(v0.7.1.9027) tibble printing
@ -1,6 +1,6 @@
|
|||||||
Package: AMR
|
Package: AMR
|
||||||
Version: 0.7.1.9026
|
Version: 0.7.1.9027
|
||||||
Date: 2019-08-06
|
Date: 2019-08-07
|
||||||
Title: Antimicrobial Resistance Analysis
|
Title: Antimicrobial Resistance Analysis
|
||||||
Authors@R: c(
|
Authors@R: c(
|
||||||
person(
|
person(
|
||||||
@ -53,6 +53,7 @@ Imports:
|
|||||||
hms,
|
hms,
|
||||||
knitr (>= 1.0.0),
|
knitr (>= 1.0.0),
|
||||||
microbenchmark,
|
microbenchmark,
|
||||||
|
pillar,
|
||||||
rlang (>= 0.3.1),
|
rlang (>= 0.3.1),
|
||||||
scales,
|
scales,
|
||||||
tidyr (>= 0.7.0)
|
tidyr (>= 0.7.0)
|
||||||
|
280
LICENSE
Normal file
@ -0,0 +1,280 @@
|
|||||||
|
GNU GENERAL PUBLIC LICENSE
|
||||||
|
Version 2, June 1991
|
||||||
|
|
||||||
|
Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
|
||||||
|
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
|
||||||
|
Everyone is permitted to copy and distribute verbatim copies
|
||||||
|
of this license document, but changing it is not allowed.
|
||||||
|
|
||||||
|
Preamble
|
||||||
|
|
||||||
|
The licenses for most software are designed to take away your
|
||||||
|
freedom to share and change it. By contrast, the GNU General Public
|
||||||
|
License is intended to guarantee your freedom to share and change free
|
||||||
|
software--to make sure the software is free for all its users. This
|
||||||
|
General Public License applies to most of the Free Software
|
||||||
|
Foundation's software and to any other program whose authors commit to
|
||||||
|
using it. (Some other Free Software Foundation software is covered by
|
||||||
|
the GNU Lesser General Public License instead.) You can apply it to
|
||||||
|
your programs, too.
|
||||||
|
|
||||||
|
When we speak of free software, we are referring to freedom, not
|
||||||
|
price. Our General Public Licenses are designed to make sure that you
|
||||||
|
have the freedom to distribute copies of free software (and charge for
|
||||||
|
this service if you wish), that you receive source code or can get it
|
||||||
|
if you want it, that you can change the software or use pieces of it
|
||||||
|
in new free programs; and that you know you can do these things.
|
||||||
|
|
||||||
|
To protect your rights, we need to make restrictions that forbid
|
||||||
|
anyone to deny you these rights or to ask you to surrender the rights.
|
||||||
|
These restrictions translate to certain responsibilities for you if you
|
||||||
|
distribute copies of the software, or if you modify it.
|
||||||
|
|
||||||
|
For example, if you distribute copies of such a program, whether
|
||||||
|
gratis or for a fee, you must give the recipients all the rights that
|
||||||
|
you have. You must make sure that they, too, receive or can get the
|
||||||
|
source code. And you must show them these terms so they know their
|
||||||
|
rights.
|
||||||
|
|
||||||
|
We protect your rights with two steps: (1) copyright the software, and
|
||||||
|
(2) offer you this license which gives you legal permission to copy,
|
||||||
|
distribute and/or modify the software.
|
||||||
|
|
||||||
|
Also, for each author's protection and ours, we want to make certain
|
||||||
|
that everyone understands that there is no warranty for this free
|
||||||
|
software. If the software is modified by someone else and passed on, we
|
||||||
|
want its recipients to know that what they have is not the original, so
|
||||||
|
that any problems introduced by others will not reflect on the original
|
||||||
|
authors' reputations.
|
||||||
|
|
||||||
|
Finally, any free program is threatened constantly by software
|
||||||
|
patents. We wish to avoid the danger that redistributors of a free
|
||||||
|
program will individually obtain patent licenses, in effect making the
|
||||||
|
program proprietary. To prevent this, we have made it clear that any
|
||||||
|
patent must be licensed for everyone's free use or not licensed at all.
|
||||||
|
|
||||||
|
The precise terms and conditions for copying, distribution and
|
||||||
|
modification follow.
|
||||||
|
|
||||||
|
GNU GENERAL PUBLIC LICENSE
|
||||||
|
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
||||||
|
|
||||||
|
0. This License applies to any program or other work which contains
|
||||||
|
a notice placed by the copyright holder saying it may be distributed
|
||||||
|
under the terms of this General Public License. The "Program", below,
|
||||||
|
refers to any such program or work, and a "work based on the Program"
|
||||||
|
means either the Program or any derivative work under copyright law:
|
||||||
|
that is to say, a work containing the Program or a portion of it,
|
||||||
|
either verbatim or with modifications and/or translated into another
|
||||||
|
language. (Hereinafter, translation is included without limitation in
|
||||||
|
the term "modification".) Each licensee is addressed as "you".
|
||||||
|
|
||||||
|
Activities other than copying, distribution and modification are not
|
||||||
|
covered by this License; they are outside its scope. The act of
|
||||||
|
running the Program is not restricted, and the output from the Program
|
||||||
|
is covered only if its contents constitute a work based on the
|
||||||
|
Program (independent of having been made by running the Program).
|
||||||
|
Whether that is true depends on what the Program does.
|
||||||
|
|
||||||
|
1. You may copy and distribute verbatim copies of the Program's
|
||||||
|
source code as you receive it, in any medium, provided that you
|
||||||
|
conspicuously and appropriately publish on each copy an appropriate
|
||||||
|
copyright notice and disclaimer of warranty; keep intact all the
|
||||||
|
notices that refer to this License and to the absence of any warranty;
|
||||||
|
and give any other recipients of the Program a copy of this License
|
||||||
|
along with the Program.
|
||||||
|
|
||||||
|
You may charge a fee for the physical act of transferring a copy, and
|
||||||
|
you may at your option offer warranty protection in exchange for a fee.
|
||||||
|
|
||||||
|
2. You may modify your copy or copies of the Program or any portion
|
||||||
|
of it, thus forming a work based on the Program, and copy and
|
||||||
|
distribute such modifications or work under the terms of Section 1
|
||||||
|
above, provided that you also meet all of these conditions:
|
||||||
|
|
||||||
|
a) You must cause the modified files to carry prominent notices
|
||||||
|
stating that you changed the files and the date of any change.
|
||||||
|
|
||||||
|
b) You must cause any work that you distribute or publish, that in
|
||||||
|
whole or in part contains or is derived from the Program or any
|
||||||
|
part thereof, to be licensed as a whole at no charge to all third
|
||||||
|
parties under the terms of this License.
|
||||||
|
|
||||||
|
c) If the modified program normally reads commands interactively
|
||||||
|
when run, you must cause it, when started running for such
|
||||||
|
interactive use in the most ordinary way, to print or display an
|
||||||
|
announcement including an appropriate copyright notice and a
|
||||||
|
notice that there is no warranty (or else, saying that you provide
|
||||||
|
a warranty) and that users may redistribute the program under
|
||||||
|
these conditions, and telling the user how to view a copy of this
|
||||||
|
License. (Exception: if the Program itself is interactive but
|
||||||
|
does not normally print such an announcement, your work based on
|
||||||
|
the Program is not required to print an announcement.)
|
||||||
|
|
||||||
|
These requirements apply to the modified work as a whole. If
|
||||||
|
identifiable sections of that work are not derived from the Program,
|
||||||
|
and can be reasonably considered independent and separate works in
|
||||||
|
themselves, then this License, and its terms, do not apply to those
|
||||||
|
sections when you distribute them as separate works. But when you
|
||||||
|
distribute the same sections as part of a whole which is a work based
|
||||||
|
on the Program, the distribution of the whole must be on the terms of
|
||||||
|
this License, whose permissions for other licensees extend to the
|
||||||
|
entire whole, and thus to each and every part regardless of who wrote it.
|
||||||
|
|
||||||
|
Thus, it is not the intent of this section to claim rights or contest
|
||||||
|
your rights to work written entirely by you; rather, the intent is to
|
||||||
|
exercise the right to control the distribution of derivative or
|
||||||
|
collective works based on the Program.
|
||||||
|
|
||||||
|
In addition, mere aggregation of another work not based on the Program
|
||||||
|
with the Program (or with a work based on the Program) on a volume of
|
||||||
|
a storage or distribution medium does not bring the other work under
|
||||||
|
the scope of this License.
|
||||||
|
|
||||||
|
3. You may copy and distribute the Program (or a work based on it,
|
||||||
|
under Section 2) in object code or executable form under the terms of
|
||||||
|
Sections 1 and 2 above provided that you also do one of the following:
|
||||||
|
|
||||||
|
a) Accompany it with the complete corresponding machine-readable
|
||||||
|
source code, which must be distributed under the terms of Sections
|
||||||
|
1 and 2 above on a medium customarily used for software interchange; or,
|
||||||
|
|
||||||
|
b) Accompany it with a written offer, valid for at least three
|
||||||
|
years, to give any third party, for a charge no more than your
|
||||||
|
cost of physically performing source distribution, a complete
|
||||||
|
machine-readable copy of the corresponding source code, to be
|
||||||
|
distributed under the terms of Sections 1 and 2 above on a medium
|
||||||
|
customarily used for software interchange; or,
|
||||||
|
|
||||||
|
c) Accompany it with the information you received as to the offer
|
||||||
|
to distribute corresponding source code. (This alternative is
|
||||||
|
allowed only for noncommercial distribution and only if you
|
||||||
|
received the program in object code or executable form with such
|
||||||
|
an offer, in accord with Subsection b above.)
|
||||||
|
|
||||||
|
The source code for a work means the preferred form of the work for
|
||||||
|
making modifications to it. For an executable work, complete source
|
||||||
|
code means all the source code for all modules it contains, plus any
|
||||||
|
associated interface definition files, plus the scripts used to
|
||||||
|
control compilation and installation of the executable. However, as a
|
||||||
|
special exception, the source code distributed need not include
|
||||||
|
anything that is normally distributed (in either source or binary
|
||||||
|
form) with the major components (compiler, kernel, and so on) of the
|
||||||
|
operating system on which the executable runs, unless that component
|
||||||
|
itself accompanies the executable.
|
||||||
|
|
||||||
|
If distribution of executable or object code is made by offering
|
||||||
|
access to copy from a designated place, then offering equivalent
|
||||||
|
access to copy the source code from the same place counts as
|
||||||
|
distribution of the source code, even though third parties are not
|
||||||
|
compelled to copy the source along with the object code.
|
||||||
|
|
||||||
|
4. You may not copy, modify, sublicense, or distribute the Program
|
||||||
|
except as expressly provided under this License. Any attempt
|
||||||
|
otherwise to copy, modify, sublicense or distribute the Program is
|
||||||
|
void, and will automatically terminate your rights under this License.
|
||||||
|
However, parties who have received copies, or rights, from you under
|
||||||
|
this License will not have their licenses terminated so long as such
|
||||||
|
parties remain in full compliance.
|
||||||
|
|
||||||
|
5. You are not required to accept this License, since you have not
|
||||||
|
signed it. However, nothing else grants you permission to modify or
|
||||||
|
distribute the Program or its derivative works. These actions are
|
||||||
|
prohibited by law if you do not accept this License. Therefore, by
|
||||||
|
modifying or distributing the Program (or any work based on the
|
||||||
|
Program), you indicate your acceptance of this License to do so, and
|
||||||
|
all its terms and conditions for copying, distributing or modifying
|
||||||
|
the Program or works based on it.
|
||||||
|
|
||||||
|
6. Each time you redistribute the Program (or any work based on the
|
||||||
|
Program), the recipient automatically receives a license from the
|
||||||
|
original licensor to copy, distribute or modify the Program subject to
|
||||||
|
these terms and conditions. You may not impose any further
|
||||||
|
restrictions on the recipients' exercise of the rights granted herein.
|
||||||
|
You are not responsible for enforcing compliance by third parties to
|
||||||
|
this License.
|
||||||
|
|
||||||
|
7. If, as a consequence of a court judgment or allegation of patent
|
||||||
|
infringement or for any other reason (not limited to patent issues),
|
||||||
|
conditions are imposed on you (whether by court order, agreement or
|
||||||
|
otherwise) that contradict the conditions of this License, they do not
|
||||||
|
excuse you from the conditions of this License. If you cannot
|
||||||
|
distribute so as to satisfy simultaneously your obligations under this
|
||||||
|
License and any other pertinent obligations, then as a consequence you
|
||||||
|
may not distribute the Program at all. For example, if a patent
|
||||||
|
license would not permit royalty-free redistribution of the Program by
|
||||||
|
all those who receive copies directly or indirectly through you, then
|
||||||
|
the only way you could satisfy both it and this License would be to
|
||||||
|
refrain entirely from distribution of the Program.
|
||||||
|
|
||||||
|
If any portion of this section is held invalid or unenforceable under
|
||||||
|
any particular circumstance, the balance of the section is intended to
|
||||||
|
apply and the section as a whole is intended to apply in other
|
||||||
|
circumstances.
|
||||||
|
|
||||||
|
It is not the purpose of this section to induce you to infringe any
|
||||||
|
patents or other property right claims or to contest validity of any
|
||||||
|
such claims; this section has the sole purpose of protecting the
|
||||||
|
integrity of the free software distribution system, which is
|
||||||
|
implemented by public license practices. Many people have made
|
||||||
|
generous contributions to the wide range of software distributed
|
||||||
|
through that system in reliance on consistent application of that
|
||||||
|
system; it is up to the author/donor to decide if he or she is willing
|
||||||
|
to distribute software through any other system and a licensee cannot
|
||||||
|
impose that choice.
|
||||||
|
|
||||||
|
This section is intended to make thoroughly clear what is believed to
|
||||||
|
be a consequence of the rest of this License.
|
||||||
|
|
||||||
|
8. If the distribution and/or use of the Program is restricted in
|
||||||
|
certain countries either by patents or by copyrighted interfaces, the
|
||||||
|
original copyright holder who places the Program under this License
|
||||||
|
may add an explicit geographical distribution limitation excluding
|
||||||
|
those countries, so that distribution is permitted only in or among
|
||||||
|
countries not thus excluded. In such case, this License incorporates
|
||||||
|
the limitation as if written in the body of this License.
|
||||||
|
|
||||||
|
9. The Free Software Foundation may publish revised and/or new versions
|
||||||
|
of the General Public License from time to time. Such new versions will
|
||||||
|
be similar in spirit to the present version, but may differ in detail to
|
||||||
|
address new problems or concerns.
|
||||||
|
|
||||||
|
Each version is given a distinguishing version number. If the Program
|
||||||
|
specifies a version number of this License which applies to it and "any
|
||||||
|
later version", you have the option of following the terms and conditions
|
||||||
|
either of that version or of any later version published by the Free
|
||||||
|
Software Foundation. If the Program does not specify a version number of
|
||||||
|
this License, you may choose any version ever published by the Free Software
|
||||||
|
Foundation.
|
||||||
|
|
||||||
|
10. If you wish to incorporate parts of the Program into other free
|
||||||
|
programs whose distribution conditions are different, write to the author
|
||||||
|
to ask for permission. For software which is copyrighted by the Free
|
||||||
|
Software Foundation, write to the Free Software Foundation; we sometimes
|
||||||
|
make exceptions for this. Our decision will be guided by the two goals
|
||||||
|
of preserving the free status of all derivatives of our free software and
|
||||||
|
of promoting the sharing and reuse of software generally.
|
||||||
|
|
||||||
|
NO WARRANTY
|
||||||
|
|
||||||
|
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
|
||||||
|
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
|
||||||
|
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
|
||||||
|
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
|
||||||
|
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||||
|
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
|
||||||
|
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
||||||
|
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
||||||
|
REPAIR OR CORRECTION.
|
||||||
|
|
||||||
|
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||||
|
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
|
||||||
|
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
|
||||||
|
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
|
||||||
|
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
|
||||||
|
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
|
||||||
|
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
|
||||||
|
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
|
||||||
|
POSSIBILITY OF SUCH DAMAGES.
|
||||||
|
|
||||||
|
END OF TERMS AND CONDITIONS
|
10
NAMESPACE
@ -18,6 +18,10 @@ S3method(freq,rsi)
|
|||||||
S3method(kurtosis,data.frame)
|
S3method(kurtosis,data.frame)
|
||||||
S3method(kurtosis,default)
|
S3method(kurtosis,default)
|
||||||
S3method(kurtosis,matrix)
|
S3method(kurtosis,matrix)
|
||||||
|
S3method(pillar_shaft,ab)
|
||||||
|
S3method(pillar_shaft,mic)
|
||||||
|
S3method(pillar_shaft,mo)
|
||||||
|
S3method(pillar_shaft,rsi)
|
||||||
S3method(plot,mic)
|
S3method(plot,mic)
|
||||||
S3method(plot,resistance_predict)
|
S3method(plot,resistance_predict)
|
||||||
S3method(plot,rsi)
|
S3method(plot,rsi)
|
||||||
@ -37,6 +41,10 @@ S3method(skewness,matrix)
|
|||||||
S3method(summary,mic)
|
S3method(summary,mic)
|
||||||
S3method(summary,mo)
|
S3method(summary,mo)
|
||||||
S3method(summary,rsi)
|
S3method(summary,rsi)
|
||||||
|
S3method(type_sum,ab)
|
||||||
|
S3method(type_sum,mic)
|
||||||
|
S3method(type_sum,mo)
|
||||||
|
S3method(type_sum,rsi)
|
||||||
export("%like%")
|
export("%like%")
|
||||||
export(ab_atc)
|
export(ab_atc)
|
||||||
export(ab_atc_group1)
|
export(ab_atc_group1)
|
||||||
@ -262,6 +270,8 @@ importFrom(graphics,plot)
|
|||||||
importFrom(graphics,points)
|
importFrom(graphics,points)
|
||||||
importFrom(graphics,text)
|
importFrom(graphics,text)
|
||||||
importFrom(microbenchmark,microbenchmark)
|
importFrom(microbenchmark,microbenchmark)
|
||||||
|
importFrom(pillar,pillar_shaft)
|
||||||
|
importFrom(pillar,type_sum)
|
||||||
importFrom(rlang,as_label)
|
importFrom(rlang,as_label)
|
||||||
importFrom(rlang,enquos)
|
importFrom(rlang,enquos)
|
||||||
importFrom(scales,percent)
|
importFrom(scales,percent)
|
||||||
|
16
NEWS.md
@ -1,4 +1,4 @@
|
|||||||
# AMR 0.7.1.9026
|
# AMR 0.7.1.9027
|
||||||
|
|
||||||
### Breaking
|
### Breaking
|
||||||
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
|
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
|
||||||
@ -35,7 +35,18 @@
|
|||||||
Since this is a major change, usage of the old `also_single_tested` will throw an informative error that it has been replaced by `only_all_tested`.
|
Since this is a major change, usage of the old `also_single_tested` will throw an informative error that it has been replaced by `only_all_tested`.
|
||||||
|
|
||||||
### Changed
|
### Changed
|
||||||
* Fixed a bug in `eucast_rules()` that caused an error when the input was a specific kind of `tibble`
|
* Added more informative errors and warnings to `eucast_rules()`
|
||||||
|
* Added tibble printing support for classes `rsi`, `mic`, `ab` and `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red:
|
||||||
|
```r
|
||||||
|
(run this on your own console, as this page does not support colour printing)
|
||||||
|
tibble(mo = sample(AMR::microorganisms$fullname, 10),
|
||||||
|
drug1 = as.rsi(sample(c("S", "I", "R"), 10, replace = TRUE,
|
||||||
|
prob = c(0.6, 0.1, 0.3))),
|
||||||
|
drug2 = as.rsi(sample(c("S", "I", "R"), 10, replace = TRUE,
|
||||||
|
prob = c(0.6, 0.1, 0.3))),
|
||||||
|
drug3 = as.rsi(sample(c("S", "I", "R"), 10, replace = TRUE,
|
||||||
|
prob = c(0.6, 0.1, 0.3))))
|
||||||
|
```
|
||||||
* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
|
* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
|
||||||
* Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
|
* Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
|
||||||
* Fix and speed improvement for `mo_shortname()`
|
* Fix and speed improvement for `mo_shortname()`
|
||||||
@ -50,6 +61,7 @@
|
|||||||
* The `antibiotics` data set is now sorted by name
|
* The `antibiotics` data set is now sorted by name
|
||||||
* Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output
|
* Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output
|
||||||
* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
|
* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
|
||||||
|
* Using factors as input for `eucast_rules()` now adds missing factors levels when the function changes antibiotic results
|
||||||
|
|
||||||
# AMR 0.7.1
|
# AMR 0.7.1
|
||||||
|
|
||||||
|
16
R/ab.R
@ -262,7 +262,7 @@ is.ab <- function(x) {
|
|||||||
#' @noRd
|
#' @noRd
|
||||||
print.ab <- function(x, ...) {
|
print.ab <- function(x, ...) {
|
||||||
cat("Class 'ab'\n")
|
cat("Class 'ab'\n")
|
||||||
print.default(as.character(x), quote = FALSE)
|
print(as.character(x), quote = FALSE)
|
||||||
}
|
}
|
||||||
|
|
||||||
#' @exportMethod as.data.frame.ab
|
#' @exportMethod as.data.frame.ab
|
||||||
@ -286,3 +286,17 @@ as.data.frame.ab <- function (x, ...) {
|
|||||||
pull.ab <- function(.data, ...) {
|
pull.ab <- function(.data, ...) {
|
||||||
pull(as.data.frame(.data), ...)
|
pull(as.data.frame(.data), ...)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar type_sum
|
||||||
|
#' @export
|
||||||
|
type_sum.ab <- function(x) {
|
||||||
|
"ab"
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar pillar_shaft
|
||||||
|
#' @export
|
||||||
|
pillar_shaft.ab <- function(x, ...) {
|
||||||
|
out <- format(x)
|
||||||
|
out[is.na(x)] <- NA
|
||||||
|
pillar::new_pillar_shaft_simple(out, align = "left", min_width = 4)
|
||||||
|
}
|
||||||
|
@ -228,18 +228,18 @@ eucast_rules <- function(x,
|
|||||||
|
|
||||||
warned <- FALSE
|
warned <- FALSE
|
||||||
|
|
||||||
txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n") }
|
txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n\n") }
|
||||||
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE }
|
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING "))) }; warned <<- TRUE }
|
||||||
txt_ok <- function(no_of_changes) {
|
txt_ok <- function(no_of_changes) {
|
||||||
if (warned == FALSE) {
|
if (warned == FALSE) {
|
||||||
if (no_of_changes > 0) {
|
if (no_of_changes > 0) {
|
||||||
if (no_of_changes == 1) {
|
if (no_of_changes == 1) {
|
||||||
cat(blue(" (1 new change)\n"))
|
cat(blue(" (1 value changed)\n"))
|
||||||
} else {
|
} else {
|
||||||
cat(blue(paste0(" (", formatnr(no_of_changes), " new changes)\n")))
|
cat(blue(paste0(" (", formatnr(no_of_changes), " values changed)\n")))
|
||||||
}
|
}
|
||||||
} else {
|
} else {
|
||||||
cat(green(" (no new changes)\n"))
|
cat(green(" (no values changed)\n"))
|
||||||
}
|
}
|
||||||
warned <<- FALSE
|
warned <<- FALSE
|
||||||
}
|
}
|
||||||
@ -402,19 +402,36 @@ eucast_rules <- function(x,
|
|||||||
x_original[rows, cols] <<- to,
|
x_original[rows, cols] <<- to,
|
||||||
warning = function(w) {
|
warning = function(w) {
|
||||||
if (w$message %like% 'invalid factor level') {
|
if (w$message %like% 'invalid factor level') {
|
||||||
warning('Value "', to, '" could not be applied to column(s) `', paste(cols, collapse = '`, `'), '` because this value is not an existing factor level. You can use as.rsi() to fix this.', call. = FALSE)
|
x_original <<- x_original %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
|
||||||
|
x <<- x %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
|
||||||
|
x_original[rows, cols] <<- to
|
||||||
|
warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = '`, `'), '` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antibiotic columns to guarantee the right structure.', call. = FALSE)
|
||||||
|
txt_warning()
|
||||||
|
warned <<- FALSE
|
||||||
} else {
|
} else {
|
||||||
warning(w$message, call. = FALSE)
|
warning(w$message, call. = FALSE)
|
||||||
}
|
|
||||||
txt_warning()
|
txt_warning()
|
||||||
|
cat("\n") # txt_warning() does not append a "\n" on itself
|
||||||
|
}
|
||||||
},
|
},
|
||||||
error = function(e) {
|
error = function(e) {
|
||||||
txt_error()
|
txt_error()
|
||||||
stop(e, call. = FALSE)
|
stop(paste0("Error in row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
|
||||||
|
'... while writing value "', to,
|
||||||
|
'" to column(s) `', paste(cols, collapse = "`, `"),
|
||||||
|
"` (data class:", paste(class(x_original), collapse = "/"), "):\n", e$message), call. = FALSE)
|
||||||
}
|
}
|
||||||
)
|
)
|
||||||
|
|
||||||
x[rows, cols] <<- x_original[rows, cols]
|
tryCatch(
|
||||||
|
x[rows, cols] <<- x_original[rows, cols],
|
||||||
|
error = function(e) {
|
||||||
|
stop(paste0("Error in row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
|
||||||
|
'... while writing value "', to,
|
||||||
|
'" to column(s) `', paste(cols, collapse = "`, `"),
|
||||||
|
"` (data class:", paste(class(x), collapse = "/"), "):\n", e$message), call. = FALSE)
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
# before_df might not be a data.frame, but a tibble or data.table instead
|
# before_df might not be a data.frame, but a tibble or data.table instead
|
||||||
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,]
|
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,]
|
||||||
@ -719,7 +736,7 @@ eucast_rules <- function(x,
|
|||||||
mutate(plural = ifelse(n > 1, "s", ""),
|
mutate(plural = ifelse(n > 1, "s", ""),
|
||||||
txt = paste0(formatnr(n), " test result", plural, " added as ", new)) %>%
|
txt = paste0(formatnr(n), " test result", plural, " added as ", new)) %>%
|
||||||
pull(txt) %>%
|
pull(txt) %>%
|
||||||
paste(" -", ., collapse = "\n") %>%
|
paste(" *", ., collapse = "\n") %>%
|
||||||
cat()
|
cat()
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -748,16 +765,16 @@ eucast_rules <- function(x,
|
|||||||
mutate(plural = ifelse(n > 1, "s", ""),
|
mutate(plural = ifelse(n > 1, "s", ""),
|
||||||
txt = paste0(formatnr(n), " test result", plural, " changed from ", old, " to ", new)) %>%
|
txt = paste0(formatnr(n), " test result", plural, " changed from ", old, " to ", new)) %>%
|
||||||
pull(txt) %>%
|
pull(txt) %>%
|
||||||
paste(" -", ., collapse = "\n") %>%
|
paste(" *", ., collapse = "\n") %>%
|
||||||
cat()
|
cat()
|
||||||
cat("\n")
|
cat("\n")
|
||||||
}
|
}
|
||||||
cat(paste0(silver(strrep("-", options()$width - 1)), "\n"))
|
cat(paste0(silver(strrep("-", options()$width - 1)), "\n"))
|
||||||
|
|
||||||
if (verbose == FALSE & nrow(verbose_info) > 0) {
|
if (verbose == FALSE & nrow(verbose_info) > 0) {
|
||||||
cat(paste("\nUse", bold("verbose = TRUE"), "(on your original data) to get a data.frame with all specified edits instead.\n"))
|
cat(paste("\nUse", bold("eucast_rules(..., verbose = TRUE)"), "(on your original data) to get a data.frame with all specified edits instead.\n\n"))
|
||||||
} else if (verbose == TRUE) {
|
} else if (verbose == TRUE) {
|
||||||
cat(paste(red("\nUsed 'Verbose mode' (verbose = TRUE)."), "This returns a data.frame with all specified edits.\nUse", bold("verbose = FALSE"), "to apply the rules on your data.\n"))
|
cat(paste(red("\nUsed 'Verbose mode' (verbose = TRUE)"), ", which returns a data.frame with all specified edits.\nUse", bold("verbose = FALSE"), "to apply the rules on your data.\n\n"))
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -45,4 +45,3 @@ scale_type.ab <- function(x) {
|
|||||||
# "Error: Discrete value supplied to continuous scale"
|
# "Error: Discrete value supplied to continuous scale"
|
||||||
"discrete"
|
"discrete"
|
||||||
}
|
}
|
||||||
|
|
||||||
|
19
R/mic.R
@ -173,9 +173,8 @@ as.mic <- function(x, na.rm = FALSE) {
|
|||||||
list_missing, call. = FALSE)
|
list_missing, call. = FALSE)
|
||||||
}
|
}
|
||||||
|
|
||||||
x <- factor(x, levels = lvls, ordered = TRUE)
|
structure(.Data = factor(x, levels = lvls, ordered = TRUE),
|
||||||
class(x) <- c('mic', 'ordered', 'factor')
|
class = c('mic', 'ordered', 'factor'))
|
||||||
x
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -279,3 +278,17 @@ barplot.mic <- function(height,
|
|||||||
...)
|
...)
|
||||||
axis(2, seq(0, max(table(droplevels.factor(height)))))
|
axis(2, seq(0, max(table(droplevels.factor(height)))))
|
||||||
}
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar type_sum
|
||||||
|
#' @export
|
||||||
|
type_sum.mic <- function(x) {
|
||||||
|
"mic"
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar pillar_shaft
|
||||||
|
#' @export
|
||||||
|
pillar_shaft.mic <- function(x, ...) {
|
||||||
|
out <- trimws(format(x))
|
||||||
|
out[is.na(x)] <- NA
|
||||||
|
pillar::new_pillar_shaft_simple(out, align = "right", min_width = 4)
|
||||||
|
}
|
||||||
|
27
R/mo.R
@ -268,13 +268,17 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
structure(.Data = y, class = "mo")
|
to_class_mo(y)
|
||||||
|
}
|
||||||
|
|
||||||
|
to_class_mo <- function(x) {
|
||||||
|
structure(.Data = x, class = "mo")
|
||||||
}
|
}
|
||||||
|
|
||||||
#' @rdname as.mo
|
#' @rdname as.mo
|
||||||
#' @export
|
#' @export
|
||||||
is.mo <- function(x) {
|
is.mo <- function(x) {
|
||||||
identical(class(x), "mo")
|
identical(class(x), class(to_class_mo(x)))
|
||||||
}
|
}
|
||||||
|
|
||||||
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
|
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
|
||||||
@ -391,8 +395,7 @@ exec_as.mo <- function(x,
|
|||||||
# all empty
|
# all empty
|
||||||
if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
|
if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
|
||||||
if (property == "mo") {
|
if (property == "mo") {
|
||||||
return(structure(rep(NA_character_, length(x_input)),
|
return(to_class_mo(rep(NA_character_, length(x_input))))
|
||||||
class = "mo"))
|
|
||||||
} else {
|
} else {
|
||||||
return(rep(NA_character_, length(x_input)))
|
return(rep(NA_character_, length(x_input)))
|
||||||
}
|
}
|
||||||
@ -1455,7 +1458,7 @@ exec_as.mo <- function(x,
|
|||||||
)
|
)
|
||||||
|
|
||||||
if (property == "mo") {
|
if (property == "mo") {
|
||||||
class(x) <- "mo"
|
x <- to_class_mo(x)
|
||||||
}
|
}
|
||||||
|
|
||||||
if (length(mo_renamed()) > 0) {
|
if (length(mo_renamed()) > 0) {
|
||||||
@ -1507,6 +1510,20 @@ print.mo <- function(x, ...) {
|
|||||||
print.default(x, quote = FALSE)
|
print.default(x, quote = FALSE)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar type_sum
|
||||||
|
#' @export
|
||||||
|
type_sum.mo <- function(x) {
|
||||||
|
"mo"
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar pillar_shaft
|
||||||
|
#' @export
|
||||||
|
pillar_shaft.mo <- function(x, ...) {
|
||||||
|
out <- format(x)
|
||||||
|
out[is.na(x)] <- NA
|
||||||
|
pillar::new_pillar_shaft_simple(out, align = "left", min_width = 11)
|
||||||
|
}
|
||||||
|
|
||||||
#' @exportMethod summary.mo
|
#' @exportMethod summary.mo
|
||||||
#' @importFrom dplyr n_distinct
|
#' @importFrom dplyr n_distinct
|
||||||
#' @importFrom clean freq top_freq
|
#' @importFrom clean freq top_freq
|
||||||
|
@ -425,11 +425,10 @@ mo_validate <- function(x, property, ...) {
|
|||||||
}
|
}
|
||||||
|
|
||||||
if (property == "mo") {
|
if (property == "mo") {
|
||||||
return(structure(x, class = "mo"))
|
return(to_class_mo(x))
|
||||||
} else if (property == "col_id") {
|
} else if (property == "col_id") {
|
||||||
return(as.integer(x))
|
return(as.integer(x))
|
||||||
} else {
|
} else {
|
||||||
return(x)
|
return(x)
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
@ -28,7 +28,7 @@
|
|||||||
#' @param year_max highest year to use in the prediction model, defaults to 10 years after today
|
#' @param year_max highest year to use in the prediction model, defaults to 10 years after today
|
||||||
#' @param year_every unit of sequence between lowest year found in the data and \code{year_max}
|
#' @param year_every unit of sequence between lowest year found in the data and \code{year_max}
|
||||||
#' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
|
#' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
|
||||||
#' @param model the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution (i.e. using \code{\link{glm}(..., family = \link{binomial})}), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.
|
#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using \code{\link{glm}(..., family = \link{binomial})}), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for all valid options.
|
||||||
#' @param I_as_S a logical to indicate whether values \code{I} should be treated as \code{S} (will otherwise be treated as \code{R})
|
#' @param I_as_S a logical to indicate whether values \code{I} should be treated as \code{S} (will otherwise be treated as \code{R})
|
||||||
#' @param preserve_measurements a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be \code{NA}.
|
#' @param preserve_measurements a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be \code{NA}.
|
||||||
#' @param info a logical to indicate whether textual analysis should be printed with the name and \code{\link{summary}} of the statistical model.
|
#' @param info a logical to indicate whether textual analysis should be printed with the name and \code{\link{summary}} of the statistical model.
|
||||||
@ -112,7 +112,7 @@ resistance_predict <- function(x,
|
|||||||
year_max = NULL,
|
year_max = NULL,
|
||||||
year_every = 1,
|
year_every = 1,
|
||||||
minimum = 30,
|
minimum = 30,
|
||||||
model = 'binomial',
|
model = NULL,
|
||||||
I_as_S = TRUE,
|
I_as_S = TRUE,
|
||||||
preserve_measurements = TRUE,
|
preserve_measurements = TRUE,
|
||||||
info = TRUE,
|
info = TRUE,
|
||||||
@ -122,6 +122,10 @@ resistance_predict <- function(x,
|
|||||||
stop('This table does not contain any observations.')
|
stop('This table does not contain any observations.')
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (is.null(model)) {
|
||||||
|
stop('Choose a regression model with the `model` parameter, e.g. resistance_predict(..., model = "binomial").')
|
||||||
|
}
|
||||||
|
|
||||||
if (!col_ab %in% colnames(x)) {
|
if (!col_ab %in% colnames(x)) {
|
||||||
stop('Column ', col_ab, ' not found.')
|
stop('Column ', col_ab, ' not found.')
|
||||||
}
|
}
|
||||||
@ -252,7 +256,7 @@ resistance_predict <- function(x,
|
|||||||
se <- predictmodel$se.fit
|
se <- predictmodel$se.fit
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
stop('No valid model selected.')
|
stop('No valid model selected. See ?resistance_predict.')
|
||||||
}
|
}
|
||||||
|
|
||||||
# prepare the output dataframe
|
# prepare the output dataframe
|
||||||
|
18
R/rsi.R
@ -472,3 +472,21 @@ barplot.rsi <- function(height,
|
|||||||
axis(side = 1, labels = levels(height), at = c(1, 2, 3) + 0.5, lwd = 0)
|
axis(side = 1, labels = levels(height), at = c(1, 2, 3) + 0.5, lwd = 0)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar type_sum
|
||||||
|
#' @export
|
||||||
|
type_sum.rsi <- function(x) {
|
||||||
|
"rsi"
|
||||||
|
}
|
||||||
|
|
||||||
|
#' @importFrom pillar pillar_shaft
|
||||||
|
#' @importFrom crayon bgGreen bgYellow bgRed white black
|
||||||
|
#' @export
|
||||||
|
pillar_shaft.rsi <- function(x, ...) {
|
||||||
|
out <- trimws(format(x))
|
||||||
|
out[is.na(x)] <- pillar::style_subtle("NA")
|
||||||
|
out[x == "S"] <- bgGreen(white(" S "))
|
||||||
|
out[x == "I"] <- bgYellow(black(" I "))
|
||||||
|
out[x == "R"] <- bgRed(white(" R "))
|
||||||
|
pillar::new_pillar_shaft_simple(out, align = "left", min_width = 4)
|
||||||
|
}
|
||||||
|
@ -78,7 +78,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<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">0.7.1.9023</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -224,17 +224,17 @@
|
|||||||
<h1>License</h1>
|
<h1>License</h1>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<pre> GNU GENERAL PUBLIC LICENSE
|
<pre>GNU GENERAL PUBLIC LICENSE
|
||||||
Version 2, June 1991
|
Version 2, June 1991
|
||||||
|
|
||||||
Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
|
Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
|
||||||
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
|
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
|
||||||
Everyone is permitted to copy and distribute verbatim copies
|
Everyone is permitted to copy and distribute verbatim copies
|
||||||
of this license document, but changing it is not allowed.
|
of this license document, but changing it is not allowed.
|
||||||
|
|
||||||
Preamble
|
Preamble
|
||||||
|
|
||||||
The licenses for most software are designed to take away your
|
The licenses for most software are designed to take away your
|
||||||
freedom to share and change it. By contrast, the GNU General Public
|
freedom to share and change it. By contrast, the GNU General Public
|
||||||
License is intended to guarantee your freedom to share and change free
|
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
|
software--to make sure the software is free for all its users. This
|
||||||
@ -279,21 +279,21 @@ program will individually obtain patent licenses, in effect making the
|
|||||||
program proprietary. To prevent this, we have made it clear that any
|
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.
|
patent must be licensed for everyone's free use or not licensed at all.
|
||||||
|
|
||||||
The precise terms and conditions for copying, distribution and
|
The precise terms and conditions for copying, distribution and
|
||||||
modification follow.
|
modification follow.
|
||||||
|
|
||||||
GNU GENERAL PUBLIC LICENSE
|
GNU GENERAL PUBLIC LICENSE
|
||||||
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
||||||
|
|
||||||
0. This License applies to any program or other work which contains
|
0. This License applies to any program or other work which contains
|
||||||
a notice placed by the copyright holder saying it may be distributed
|
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"
|
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:
|
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
|
either verbatim or with modifications and/or translated into another
|
||||||
language. (Hereinafter, translation is included without limitation in
|
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
|
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
|
||||||
@ -302,7 +302,7 @@ is covered only if its contents constitute a work based on the
|
|||||||
Program (independent of having been made by running the Program).
|
Program (independent of having been made by running the Program).
|
||||||
Whether that is true depends on what the Program does.
|
Whether that is true depends on what the Program does.
|
||||||
|
|
||||||
1. You may copy and distribute verbatim copies of the Program's
|
1. You may copy and distribute verbatim copies of the Program's
|
||||||
source code as you receive it, in any medium, provided that you
|
source code as you receive it, in any medium, provided that you
|
||||||
conspicuously and appropriately publish on each copy an appropriate
|
conspicuously and appropriately publish on each copy an appropriate
|
||||||
copyright notice and disclaimer of warranty; keep intact all the
|
copyright notice and disclaimer of warranty; keep intact all the
|
||||||
@ -420,10 +420,10 @@ restrictions on the recipients' exercise of the rights granted herein.
|
|||||||
You are not responsible for enforcing compliance by third parties to
|
You are not responsible for enforcing compliance by third parties to
|
||||||
this License.
|
this License.
|
||||||
|
|
||||||
7. If, as a consequence of a court judgment or allegation of patent
|
7. If, as a consequence of a court judgment or allegation of patent
|
||||||
infringement or for any other reason (not limited to patent issues),
|
infringement or for any other reason (not limited to patent issues),
|
||||||
conditions are imposed on you (whether by court order, agreement or
|
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
|
excuse you from the conditions of this License. If you cannot
|
||||||
distribute so as to satisfy simultaneously your obligations under this
|
distribute so as to satisfy simultaneously your obligations under this
|
||||||
License and any other pertinent obligations, then as a consequence you
|
License and any other pertinent obligations, then as a consequence you
|
||||||
@ -452,7 +452,7 @@ impose that choice.
|
|||||||
This section is intended to make thoroughly clear what is believed to
|
This section is intended to make thoroughly clear what is believed to
|
||||||
be a consequence of the rest of this License.
|
be a consequence of the rest of this License.
|
||||||
|
|
||||||
8. If the distribution and/or use of the Program is restricted in
|
8. If the distribution and/or use of the Program is restricted in
|
||||||
certain countries either by patents or by copyrighted interfaces, the
|
certain countries either by patents or by copyrighted interfaces, the
|
||||||
original copyright holder who places the Program under this License
|
original copyright holder who places the Program under this License
|
||||||
may add an explicit geographical distribution limitation excluding
|
may add an explicit geographical distribution limitation excluding
|
||||||
@ -460,7 +460,7 @@ 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.
|
the limitation as if written in the body of this License.
|
||||||
|
|
||||||
9. The Free Software Foundation may publish revised and/or new versions
|
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
|
be similar in spirit to the present version, but may differ in detail to
|
||||||
address new problems or concerns.
|
address new problems or concerns.
|
||||||
@ -473,7 +473,7 @@ 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
|
this License, you may choose any version ever published by the Free Software
|
||||||
Foundation.
|
Foundation.
|
||||||
|
|
||||||
10. If you wish to incorporate parts of the Program into other free
|
10. If you wish to incorporate parts of the Program into other free
|
||||||
programs whose distribution conditions are different, write to the author
|
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
|
Software Foundation, write to the Free Software Foundation; we sometimes
|
||||||
@ -481,9 +481,9 @@ 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 preserving the free status of all derivatives of our free software and
|
||||||
of promoting the sharing and reuse of software generally.
|
of promoting the sharing and reuse of software generally.
|
||||||
|
|
||||||
NO WARRANTY
|
NO WARRANTY
|
||||||
|
|
||||||
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS 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
|
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
|
||||||
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
|
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
|
||||||
@ -493,76 +493,17 @@ TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
|||||||
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
||||||
REPAIR OR CORRECTION.
|
REPAIR OR CORRECTION.
|
||||||
|
|
||||||
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||||
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
|
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,
|
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
|
||||||
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
|
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
|
||||||
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
|
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
|
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
|
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
|
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
|
||||||
POSSIBILITY OF SUCH DAMAGES.
|
POSSIBILITY OF SUCH DAMAGES.
|
||||||
|
|
||||||
END OF TERMS AND CONDITIONS
|
END OF TERMS AND CONDITIONS
|
||||||
|
|
||||||
How to Apply These Terms to Your New Programs
|
|
||||||
|
|
||||||
If you develop a new program, and you want it to be of the greatest
|
|
||||||
possible use to the public, the best way to achieve this is to make it
|
|
||||||
free software which everyone can redistribute and change under these terms.
|
|
||||||
|
|
||||||
To do so, attach the following notices to the program. It is safest
|
|
||||||
to attach them to the start of each source file to most effectively
|
|
||||||
convey the exclusion of warranty; and each file should have at least
|
|
||||||
the "copyright" line and a pointer to where the full notice is found.
|
|
||||||
|
|
||||||
{description}
|
|
||||||
Copyright (C) {year} {fullname}
|
|
||||||
|
|
||||||
This program is free software; you can redistribute it and/or modify
|
|
||||||
it under the terms of the GNU General Public License as published by
|
|
||||||
the Free Software Foundation; either version 2 of the License, or
|
|
||||||
(at your option) any later version.
|
|
||||||
|
|
||||||
This program is distributed in the hope that it will be useful,
|
|
||||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
||||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
||||||
GNU General Public License for more details.
|
|
||||||
|
|
||||||
You should have received a copy of the GNU General Public License along
|
|
||||||
with this program; if not, write to the Free Software Foundation, Inc.,
|
|
||||||
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
|
||||||
|
|
||||||
Also add information on how to contact you by electronic and paper mail.
|
|
||||||
|
|
||||||
If the program is interactive, make it output a short notice like this
|
|
||||||
when it starts in an interactive mode:
|
|
||||||
|
|
||||||
Gnomovision version 69, Copyright (C) year name of author
|
|
||||||
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
|
|
||||||
This is free software, and you are welcome to redistribute it
|
|
||||||
under certain conditions; type `show c' for details.
|
|
||||||
|
|
||||||
The hypothetical commands `show w' and `show c' should show the appropriate
|
|
||||||
parts of the General Public License. Of course, the commands you use may
|
|
||||||
be called something other than `show w' and `show c'; they could even be
|
|
||||||
mouse-clicks or menu items--whatever suits your program.
|
|
||||||
|
|
||||||
You should also get your employer (if you work as a programmer) or your
|
|
||||||
school, if any, to sign a "copyright disclaimer" for the program, if
|
|
||||||
necessary. Here is a sample; alter the names:
|
|
||||||
|
|
||||||
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
|
|
||||||
`Gnomovision' (which makes passes at compilers) written by James Hacker.
|
|
||||||
|
|
||||||
{signature of Ty Coon}, 1 April 1989
|
|
||||||
Ty Coon, President of Vice
|
|
||||||
|
|
||||||
This General Public License does not permit incorporating your program into
|
|
||||||
proprietary programs. If your program is a subroutine library, you may
|
|
||||||
consider it more useful to permit linking proprietary applications with the
|
|
||||||
library. If this is what you want to do, use the GNU Lesser General
|
|
||||||
Public License instead of this License.
|
|
||||||
</pre>
|
</pre>
|
||||||
|
|
||||||
</div>
|
</div>
|
||||||
|
@ -40,7 +40,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -185,7 +185,7 @@
|
|||||||
<h1>How to conduct AMR analysis</h1>
|
<h1>How to conduct AMR analysis</h1>
|
||||||
<h4 class="author">Matthijs S. Berends</h4>
|
<h4 class="author">Matthijs S. Berends</h4>
|
||||||
|
|
||||||
<h4 class="date">06 August 2019</h4>
|
<h4 class="date">07 August 2019</h4>
|
||||||
|
|
||||||
|
|
||||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||||
@ -194,7 +194,7 @@
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 06 August 2019.</p>
|
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 07 August 2019.</p>
|
||||||
<div id="introduction" class="section level1">
|
<div id="introduction" class="section level1">
|
||||||
<h1 class="hasAnchor">
|
<h1 class="hasAnchor">
|
||||||
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
||||||
@ -210,21 +210,21 @@
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2019-08-06</td>
|
<td align="center">2019-08-07</td>
|
||||||
<td align="center">abcd</td>
|
<td align="center">abcd</td>
|
||||||
<td align="center">Escherichia coli</td>
|
<td align="center">Escherichia coli</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">2019-08-06</td>
|
<td align="center">2019-08-07</td>
|
||||||
<td align="center">abcd</td>
|
<td align="center">abcd</td>
|
||||||
<td align="center">Escherichia coli</td>
|
<td align="center">Escherichia coli</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2019-08-06</td>
|
<td align="center">2019-08-07</td>
|
||||||
<td align="center">efgh</td>
|
<td align="center">efgh</td>
|
||||||
<td align="center">Escherichia coli</td>
|
<td align="center">Escherichia coli</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
@ -320,71 +320,71 @@
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">2017-03-10</td>
|
<td align="center">2017-01-02</td>
|
||||||
<td align="center">Q5</td>
|
<td align="center">V8</td>
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">Escherichia coli</td>
|
<td align="center">Klebsiella pneumoniae</td>
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
|
<td align="center">I</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">2011-12-26</td>
|
<td align="center">2013-05-08</td>
|
||||||
<td align="center">G6</td>
|
<td align="center">W2</td>
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital B</td>
|
||||||
|
<td align="center">Staphylococcus aureus</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="center">2015-08-15</td>
|
||||||
|
<td align="center">R1</td>
|
||||||
|
<td align="center">Hospital B</td>
|
||||||
|
<td align="center">Streptococcus pneumoniae</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2012-01-09</td>
|
||||||
|
<td align="center">X9</td>
|
||||||
|
<td align="center">Hospital D</td>
|
||||||
|
<td align="center">Staphylococcus aureus</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">I</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td align="center">2014-06-18</td>
|
||||||
|
<td align="center">Z7</td>
|
||||||
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">Streptococcus pneumoniae</td>
|
<td align="center">Streptococcus pneumoniae</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">M</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="center">2011-07-01</td>
|
|
||||||
<td align="center">L6</td>
|
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">Escherichia coli</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2015-08-22</td>
|
|
||||||
<td align="center">A9</td>
|
|
||||||
<td align="center">Hospital B</td>
|
|
||||||
<td align="center">Escherichia coli</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd">
|
|
||||||
<td align="center">2017-03-16</td>
|
|
||||||
<td align="center">H1</td>
|
|
||||||
<td align="center">Hospital A</td>
|
|
||||||
<td align="center">Staphylococcus aureus</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">I</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td align="center">2017-06-20</td>
|
|
||||||
<td align="center">V2</td>
|
|
||||||
<td align="center">Hospital D</td>
|
|
||||||
<td align="center">Escherichia coli</td>
|
|
||||||
<td align="center">I</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td align="center">2015-02-18</td>
|
||||||
|
<td align="center">F4</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
|
<td align="center">Escherichia coli</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">M</td>
|
||||||
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
<p>Now, let’s start the cleaning and the analysis!</p>
|
<p>Now, let’s start the cleaning and the analysis!</p>
|
||||||
@ -406,8 +406,8 @@
|
|||||||
#
|
#
|
||||||
# Item Count Percent Cum. Count Cum. Percent
|
# Item Count Percent Cum. Count Cum. Percent
|
||||||
# --- ----- ------- -------- ----------- -------------
|
# --- ----- ------- -------- ----------- -------------
|
||||||
# 1 M 10,366 51.8% 10,366 51.8%
|
# 1 M 10,401 52.0% 10,401 52.0%
|
||||||
# 2 F 9,634 48.2% 20,000 100.0%</code></pre>
|
# 2 F 9,599 48.0% 20,000 100.0%</code></pre>
|
||||||
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p>
|
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p>
|
||||||
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
|
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
|
||||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data <-<span class="st"> </span>data <span class="op">%>%</span></a>
|
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data <-<span class="st"> </span>data <span class="op">%>%</span></a>
|
||||||
@ -423,56 +423,56 @@
|
|||||||
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="co"># http://eucast.org/</span></a>
|
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="co"># http://eucast.org/</span></a>
|
||||||
<a class="sourceLine" id="cb15-5" data-line-number="5"><span class="co"># </span></a>
|
<a class="sourceLine" id="cb15-5" data-line-number="5"><span class="co"># </span></a>
|
||||||
<a class="sourceLine" id="cb15-6" data-line-number="6"><span class="co"># EUCAST Clinical Breakpoints (v9.0, 2019)</span></a>
|
<a class="sourceLine" id="cb15-6" data-line-number="6"><span class="co"># EUCAST Clinical Breakpoints (v9.0, 2019)</span></a>
|
||||||
<a class="sourceLine" id="cb15-7" data-line-number="7"><span class="co"># Aerococcus sanguinicola (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-7" data-line-number="7"><span class="co"># Aerococcus sanguinicola (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="co"># Aerococcus urinae (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="co"># Aerococcus urinae (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-9" data-line-number="9"><span class="co"># Anaerobic Gram-negatives (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-9" data-line-number="9"><span class="co"># Anaerobic Gram-negatives (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="co"># Anaerobic Gram-positives (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="co"># Anaerobic Gram-positives (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-11" data-line-number="11"><span class="co"># Campylobacter coli (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-11" data-line-number="11"><span class="co"># Campylobacter coli (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-12" data-line-number="12"><span class="co"># Campylobacter jejuni (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-12" data-line-number="12"><span class="co"># Campylobacter jejuni (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-13" data-line-number="13"><span class="co"># Enterobacteriales (Order) (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-13" data-line-number="13"><span class="co"># Enterobacteriales (Order) (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-14" data-line-number="14"><span class="co"># Enterococcus (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-14" data-line-number="14"><span class="co"># Enterococcus (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-15" data-line-number="15"><span class="co"># Haemophilus influenzae (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-15" data-line-number="15"><span class="co"># Haemophilus influenzae (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-16" data-line-number="16"><span class="co"># Kingella kingae (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-16" data-line-number="16"><span class="co"># Kingella kingae (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-17" data-line-number="17"><span class="co"># Moraxella catarrhalis (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-17" data-line-number="17"><span class="co"># Moraxella catarrhalis (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,439 new changes)</span></a>
|
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,456 values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a>
|
<a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a>
|
||||||
<a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
|
<a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
|
||||||
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,329 new changes)</span></a>
|
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,287 values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,679 new changes)</span></a>
|
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,759 values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-32" data-line-number="32"><span class="co"># Table 12: Interpretive rules for aminoglycosides (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-32" data-line-number="32"><span class="co"># Table 12: Interpretive rules for aminoglycosides (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a>
|
<a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a>
|
||||||
<a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a>
|
<a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a>
|
||||||
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,347 new changes)</span></a>
|
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,330 values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (114 new changes)</span></a>
|
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (108 values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
|
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no values changed)</span></a>
|
||||||
<a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a>
|
<a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a>
|
||||||
<a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
|
<a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
|
||||||
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,589 out of 20,000 rows, making a total of 7,908 edits</span></a>
|
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,604 out of 20,000 rows, making a total of 7,940 edits</span></a>
|
||||||
<a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># => added 0 test results</span></a>
|
<a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># => added 0 test results</span></a>
|
||||||
<a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a>
|
<a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a>
|
||||||
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># => changed 7,908 test results</span></a>
|
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># => changed 7,940 test results</span></a>
|
||||||
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 110 test results changed from S to I</span></a>
|
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># * 110 test results changed from S to I</span></a>
|
||||||
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,680 test results changed from S to R</span></a>
|
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># * 4,715 test results changed from S to R</span></a>
|
||||||
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,068 test results changed from I to S</span></a>
|
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># * 1,119 test results changed from I to S</span></a>
|
||||||
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 326 test results changed from I to R</span></a>
|
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># * 307 test results changed from I to R</span></a>
|
||||||
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,711 test results changed from R to S</span></a>
|
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># * 1,664 test results changed from R to S</span></a>
|
||||||
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 13 test results changed from R to I</span></a>
|
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># * 25 test results changed from R to I</span></a>
|
||||||
<a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
|
<a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
|
||||||
<a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a>
|
<a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a>
|
||||||
<a class="sourceLine" id="cb15-56" data-line-number="56"><span class="co"># Use verbose = TRUE (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
|
<a class="sourceLine" id="cb15-56" data-line-number="56"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
<div id="adding-new-variables" class="section level1">
|
<div id="adding-new-variables" class="section level1">
|
||||||
<h1 class="hasAnchor">
|
<h1 class="hasAnchor">
|
||||||
@ -497,7 +497,7 @@
|
|||||||
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
|
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
|
||||||
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
|
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
|
||||||
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
|
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
|
||||||
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># => Found 5,681 first isolates (28.4% of total)</span></a></code></pre></div>
|
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># => Found 5,676 first isolates (28.4% of total)</span></a></code></pre></div>
|
||||||
<p>So only is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
<p>So only is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
|
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
|
||||||
@ -508,7 +508,7 @@
|
|||||||
<div id="first-weighted-isolates" class="section level2">
|
<div id="first-weighted-isolates" class="section level2">
|
||||||
<h2 class="hasAnchor">
|
<h2 class="hasAnchor">
|
||||||
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
|
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
|
||||||
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient C10, sorted on date:</p>
|
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient M4, sorted on date:</p>
|
||||||
<table class="table">
|
<table class="table">
|
||||||
<thead><tr class="header">
|
<thead><tr class="header">
|
||||||
<th align="center">isolate</th>
|
<th align="center">isolate</th>
|
||||||
@ -524,21 +524,21 @@
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">1</td>
|
<td align="center">1</td>
|
||||||
<td align="center">2010-07-24</td>
|
<td align="center">2010-04-02</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">2</td>
|
<td align="center">2</td>
|
||||||
<td align="center">2010-12-03</td>
|
<td align="center">2010-05-26</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -546,10 +546,10 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">3</td>
|
<td align="center">3</td>
|
||||||
<td align="center">2010-12-19</td>
|
<td align="center">2010-07-15</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -557,10 +557,10 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">4</td>
|
<td align="center">4</td>
|
||||||
<td align="center">2011-02-18</td>
|
<td align="center">2010-09-11</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -568,21 +568,21 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">5</td>
|
<td align="center">5</td>
|
||||||
<td align="center">2011-06-26</td>
|
<td align="center">2010-11-13</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">FALSE</td>
|
<td align="center">FALSE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">6</td>
|
<td align="center">6</td>
|
||||||
<td align="center">2011-06-28</td>
|
<td align="center">2010-11-16</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -590,43 +590,43 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">7</td>
|
<td align="center">7</td>
|
||||||
<td align="center">2011-06-30</td>
|
<td align="center">2011-01-03</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
<td align="center">FALSE</td>
|
<td align="center">FALSE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">8</td>
|
<td align="center">8</td>
|
||||||
<td align="center">2011-08-29</td>
|
<td align="center">2011-03-16</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">FALSE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">9</td>
|
<td align="center">9</td>
|
||||||
<td align="center">2011-10-03</td>
|
<td align="center">2011-04-21</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">FALSE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">10</td>
|
<td align="center">10</td>
|
||||||
<td align="center">2011-12-30</td>
|
<td align="center">2011-04-24</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -645,7 +645,7 @@
|
|||||||
<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
|
<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
|
||||||
<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
|
<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
|
||||||
<a class="sourceLine" id="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
|
<a class="sourceLine" id="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
|
||||||
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># => Found 15,027 first weighted isolates (75.1% of total)</span></a></code></pre></div>
|
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># => Found 14,973 first weighted isolates (74.9% of total)</span></a></code></pre></div>
|
||||||
<table class="table">
|
<table class="table">
|
||||||
<thead><tr class="header">
|
<thead><tr class="header">
|
||||||
<th align="center">isolate</th>
|
<th align="center">isolate</th>
|
||||||
@ -662,22 +662,22 @@
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">1</td>
|
<td align="center">1</td>
|
||||||
<td align="center">2010-07-24</td>
|
<td align="center">2010-04-02</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">2</td>
|
<td align="center">2</td>
|
||||||
<td align="center">2010-12-03</td>
|
<td align="center">2010-05-26</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -686,10 +686,10 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">3</td>
|
<td align="center">3</td>
|
||||||
<td align="center">2010-12-19</td>
|
<td align="center">2010-07-15</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -698,10 +698,10 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">4</td>
|
<td align="center">4</td>
|
||||||
<td align="center">2011-02-18</td>
|
<td align="center">2010-09-11</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
@ -710,83 +710,83 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">5</td>
|
<td align="center">5</td>
|
||||||
<td align="center">2011-06-26</td>
|
<td align="center">2010-11-13</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">FALSE</td>
|
<td align="center">FALSE</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">6</td>
|
<td align="center">6</td>
|
||||||
<td align="center">2011-06-28</td>
|
<td align="center">2010-11-16</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">FALSE</td>
|
<td align="center">FALSE</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">FALSE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">7</td>
|
<td align="center">7</td>
|
||||||
<td align="center">2011-06-30</td>
|
<td align="center">2011-01-03</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">FALSE</td>
|
||||||
<td align="center">FALSE</td>
|
<td align="center">FALSE</td>
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">8</td>
|
<td align="center">8</td>
|
||||||
<td align="center">2011-08-29</td>
|
<td align="center">2011-03-16</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">FALSE</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">9</td>
|
<td align="center">9</td>
|
||||||
<td align="center">2011-10-03</td>
|
<td align="center">2011-04-21</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">FALSE</td>
|
<td align="center">TRUE</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">10</td>
|
<td align="center">10</td>
|
||||||
<td align="center">2011-12-30</td>
|
<td align="center">2011-04-24</td>
|
||||||
<td align="center">C10</td>
|
<td align="center">M4</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">FALSE</td>
|
<td align="center">FALSE</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">FALSE</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
<p>Instead of 2, now 10 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
|
<p>Instead of 2, now 7 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
|
||||||
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
|
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
|
||||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
|
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
|
||||||
<p>So we end up with 15,027 isolates for analysis.</p>
|
<p>So we end up with 14,973 isolates for analysis.</p>
|
||||||
<p>We can remove unneeded columns:</p>
|
<p>We can remove unneeded columns:</p>
|
||||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st <-<span class="st"> </span>data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st <-<span class="st"> </span>data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
|
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
|
||||||
@ -811,64 +811,64 @@
|
|||||||
</tr></thead>
|
</tr></thead>
|
||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td>1</td>
|
<td>3</td>
|
||||||
<td align="center">2017-03-10</td>
|
<td align="center">2015-08-15</td>
|
||||||
<td align="center">Q5</td>
|
<td align="center">R1</td>
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">F</td>
|
|
||||||
<td align="center">Gram-negative</td>
|
|
||||||
<td align="center">Escherichia</td>
|
|
||||||
<td align="center">coli</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
|
||||||
<td>2</td>
|
|
||||||
<td align="center">2011-12-26</td>
|
|
||||||
<td align="center">G6</td>
|
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">B_STRPT_PNE</td>
|
<td align="center">B_STRPT_PNE</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">M</td>
|
<td align="center">F</td>
|
||||||
<td align="center">Gram-positive</td>
|
<td align="center">Gram-positive</td>
|
||||||
<td align="center">Streptococcus</td>
|
<td align="center">Streptococcus</td>
|
||||||
<td align="center">pneumoniae</td>
|
<td align="center">pneumoniae</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
|
||||||
<td>3</td>
|
|
||||||
<td align="center">2011-07-01</td>
|
|
||||||
<td align="center">L6</td>
|
|
||||||
<td align="center">Hospital C</td>
|
|
||||||
<td align="center">B_ESCHR_COL</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">S</td>
|
|
||||||
<td align="center">M</td>
|
|
||||||
<td align="center">Gram-negative</td>
|
|
||||||
<td align="center">Escherichia</td>
|
|
||||||
<td align="center">coli</td>
|
|
||||||
<td align="center">TRUE</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td>6</td>
|
<td>4</td>
|
||||||
<td align="center">2017-06-20</td>
|
<td align="center">2012-01-09</td>
|
||||||
<td align="center">V2</td>
|
<td align="center">X9</td>
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">B_ESCHR_COL</td>
|
<td align="center">B_STPHY_AUR</td>
|
||||||
<td align="center">I</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">F</td>
|
<td align="center">F</td>
|
||||||
|
<td align="center">Gram-positive</td>
|
||||||
|
<td align="center">Staphylococcus</td>
|
||||||
|
<td align="center">aureus</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>5</td>
|
||||||
|
<td align="center">2014-06-18</td>
|
||||||
|
<td align="center">Z7</td>
|
||||||
|
<td align="center">Hospital D</td>
|
||||||
|
<td align="center">B_STRPT_PNE</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">F</td>
|
||||||
|
<td align="center">Gram-positive</td>
|
||||||
|
<td align="center">Streptococcus</td>
|
||||||
|
<td align="center">pneumoniae</td>
|
||||||
|
<td align="center">TRUE</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>6</td>
|
||||||
|
<td align="center">2015-02-18</td>
|
||||||
|
<td align="center">F4</td>
|
||||||
|
<td align="center">Hospital A</td>
|
||||||
|
<td align="center">B_ESCHR_COL</td>
|
||||||
|
<td align="center">R</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">S</td>
|
||||||
|
<td align="center">M</td>
|
||||||
<td align="center">Gram-negative</td>
|
<td align="center">Gram-negative</td>
|
||||||
<td align="center">Escherichia</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">coli</td>
|
<td align="center">coli</td>
|
||||||
@ -876,34 +876,34 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td>7</td>
|
<td>7</td>
|
||||||
<td align="center">2012-02-10</td>
|
<td align="center">2010-11-14</td>
|
||||||
<td align="center">D1</td>
|
<td align="center">W5</td>
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">B_STRPT_PNE</td>
|
<td align="center">B_STPHY_AUR</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
<td align="center">R</td>
|
||||||
<td align="center">R</td>
|
<td align="center">S</td>
|
||||||
<td align="center">M</td>
|
<td align="center">F</td>
|
||||||
<td align="center">Gram-positive</td>
|
<td align="center">Gram-positive</td>
|
||||||
<td align="center">Streptococcus</td>
|
<td align="center">Staphylococcus</td>
|
||||||
<td align="center">pneumoniae</td>
|
<td align="center">aureus</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td>8</td>
|
<td>8</td>
|
||||||
<td align="center">2010-05-01</td>
|
<td align="center">2010-12-25</td>
|
||||||
<td align="center">E1</td>
|
<td align="center">F4</td>
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">B_STRPT_PNE</td>
|
<td align="center">B_ESCHR_COL</td>
|
||||||
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">S</td>
|
<td align="center">S</td>
|
||||||
<td align="center">R</td>
|
|
||||||
<td align="center">M</td>
|
<td align="center">M</td>
|
||||||
<td align="center">Gram-positive</td>
|
<td align="center">Gram-negative</td>
|
||||||
<td align="center">Streptococcus</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">pneumoniae</td>
|
<td align="center">coli</td>
|
||||||
<td align="center">TRUE</td>
|
<td align="center">TRUE</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
@ -925,7 +925,7 @@
|
|||||||
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus, species)</a></code></pre></div>
|
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus, species)</a></code></pre></div>
|
||||||
<p><strong>Frequency table</strong></p>
|
<p><strong>Frequency table</strong></p>
|
||||||
<p>Class: character<br>
|
<p>Class: character<br>
|
||||||
Length: 15,027 (of which NA: 0 = 0.00%)<br>
|
Length: 14,973 (of which NA: 0 = 0.00%)<br>
|
||||||
Unique: 4</p>
|
Unique: 4</p>
|
||||||
<p>Shortest: 16<br>
|
<p>Shortest: 16<br>
|
||||||
Longest: 24</p>
|
Longest: 24</p>
|
||||||
@ -942,33 +942,33 @@ Longest: 24</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="left">Escherichia coli</td>
|
<td align="left">Escherichia coli</td>
|
||||||
<td align="right">7,456</td>
|
<td align="right">7,385</td>
|
||||||
<td align="right">49.6%</td>
|
<td align="right">49.3%</td>
|
||||||
<td align="right">7,456</td>
|
<td align="right">7,385</td>
|
||||||
<td align="right">49.6%</td>
|
<td align="right">49.3%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">2</td>
|
||||||
<td align="left">Staphylococcus aureus</td>
|
<td align="left">Staphylococcus aureus</td>
|
||||||
<td align="right">3,709</td>
|
<td align="right">3,709</td>
|
||||||
<td align="right">24.7%</td>
|
<td align="right">24.8%</td>
|
||||||
<td align="right">11,165</td>
|
<td align="right">11,094</td>
|
||||||
<td align="right">74.3%</td>
|
<td align="right">74.1%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">3</td>
|
<td align="left">3</td>
|
||||||
<td align="left">Streptococcus pneumoniae</td>
|
<td align="left">Streptococcus pneumoniae</td>
|
||||||
<td align="right">2,267</td>
|
<td align="right">2,340</td>
|
||||||
<td align="right">15.1%</td>
|
<td align="right">15.6%</td>
|
||||||
<td align="right">13,432</td>
|
<td align="right">13,434</td>
|
||||||
<td align="right">89.4%</td>
|
<td align="right">89.7%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">4</td>
|
<td align="left">4</td>
|
||||||
<td align="left">Klebsiella pneumoniae</td>
|
<td align="left">Klebsiella pneumoniae</td>
|
||||||
<td align="right">1,595</td>
|
<td align="right">1,539</td>
|
||||||
<td align="right">10.6%</td>
|
<td align="right">10.3%</td>
|
||||||
<td align="right">15,027</td>
|
<td align="right">14,973</td>
|
||||||
<td align="right">100.0%</td>
|
<td align="right">100.0%</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
@ -979,7 +979,7 @@ Longest: 24</p>
|
|||||||
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
|
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
|
||||||
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
|
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
|
||||||
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
|
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
|
||||||
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4685566</span></a></code></pre></div>
|
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4646363</span></a></code></pre></div>
|
||||||
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||||
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
@ -992,19 +992,19 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">0.4574111</td>
|
<td align="center">0.4721851</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">0.4789054</td>
|
<td align="center">0.4554570</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">0.4639895</td>
|
<td align="center">0.4683715</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">0.4705098</td>
|
<td align="center">0.4663838</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -1022,23 +1022,23 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital A</td>
|
<td align="center">Hospital A</td>
|
||||||
<td align="center">0.4574111</td>
|
<td align="center">0.4721851</td>
|
||||||
<td align="center">4473</td>
|
<td align="center">4494</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital B</td>
|
<td align="center">Hospital B</td>
|
||||||
<td align="center">0.4789054</td>
|
<td align="center">0.4554570</td>
|
||||||
<td align="center">5262</td>
|
<td align="center">5186</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Hospital C</td>
|
<td align="center">Hospital C</td>
|
||||||
<td align="center">0.4639895</td>
|
<td align="center">0.4683715</td>
|
||||||
<td align="center">2291</td>
|
<td align="center">2229</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Hospital D</td>
|
<td align="center">Hospital D</td>
|
||||||
<td align="center">0.4705098</td>
|
<td align="center">0.4663838</td>
|
||||||
<td align="center">3001</td>
|
<td align="center">3064</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@ -1058,27 +1058,27 @@ Longest: 24</p>
|
|||||||
<tbody>
|
<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Escherichia</td>
|
<td align="center">Escherichia</td>
|
||||||
<td align="center">0.9244903</td>
|
<td align="center">0.9243060</td>
|
||||||
<td align="center">0.8964592</td>
|
<td align="center">0.8958700</td>
|
||||||
<td align="center">0.9936964</td>
|
<td align="center">0.9932295</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Klebsiella</td>
|
<td align="center">Klebsiella</td>
|
||||||
<td align="center">0.8244514</td>
|
<td align="center">0.8401559</td>
|
||||||
<td align="center">0.9059561</td>
|
<td align="center">0.8992853</td>
|
||||||
<td align="center">0.9811912</td>
|
<td align="center">0.9837557</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="center">Staphylococcus</td>
|
<td align="center">Staphylococcus</td>
|
||||||
<td align="center">0.9266649</td>
|
<td align="center">0.9280129</td>
|
||||||
<td align="center">0.9201941</td>
|
<td align="center">0.9263953</td>
|
||||||
<td align="center">0.9935293</td>
|
<td align="center">0.9967646</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="center">Streptococcus</td>
|
<td align="center">Streptococcus</td>
|
||||||
<td align="center">0.6060873</td>
|
<td align="center">0.6303419</td>
|
||||||
<td align="center">0.0000000</td>
|
<td align="center">0.0000000</td>
|
||||||
<td align="center">0.6060873</td>
|
<td align="center">0.6303419</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
|
Before Width: | Height: | Size: 63 KiB After Width: | Height: | Size: 63 KiB |
Before Width: | Height: | Size: 51 KiB After Width: | Height: | Size: 51 KiB |
Before Width: | Height: | Size: 102 KiB After Width: | Height: | Size: 102 KiB |
Before Width: | Height: | Size: 77 KiB After Width: | Height: | Size: 77 KiB |
@ -40,7 +40,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -185,7 +185,7 @@
|
|||||||
<h1>How to determine multi-drug resistance (MDR)</h1>
|
<h1>How to determine multi-drug resistance (MDR)</h1>
|
||||||
<h4 class="author">Matthijs S. Berends</h4>
|
<h4 class="author">Matthijs S. Berends</h4>
|
||||||
|
|
||||||
<h4 class="date">06 August 2019</h4>
|
<h4 class="date">07 August 2019</h4>
|
||||||
|
|
||||||
|
|
||||||
<div class="hidden name"><code>MDR.Rmd</code></div>
|
<div class="hidden name"><code>MDR.Rmd</code></div>
|
||||||
@ -228,16 +228,16 @@
|
|||||||
<p>The data set looks like this now:</p>
|
<p>The data set looks like this now:</p>
|
||||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
|
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
|
||||||
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
|
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
|
||||||
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R R S R S S</span></a>
|
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R R S S I S</span></a>
|
||||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R R S R S S</span></a>
|
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 S S S R R R</span></a>
|
||||||
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R S R S S R</span></a>
|
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 S S S S R R</span></a>
|
||||||
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 R I S R R R</span></a>
|
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S S R S R</span></a>
|
||||||
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 I S S R I S</span></a>
|
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 S R R R R R</span></a>
|
||||||
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R R R S I S</span></a>
|
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 S S R S S I</span></a>
|
||||||
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
|
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
|
||||||
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 I</span></a>
|
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 S</span></a>
|
||||||
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</span></a>
|
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 R</span></a>
|
||||||
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 I</span></a>
|
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 S</span></a>
|
||||||
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 S</span></a>
|
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 S</span></a>
|
||||||
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 S</span></a>
|
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 S</span></a>
|
||||||
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
|
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
|
||||||
@ -272,39 +272,39 @@ Unique: 5</p>
|
|||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">1</td>
|
<td align="left">1</td>
|
||||||
<td align="left">Mono-resistance</td>
|
<td align="left">Mono-resistance</td>
|
||||||
<td align="right">3264</td>
|
<td align="right">3271</td>
|
||||||
<td align="right">65.3%</td>
|
<td align="right">65.4%</td>
|
||||||
<td align="right">3264</td>
|
<td align="right">3271</td>
|
||||||
<td align="right">65.3%</td>
|
<td align="right">65.4%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">2</td>
|
<td align="left">2</td>
|
||||||
<td align="left">Negative</td>
|
<td align="left">Negative</td>
|
||||||
<td align="right">627</td>
|
<td align="right">643</td>
|
||||||
<td align="right">12.5%</td>
|
<td align="right">12.9%</td>
|
||||||
<td align="right">3891</td>
|
<td align="right">3914</td>
|
||||||
<td align="right">77.8%</td>
|
<td align="right">78.3%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">3</td>
|
<td align="left">3</td>
|
||||||
<td align="left">Multidrug resistance</td>
|
<td align="left">Multidrug resistance</td>
|
||||||
<td align="right">607</td>
|
<td align="right">582</td>
|
||||||
<td align="right">12.1%</td>
|
<td align="right">11.6%</td>
|
||||||
<td align="right">4498</td>
|
<td align="right">4496</td>
|
||||||
<td align="right">90.0%</td>
|
<td align="right">89.9%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">4</td>
|
<td align="left">4</td>
|
||||||
<td align="left">Poly-resistance</td>
|
<td align="left">Poly-resistance</td>
|
||||||
<td align="right">288</td>
|
<td align="right">287</td>
|
||||||
<td align="right">5.8%</td>
|
<td align="right">5.7%</td>
|
||||||
<td align="right">4786</td>
|
<td align="right">4783</td>
|
||||||
<td align="right">95.7%</td>
|
<td align="right">95.7%</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">5</td>
|
<td align="left">5</td>
|
||||||
<td align="left">Extensive drug resistance</td>
|
<td align="left">Extensive drug resistance</td>
|
||||||
<td align="right">214</td>
|
<td align="right">217</td>
|
||||||
<td align="right">4.3%</td>
|
<td align="right">4.3%</td>
|
||||||
<td align="right">5000</td>
|
<td align="right">5000</td>
|
||||||
<td align="right">100.0%</td>
|
<td align="right">100.0%</td>
|
||||||
|
@ -40,7 +40,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -185,7 +185,7 @@
|
|||||||
<h1>How to work with WHONET data</h1>
|
<h1>How to work with WHONET data</h1>
|
||||||
<h4 class="author">Matthijs S. Berends</h4>
|
<h4 class="author">Matthijs S. Berends</h4>
|
||||||
|
|
||||||
<h4 class="date">06 August 2019</h4>
|
<h4 class="date">07 August 2019</h4>
|
||||||
|
|
||||||
|
|
||||||
<div class="hidden name"><code>WHONET.Rmd</code></div>
|
<div class="hidden name"><code>WHONET.Rmd</code></div>
|
||||||
|
@ -78,7 +78,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -78,7 +78,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -42,7 +42,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -78,7 +78,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -225,9 +225,9 @@
|
|||||||
|
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div id="amr-0-7-1-9026" class="section level1">
|
<div id="amr-0-7-1-9027" class="section level1">
|
||||||
<h1 class="page-header">
|
<h1 class="page-header">
|
||||||
<a href="#amr-0-7-1-9026" class="anchor"></a>AMR 0.7.1.9026<small> Unreleased </small>
|
<a href="#amr-0-7-1-9027" class="anchor"></a>AMR 0.7.1.9027<small> Unreleased </small>
|
||||||
</h1>
|
</h1>
|
||||||
<div id="breaking" class="section level3">
|
<div id="breaking" class="section level3">
|
||||||
<h3 class="hasAnchor">
|
<h3 class="hasAnchor">
|
||||||
@ -273,7 +273,18 @@
|
|||||||
<h3 class="hasAnchor">
|
<h3 class="hasAnchor">
|
||||||
<a href="#changed" class="anchor"></a>Changed</h3>
|
<a href="#changed" class="anchor"></a>Changed</h3>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> that caused an error when the input was a specific kind of <code>tibble</code>
|
<li>Added more informative errors and warnings to <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Added tibble printing support for classes <code>rsi</code>, <code>mic</code>, <code>ab</code> and <code>mo</code>. When using tibbles containing antibiotic columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red:</p>
|
||||||
|
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">(run this on your own console, as this page does not support colour printing)</a>
|
||||||
|
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">tibble</span>(<span class="dt">mo =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(AMR<span class="op">::</span>microorganisms<span class="op">$</span>fullname, <span class="dv">10</span>),</a>
|
||||||
|
<a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="dt">drug1 =</span> <span class="kw"><a href="../reference/as.rsi.html">as.rsi</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>), <span class="dv">10</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>, </a>
|
||||||
|
<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.6</span>, <span class="fl">0.1</span>, <span class="fl">0.3</span>))),</a>
|
||||||
|
<a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="dt">drug2 =</span> <span class="kw"><a href="../reference/as.rsi.html">as.rsi</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>), <span class="dv">10</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</a>
|
||||||
|
<a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.6</span>, <span class="fl">0.1</span>, <span class="fl">0.3</span>))),</a>
|
||||||
|
<a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="dt">drug3 =</span> <span class="kw"><a href="../reference/as.rsi.html">as.rsi</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>), <span class="dv">10</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</a>
|
||||||
|
<a class="sourceLine" id="cb2-8" data-line-number="8"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.6</span>, <span class="fl">0.1</span>, <span class="fl">0.3</span>))))</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li>
|
<li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li>
|
||||||
<li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code>
|
<li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code>
|
||||||
@ -294,6 +305,7 @@
|
|||||||
<li>The <code>antibiotics</code> data set is now sorted by name</li>
|
<li>The <code>antibiotics</code> data set is now sorted by name</li>
|
||||||
<li>Using verbose mode with <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> returns more informative and readable output</li>
|
<li>Using verbose mode with <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> returns more informative and readable output</li>
|
||||||
<li>Speed improvement for <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30 times faster for antibiotic abbreviations</li>
|
<li>Speed improvement for <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30 times faster for antibiotic abbreviations</li>
|
||||||
|
<li><p>Using factors as input for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now adds missing factors levels when the function changes antibiotic results</p></li>
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
@ -307,14 +319,14 @@
|
|||||||
<ul>
|
<ul>
|
||||||
<li>
|
<li>
|
||||||
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
|
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
|
||||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="st"> </span><span class="kw">select</span>(AMX, CIP) <span class="op">%>%</span></a>
|
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="st"> </span><span class="kw">select</span>(AMX, CIP) <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
|
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a>
|
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a>
|
||||||
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
|
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
|
||||||
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
|
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
|
||||||
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
|
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
|
||||||
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
|
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
|
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
|
||||||
@ -332,12 +344,12 @@
|
|||||||
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
|
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
|
||||||
</ul>
|
</ul>
|
||||||
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
|
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
|
||||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
|
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||||
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a>
|
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a>
|
||||||
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
|
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a>
|
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a>
|
||||||
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
|
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
|
||||||
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
|
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
|
<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
|
||||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
||||||
@ -436,14 +448,14 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
|
|||||||
<li>when all values are unique it now shows a message instead of a warning</li>
|
<li>when all values are unique it now shows a message instead of a warning</li>
|
||||||
<li>
|
<li>
|
||||||
<p>support for boxplots:</p>
|
<p>support for boxplots:</p>
|
||||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="st"> </span><span class="kw">freq</span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="st"> </span><span class="kw">freq</span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
|
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
|
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
|
||||||
<a class="sourceLine" id="cb4-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb5-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="st"> </span><span class="kw">freq</span>(age) <span class="op">%>%</span></a>
|
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="st"> </span><span class="kw">freq</span>(age) <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
|
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
@ -528,32 +540,32 @@ This data is updated annually - check the included version with the new function
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
||||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||||
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
||||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||||
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||||
<a class="sourceLine" id="cb6-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
<a class="sourceLine" id="cb7-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||||
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">ab_property -><span class="st"> </span><span class="kw">atc_property</span>()</a>
|
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">ab_property -><span class="st"> </span><span class="kw">atc_property</span>()</a>
|
||||||
<a class="sourceLine" id="cb7-2" data-line-number="2">ab_name -><span class="st"> </span><span class="kw">atc_name</span>()</a>
|
<a class="sourceLine" id="cb8-2" data-line-number="2">ab_name -><span class="st"> </span><span class="kw">atc_name</span>()</a>
|
||||||
<a class="sourceLine" id="cb7-3" data-line-number="3">ab_official -><span class="st"> </span><span class="kw">atc_official</span>()</a>
|
<a class="sourceLine" id="cb8-3" data-line-number="3">ab_official -><span class="st"> </span><span class="kw">atc_official</span>()</a>
|
||||||
<a class="sourceLine" id="cb7-4" data-line-number="4">ab_trivial_nl -><span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
|
<a class="sourceLine" id="cb8-4" data-line-number="4">ab_trivial_nl -><span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
|
||||||
<a class="sourceLine" id="cb7-5" data-line-number="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
<a class="sourceLine" id="cb8-5" data-line-number="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||||
<a class="sourceLine" id="cb7-6" data-line-number="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
<a class="sourceLine" id="cb8-6" data-line-number="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||||
<a class="sourceLine" id="cb7-7" data-line-number="7">ab_tradenames -><span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
|
<a class="sourceLine" id="cb8-7" data-line-number="7">ab_tradenames -><span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
|
||||||
These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
|
These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
|
||||||
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
|
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
|
||||||
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
|
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
|
||||||
@ -565,20 +577,20 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
|
|||||||
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
|
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
|
||||||
<li>
|
<li>
|
||||||
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
||||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||||
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
|
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
|
||||||
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
|
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
|
||||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
||||||
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="co"># or</span></a>
|
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># or</span></a>
|
||||||
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
||||||
<p>is equal to:</p>
|
<p>is equal to:</p>
|
||||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
<a class="sourceLine" id="cb11-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
|
<li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
|
||||||
</li>
|
</li>
|
||||||
@ -607,33 +619,33 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
|
|||||||
<ul>
|
<ul>
|
||||||
<li>
|
<li>
|
||||||
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
|
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
|
||||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
||||||
<a class="sourceLine" id="cb11-2" data-line-number="2"></a>
|
<a class="sourceLine" id="cb12-2" data-line-number="2"></a>
|
||||||
<a class="sourceLine" id="cb11-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
<a class="sourceLine" id="cb12-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
||||||
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
<a class="sourceLine" id="cb12-4" data-line-number="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
||||||
<a class="sourceLine" id="cb11-5" data-line-number="5"></a>
|
<a class="sourceLine" id="cb12-5" data-line-number="5"></a>
|
||||||
<a class="sourceLine" id="cb11-6" data-line-number="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
<a class="sourceLine" id="cb12-6" data-line-number="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
||||||
<a class="sourceLine" id="cb11-7" data-line-number="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></pre></div>
|
<a class="sourceLine" id="cb12-7" data-line-number="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
|
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
|
||||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="co"># equal:</span></a>
|
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="co"># equal:</span></a>
|
||||||
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
||||||
<a class="sourceLine" id="cb12-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
||||||
<a class="sourceLine" id="cb12-4" data-line-number="4"></a>
|
<a class="sourceLine" id="cb13-4" data-line-number="4"></a>
|
||||||
<a class="sourceLine" id="cb12-5" data-line-number="5"><span class="co"># also equal:</span></a>
|
<a class="sourceLine" id="cb13-5" data-line-number="5"><span class="co"># also equal:</span></a>
|
||||||
<a class="sourceLine" id="cb12-6" data-line-number="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
<a class="sourceLine" id="cb13-6" data-line-number="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
||||||
<a class="sourceLine" id="cb12-7" data-line-number="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
<a class="sourceLine" id="cb13-7" data-line-number="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
||||||
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
|
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
|
||||||
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
|
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
|
||||||
</li>
|
</li>
|
||||||
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
|
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
||||||
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="co"># Warning: </span></a>
|
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="co"># Warning: </span></a>
|
||||||
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
||||||
<a class="sourceLine" id="cb13-4" data-line-number="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
<a class="sourceLine" id="cb14-4" data-line-number="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Fix for vector containing only empty values</li>
|
<li>Fix for vector containing only empty values</li>
|
||||||
<li>Finds better results when input is in other languages</li>
|
<li>Finds better results when input is in other languages</li>
|
||||||
@ -679,19 +691,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
<ul>
|
<ul>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
||||||
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
|
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
|
||||||
<a class="sourceLine" id="cb14-3" data-line-number="3">septic_patients <span class="op">%>%</span></a>
|
<a class="sourceLine" id="cb15-3" data-line-number="3">septic_patients <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb14-4" data-line-number="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb14-5" data-line-number="5"><span class="st"> </span><span class="kw">freq</span>(genus)</a>
|
<a class="sourceLine" id="cb15-5" data-line-number="5"><span class="st"> </span><span class="kw">freq</span>(genus)</a>
|
||||||
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
|
<a class="sourceLine" id="cb15-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
|
||||||
<a class="sourceLine" id="cb14-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb15-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb14-8" data-line-number="8"><span class="st"> </span><span class="kw">freq</span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="st"> </span><span class="kw">freq</span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||||
<a class="sourceLine" id="cb14-9" data-line-number="9"></a>
|
<a class="sourceLine" id="cb15-9" data-line-number="9"></a>
|
||||||
<a class="sourceLine" id="cb14-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
|
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||||
<a class="sourceLine" id="cb14-11" data-line-number="11">septic_patients <span class="op">%>%</span></a>
|
<a class="sourceLine" id="cb15-11" data-line-number="11">septic_patients <span class="op">%>%</span></a>
|
||||||
<a class="sourceLine" id="cb14-12" data-line-number="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb15-12" data-line-number="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb14-13" data-line-number="13"><span class="st"> </span><span class="kw">freq</span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
<a class="sourceLine" id="cb15-13" data-line-number="13"><span class="st"> </span><span class="kw">freq</span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Header info is now available as a list, with the <code>header</code> function</li>
|
<li>Header info is now available as a list, with the <code>header</code> function</li>
|
||||||
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
|
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
|
||||||
@ -766,10 +778,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
|
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
|
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
|
||||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
||||||
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
<a class="sourceLine" id="cb16-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
||||||
<a class="sourceLine" id="cb15-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
||||||
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
|
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
|
||||||
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
|
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
|
||||||
@ -782,15 +794,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
<ul>
|
<ul>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for grouping variables, test with:</p>
|
<p>Support for grouping variables, test with:</p>
|
||||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb16-2" data-line-number="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div>
|
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for (un)selecting columns:</p>
|
<p>Support for (un)selecting columns:</p>
|
||||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="st"> </span><span class="kw">freq</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw">freq</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||||
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
<a class="sourceLine" id="cb18-3" data-line-number="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/Deprecated">hms::is.hms</a></code>
|
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/Deprecated">hms::is.hms</a></code>
|
||||||
</li>
|
</li>
|
||||||
@ -870,18 +882,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||||
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
|
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
|
||||||
<a class="sourceLine" id="cb18-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
<a class="sourceLine" id="cb19-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
||||||
<a class="sourceLine" id="cb18-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
<a class="sourceLine" id="cb19-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
||||||
<a class="sourceLine" id="cb18-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
<a class="sourceLine" id="cb19-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
||||||
<a class="sourceLine" id="cb18-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
|
<a class="sourceLine" id="cb19-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
|
||||||
<a class="sourceLine" id="cb18-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
<a class="sourceLine" id="cb19-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
||||||
<a class="sourceLine" id="cb18-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
||||||
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
||||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
||||||
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
||||||
<a class="sourceLine" id="cb19-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
<a class="sourceLine" id="cb20-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
|
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
|
||||||
<ul>
|
<ul>
|
||||||
@ -892,18 +904,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
|
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
|
||||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||||
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
||||||
<a class="sourceLine" id="cb20-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
||||||
<a class="sourceLine" id="cb20-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
<a class="sourceLine" id="cb21-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
||||||
<a class="sourceLine" id="cb20-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
<a class="sourceLine" id="cb21-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||||
<a class="sourceLine" id="cb20-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
<a class="sourceLine" id="cb21-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||||
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
||||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||||
<a class="sourceLine" id="cb21-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
<a class="sourceLine" id="cb22-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||||
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
|
<a class="sourceLine" id="cb22-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
|
||||||
<a class="sourceLine" id="cb21-4" data-line-number="4"><span class="co"># min median max neval</span></a>
|
<a class="sourceLine" id="cb22-4" data-line-number="4"><span class="co"># min median max neval</span></a>
|
||||||
<a class="sourceLine" id="cb21-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
<a class="sourceLine" id="cb22-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
|
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
|
||||||
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
|
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
|
||||||
@ -931,12 +943,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
|
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
|
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
|
||||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a>
|
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a>
|
||||||
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
|
<a class="sourceLine" id="cb23-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||||
<a class="sourceLine" id="cb22-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
<a class="sourceLine" id="cb23-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||||
<a class="sourceLine" id="cb22-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
<a class="sourceLine" id="cb23-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||||
<a class="sourceLine" id="cb22-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
<a class="sourceLine" id="cb23-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||||
<a class="sourceLine" id="cb22-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
<a class="sourceLine" id="cb23-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
|
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
|
||||||
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
|
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
|
||||||
@ -947,13 +959,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
||||||
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
||||||
<a class="sourceLine" id="cb23-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
|
<a class="sourceLine" id="cb24-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
|
||||||
<a class="sourceLine" id="cb23-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
<a class="sourceLine" id="cb24-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
||||||
<a class="sourceLine" id="cb23-4" data-line-number="4"></a>
|
<a class="sourceLine" id="cb24-4" data-line-number="4"></a>
|
||||||
<a class="sourceLine" id="cb23-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
|
<a class="sourceLine" id="cb24-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
|
||||||
<a class="sourceLine" id="cb23-6" data-line-number="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
|
<a class="sourceLine" id="cb24-6" data-line-number="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
|
||||||
<a class="sourceLine" id="cb23-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
<a class="sourceLine" id="cb24-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
|
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
|
||||||
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
|
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
|
||||||
@ -967,12 +979,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||||
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||||
<a class="sourceLine" id="cb24-2" data-line-number="2"><span class="kw">freq</span>(my_matrix)</a></code></pre></div>
|
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="kw">freq</span>(my_matrix)</a></code></pre></div>
|
||||||
<p>For lists, subsetting is possible:</p>
|
<p>For lists, subsetting is possible:</p>
|
||||||
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||||
<a class="sourceLine" id="cb25-2" data-line-number="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw">freq</span>(age)</a>
|
<a class="sourceLine" id="cb26-2" data-line-number="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw">freq</span>(age)</a>
|
||||||
<a class="sourceLine" id="cb25-3" data-line-number="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div>
|
<a class="sourceLine" id="cb26-3" data-line-number="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
@ -1206,7 +1218,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||||||
<div id="tocnav">
|
<div id="tocnav">
|
||||||
<h2>Contents</h2>
|
<h2>Contents</h2>
|
||||||
<ul class="nav nav-pills nav-stacked">
|
<ul class="nav nav-pills nav-stacked">
|
||||||
<li><a href="#amr-0-7-1-9026">0.7.1.9026</a></li>
|
<li><a href="#amr-0-7-1-9027">0.7.1.9027</a></li>
|
||||||
<li><a href="#amr-0-7-1">0.7.1</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-0-7-0">0.7.0</a></li>
|
||||||
<li><a href="#amr-0-6-1">0.6.1</a></li>
|
<li><a href="#amr-0-6-1">0.6.1</a></li>
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9015</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
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</span>
|
||||||
</div>
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||||||
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|
||||||
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@ -78,7 +78,7 @@
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|||||||
</button>
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</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
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|
||||||
|
|
||||||
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@ -80,7 +80,7 @@
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|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -80,7 +80,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
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|
||||||
</div>
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||||||
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@ -80,7 +80,7 @@
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</button>
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</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
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|
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@ -80,7 +80,7 @@
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</button>
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</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
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</span>
|
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</div>
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@ -80,7 +80,7 @@
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|||||||
</button>
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</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">0.7.1.9026</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
|
||||||
</span>
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|
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</div>
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@ -235,14 +235,12 @@
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</div>
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|
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<pre class="usage"><span class='fu'>resistance_predict</span>(<span class='no'>x</span>, <span class='no'>col_ab</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
<pre class="usage"><span class='fu'>resistance_predict</span>(<span class='no'>x</span>, <span class='no'>col_ab</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
||||||
<span class='kw'>year_max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_every</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
|
<span class='kw'>year_max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_every</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
||||||
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>, <span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
<span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||||
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
|
||||||
|
|
||||||
<span class='fu'>rsi_predict</span>(<span class='no'>x</span>, <span class='no'>col_ab</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
<span class='fu'>rsi_predict</span>(<span class='no'>x</span>, <span class='no'>col_ab</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
||||||
<span class='kw'>year_max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_every</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
|
<span class='kw'>year_max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year_every</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
||||||
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>, <span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
<span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||||
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
|
||||||
|
|
||||||
<span class='co'># S3 method for resistance_predict</span>
|
<span class='co'># S3 method for resistance_predict</span>
|
||||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>,
|
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>,
|
||||||
@ -284,7 +282,7 @@
|
|||||||
</tr>
|
</tr>
|
||||||
<tr>
|
<tr>
|
||||||
<th>model</th>
|
<th>model</th>
|
||||||
<td><p>the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution (i.e. using <code><a href='https://www.rdocumentation.org/packages/stats/topics/glm'>glm</a>(..., family = <a href='https://www.rdocumentation.org/packages/stats/topics/family'>binomial</a>)</code>), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.</p></td>
|
<td><p>the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using <code><a href='https://www.rdocumentation.org/packages/stats/topics/glm'>glm</a>(..., family = <a href='https://www.rdocumentation.org/packages/stats/topics/family'>binomial</a>)</code>), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for all valid options.</p></td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr>
|
<tr>
|
||||||
<th>I_as_S</th>
|
<th>I_as_S</th>
|
||||||
|
@ -8,14 +8,12 @@
|
|||||||
\title{Predict antimicrobial resistance}
|
\title{Predict antimicrobial resistance}
|
||||||
\usage{
|
\usage{
|
||||||
resistance_predict(x, col_ab, col_date = NULL, year_min = NULL,
|
resistance_predict(x, col_ab, col_date = NULL, year_min = NULL,
|
||||||
year_max = NULL, year_every = 1, minimum = 30,
|
year_max = NULL, year_every = 1, minimum = 30, model = NULL,
|
||||||
model = "binomial", I_as_S = TRUE, preserve_measurements = TRUE,
|
I_as_S = TRUE, preserve_measurements = TRUE, info = TRUE, ...)
|
||||||
info = TRUE, ...)
|
|
||||||
|
|
||||||
rsi_predict(x, col_ab, col_date = NULL, year_min = NULL,
|
rsi_predict(x, col_ab, col_date = NULL, year_min = NULL,
|
||||||
year_max = NULL, year_every = 1, minimum = 30,
|
year_max = NULL, year_every = 1, minimum = 30, model = NULL,
|
||||||
model = "binomial", I_as_S = TRUE, preserve_measurements = TRUE,
|
I_as_S = TRUE, preserve_measurements = TRUE, info = TRUE, ...)
|
||||||
info = TRUE, ...)
|
|
||||||
|
|
||||||
\method{plot}{resistance_predict}(x,
|
\method{plot}{resistance_predict}(x,
|
||||||
main = paste("Resistance Prediction of", x_name), ...)
|
main = paste("Resistance Prediction of", x_name), ...)
|
||||||
@ -38,7 +36,7 @@ ggplot_rsi_predict(x, main = paste("Resistance Prediction of", x_name),
|
|||||||
|
|
||||||
\item{minimum}{minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.}
|
\item{minimum}{minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.}
|
||||||
|
|
||||||
\item{model}{the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution (i.e. using \code{\link{glm}(..., family = \link{binomial})}), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.}
|
\item{model}{the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using \code{\link{glm}(..., family = \link{binomial})}), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for all valid options.}
|
||||||
|
|
||||||
\item{I_as_S}{a logical to indicate whether values \code{I} should be treated as \code{S} (will otherwise be treated as \code{R})}
|
\item{I_as_S}{a logical to indicate whether values \code{I} should be treated as \code{S} (will otherwise be treated as \code{R})}
|
||||||
|
|
||||||
|
@ -35,6 +35,8 @@ test_that("EUCAST rules work", {
|
|||||||
expect_error(eucast_rules(data.frame(a = "test")))
|
expect_error(eucast_rules(data.frame(a = "test")))
|
||||||
expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
|
expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
|
||||||
|
|
||||||
|
expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S")))
|
||||||
|
|
||||||
expect_identical(colnames(septic_patients),
|
expect_identical(colnames(septic_patients),
|
||||||
colnames(suppressWarnings(eucast_rules(septic_patients))))
|
colnames(suppressWarnings(eucast_rules(septic_patients))))
|
||||||
|
|
||||||
|
@ -116,5 +116,6 @@ test_that("portions works", {
|
|||||||
septic_patients$AMX %>% portion_R())
|
septic_patients$AMX %>% portion_R())
|
||||||
)
|
)
|
||||||
|
|
||||||
|
expect_error(portion_df(c("A", "B", "C")))
|
||||||
|
expect_error(portion_df(septic_patients[,"date"]))
|
||||||
})
|
})
|
||||||
|
@ -32,7 +32,7 @@ test_that("prediction of rsi works", {
|
|||||||
# # AMX resistance will increase according to data set `septic_patients`
|
# # AMX resistance will increase according to data set `septic_patients`
|
||||||
# expect_true(AMX_R[3] < AMX_R[20])
|
# expect_true(AMX_R[3] < AMX_R[20])
|
||||||
|
|
||||||
x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)
|
x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010, model = "binomial")
|
||||||
plot(x)
|
plot(x)
|
||||||
ggplot_rsi_predict(x)
|
ggplot_rsi_predict(x)
|
||||||
expect_error(ggplot_rsi_predict(septic_patients))
|
expect_error(ggplot_rsi_predict(septic_patients))
|
||||||
@ -61,19 +61,27 @@ test_that("prediction of rsi works", {
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col_date = "date",
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col_date = "date",
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info = TRUE))
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info = TRUE))
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expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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model = "binomial",
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col_ab = "NOT EXISTING COLUMN",
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col_ab = "NOT EXISTING COLUMN",
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col_date = "date",
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col_date = "date",
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info = TRUE))
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info = TRUE))
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expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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model = "binomial",
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col_ab = "AMX",
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col_date = "NOT EXISTING COLUMN",
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info = TRUE))
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expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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col_ab = "AMX",
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col_ab = "AMX",
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col_date = "NOT EXISTING COLUMN",
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col_date = "NOT EXISTING COLUMN",
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info = TRUE))
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info = TRUE))
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expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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col_ab = "AMX",
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col_date = "date",
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info = TRUE))
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# almost all E. coli are MEM S in the Netherlands :)
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# almost all E. coli are MEM S in the Netherlands :)
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expect_error(resistance_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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expect_error(resistance_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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model = "binomial",
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col_ab = "MEM",
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col_ab = "MEM",
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col_date = "date",
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col_date = "date",
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info = TRUE))
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info = TRUE))
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expect_error(portion_df(c("A", "B", "C")))
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expect_error(portion_df(septic_patients[,"date"]))
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})
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})
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