not copy, modify, sublicense, or distribute the Program
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4. You may not copy, modify, sublicense, or distribute the Program
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except as expressly provided under this License. Any attempt
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otherwise to copy, modify, sublicense or distribute the Program is
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void, and will automatically terminate your rights under this License.
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@ -177,7 +145,7 @@ However, parties who have received copies, or rights, from you under
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this License will not have their licenses terminated so long as such
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parties remain in full compliance.
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5. You are not required to accept this License, since you have not
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5. You are not required to accept this License, since you have not
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signed it. However, nothing else grants you permission to modify or
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distribute the Program or its derivative works. These actions are
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prohibited by law if you do not accept this License. Therefore, by
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@ -186,7 +154,7 @@ Program), you indicate your acceptance of this License to do so, and
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all its terms and conditions for copying, distributing or modifying
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the Program or works based on it.
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||||
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||||
6. Each time you redistribute the Program (or any work based on the
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6. Each time you redistribute the Program (or any work based on the
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Program), the recipient automatically receives a license from the
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original licensor to copy, distribute or modify the Program subject to
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these terms and conditions. You may not impose any further
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@ -197,7 +165,7 @@ this License.
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7. If, as a consequence of a court judgment or allegation of patent
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infringement or for any other reason (not limited to patent issues),
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conditions are imposed on you (whether by court order, agreement or
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otherwise) that contradict the conditions of this License, they do not
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otherwise) that contradict the conditions of this License, they do not
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excuse you from the conditions of this License. If you cannot
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distribute so as to satisfy simultaneously your obligations under this
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License and any other pertinent obligations, then as a consequence you
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@ -272,9 +240,9 @@ WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
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INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
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OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
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TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
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YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
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PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
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TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
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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.
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||||
|
||||
END OF TERMS AND CONDITIONS
|
||||
|
|
|
|||
2
NEWS.md
2
NEWS.md
|
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@ -1,4 +1,4 @@
|
|||
# AMR 0.7.1.9067
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# AMR 0.7.1.9068
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### Breaking
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* 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`:
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|
|
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19
R/freq.R
19
R/freq.R
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@ -29,11 +29,22 @@ clean::freq
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#' @export
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#' @noRd
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freq.mo <- function(x, ...) {
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x_noNA <- x[!is.na(x)]
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grams <- mo_gramstain(x_noNA, language = NULL)
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freq.default(x = x, ...,
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.add_header = list(families = n_distinct(mo_family(x, language = NULL)),
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genera = n_distinct(mo_genus(x, language = NULL)),
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species = n_distinct(paste(mo_genus(x, language = NULL),
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mo_species(x, language = NULL)))))
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.add_header = list(`Gram-negative` = paste0(format(sum(grams == "Gram-negative", na.rm = TRUE),
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big.mark = ",",
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decimal.mark = "."),
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" (", percent(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), force_zero = TRUE),
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" of total)"),
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`Gram-positive` = paste0(format(sum(grams == "Gram-positive", na.rm = TRUE),
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big.mark = ",",
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decimal.mark = "."),
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" (", percent(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), force_zero = TRUE),
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" of total)"),
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genera = n_distinct(mo_genus(x_noNA, language = NULL)),
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species = n_distinct(paste(mo_genus(x_noNA, language = NULL),
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mo_species(x_noNA, language = NULL)))))
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}
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#' @exportMethod freq.rsi
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|
|
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53
README.md
53
README.md
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|
@ -4,26 +4,26 @@
|
|||
<img src="man/figures/logo.png" align="right" height="120px" />
|
||||
|
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### 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.
|
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|
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## Authors
|
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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>,
|
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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>,
|
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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>,
|
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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>,
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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>
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Matthijs S. Berends<sup>1,2</sup>,
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Christian F. Luz<sup>1</sup>,
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Alex W. Friedrich1</sup>,
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Bhanu N.M. Sinha<sup>1</sup>,
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Casper J. Albers<sup>3</sup>,
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Corinna Glasner<sup>1</sup>
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||||
<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>
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<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>
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<sup>a</sup> Thesis dissertant<br>
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||||
<sup>b</sup> Thesis advisor
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<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
|
||||
[](https://CRAN.R-project.org/package=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
|
||||
[](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 | [](https://gitlab.com/msberends/AMR/commits/master) | GitLab CI [[ref 1]](https://gitlab.com/msberends/AMR)
|
||||
All functions checked on Windows | [](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 | [](https://codecov.io/gl/msberends/AMR) [](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
|
||||
|
||||
|
|
|
|||
|
|
@ -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>
|
||||
|
||||
|
|
@ -232,55 +232,23 @@ 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
|
||||
A SUMMARY OF THIS LICENSE BY THE ORIGINAL AUTHORS OF THE AMR R PACKAGE
|
||||
|
||||
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.
|
||||
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
|
||||
|
||||
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.
|
||||
END OF THE SUMMARY
|
||||
|
||||
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
|
||||
|
|
@ -290,10 +258,10 @@ 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,
|
||||
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".
|
||||
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
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
||||
|
|
@ -395,7 +363,7 @@ 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
|
||||
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.
|
||||
|
|
@ -403,7 +371,7 @@ 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
|
||||
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
|
||||
|
|
@ -412,7 +380,7 @@ 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
|
||||
|
|
@ -423,7 +391,7 @@ 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
|
||||
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
|
||||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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>
|
||||
|
||||
|
|
|
|||
|
|
@ -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>
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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 & 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 & 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>
|
||||
|
|
|
|||
|
|
@ -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>
|
||||
|
|
|
|||
|
|
@ -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
27
index.md
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -77,14 +77,17 @@ $( document ).ready(function() {
|
|||
// doctoral titles of authors
|
||||
function doct_tit(x) {
|
||||
if (typeof(x) != "undefined") {
|
||||
x = x.replace("Alex", "Prof Dr Alex");
|
||||
x = x.replace("Bhanu", "Prof Dr Bhanu");
|
||||
// authors
|
||||
x = x.replace(/Author, maintainer/g, "Main developer");
|
||||
x = x.replace(/Author, contributor/g, "Main contributor");
|
||||
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
|
||||
x = x.replace("Alex", "Prof. Dr Alex");
|
||||
x = x.replace("Bhanu", "Prof. Dr Bhanu");
|
||||
x = x.replace("Casper", "Prof. Dr Casper");
|
||||
x = x.replace("Corinna", "Dr Corinna");
|
||||
x = x.replace("Casper", "Prof Dr Casper");
|
||||
// others
|
||||
x = x.replace("Bart", "Dr Bart");
|
||||
x = x.replace("Dennis", "Dr Dennis");
|
||||
x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
|
||||
x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
|
||||
}
|
||||
return(x);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -25,9 +25,13 @@ test_that("frequency table works", {
|
|||
library(clean)
|
||||
# mo
|
||||
expect_true(is.freq(freq(example_isolates$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")
|
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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)))
|
||||
})
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue