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(v0.7.1.9027) tibble printing

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dr. M.S. (Matthijs) Berends 2019-08-07 15:37:39 +02:00
parent 14c47da656
commit 90c874025a
42 changed files with 946 additions and 602 deletions
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5
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9026
Date: 2019-08-06
Version: 0.7.1.9027
Date: 2019-08-07
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(
@ -53,6 +53,7 @@ Imports:
hms,
knitr (>= 1.0.0),
microbenchmark,
pillar,
rlang (>= 0.3.1),
scales,
tidyr (>= 0.7.0)

280
LICENSE Normal file
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@ -0,0 +1,280 @@
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10
NAMESPACE
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@ -18,6 +18,10 @@ S3method(freq,rsi)
S3method(kurtosis,data.frame)
S3method(kurtosis,default)
S3method(kurtosis,matrix)
S3method(pillar_shaft,ab)
S3method(pillar_shaft,mic)
S3method(pillar_shaft,mo)
S3method(pillar_shaft,rsi)
S3method(plot,mic)
S3method(plot,resistance_predict)
S3method(plot,rsi)
@ -37,6 +41,10 @@ S3method(skewness,matrix)
S3method(summary,mic)
S3method(summary,mo)
S3method(summary,rsi)
S3method(type_sum,ab)
S3method(type_sum,mic)
S3method(type_sum,mo)
S3method(type_sum,rsi)
export("%like%")
export(ab_atc)
export(ab_atc_group1)
@ -262,6 +270,8 @@ importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(microbenchmark,microbenchmark)
importFrom(pillar,pillar_shaft)
importFrom(pillar,type_sum)
importFrom(rlang,as_label)
importFrom(rlang,enquos)
importFrom(scales,percent)

16
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9026
# AMR 0.7.1.9027
### 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.
@ -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`.
### 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 deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
* Fix and speed improvement for `mo_shortname()`
@ -50,6 +61,7 @@
* The `antibiotics` data set is now sorted by name
* 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
* Using factors as input for `eucast_rules()` now adds missing factors levels when the function changes antibiotic results
# AMR 0.7.1

16
R/ab.R
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@ -262,7 +262,7 @@ is.ab <- function(x) {
#' @noRd
print.ab <- function(x, ...) {
cat("Class 'ab'\n")
print.default(as.character(x), quote = FALSE)
print(as.character(x), quote = FALSE)
}
#' @exportMethod as.data.frame.ab
@ -286,3 +286,17 @@ as.data.frame.ab <- function (x, ...) {
pull.ab <- function(.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)
}

47
R/eucast_rules.R
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@ -228,18 +228,18 @@ eucast_rules <- function(x,
warned <- FALSE
txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n") }
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE }
txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n\n") }
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING "))) }; warned <<- TRUE }
txt_ok <- function(no_of_changes) {
if (warned == FALSE) {
if (no_of_changes > 0) {
if (no_of_changes == 1) {
cat(blue(" (1 new change)\n"))
cat(blue(" (1 value changed)\n"))
} else {
cat(blue(paste0(" (", formatnr(no_of_changes), " new changes)\n")))
cat(blue(paste0(" (", formatnr(no_of_changes), " values changed)\n")))
}
} else {
cat(green(" (no new changes)\n"))
cat(green(" (no values changed)\n"))
}
warned <<- FALSE
}
@ -402,20 +402,37 @@ eucast_rules <- function(x,
x_original[rows, cols] <<- to,
warning = function(w) {
if (w$message %like% 'invalid factor level') {
warning('Value "', to, '" could not be applied to column(s) `', paste(cols, collapse = '`, `'), '` because this value is not an existing factor level. You can use as.rsi() to fix this.', call. = FALSE)
x_original <<- x_original %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
x <<- x %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
x_original[rows, cols] <<- to
warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = '`, `'), '` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antibiotic columns to guarantee the right structure.', call. = FALSE)
txt_warning()
warned <<- FALSE
} else {
warning(w$message, call. = FALSE)
txt_warning()
cat("\n") # txt_warning() does not append a "\n" on itself
}
txt_warning()
},
error = function(e) {
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
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,]
no_of_changes_this_run <- 0
@ -719,7 +736,7 @@ eucast_rules <- function(x,
mutate(plural = ifelse(n > 1, "s", ""),
txt = paste0(formatnr(n), " test result", plural, " added as ", new)) %>%
pull(txt) %>%
paste(" -", ., collapse = "\n") %>%
paste(" *", ., collapse = "\n") %>%
cat()
}
@ -748,16 +765,16 @@ eucast_rules <- function(x,
mutate(plural = ifelse(n > 1, "s", ""),
txt = paste0(formatnr(n), " test result", plural, " changed from ", old, " to ", new)) %>%
pull(txt) %>%
paste(" -", ., collapse = "\n") %>%
paste(" *", ., collapse = "\n") %>%
cat()
cat("\n")
}
cat(paste0(silver(strrep("-", options()$width - 1)), "\n"))
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) {
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"))
}
}

1
R/extended.R
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@ -45,4 +45,3 @@ scale_type.ab <- function(x) {
# "Error: Discrete value supplied to continuous scale"
"discrete"
}

19
R/mic.R
View File

@ -173,9 +173,8 @@ as.mic <- function(x, na.rm = FALSE) {
list_missing, call. = FALSE)
}
x <- factor(x, levels = lvls, ordered = TRUE)
class(x) <- c('mic', 'ordered', 'factor')
x
structure(.Data = factor(x, levels = lvls, ordered = TRUE),
class = c('mic', 'ordered', 'factor'))
}
}
@ -279,3 +278,17 @@ barplot.mic <- function(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
View File

@ -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
#' @export
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
@ -391,8 +395,7 @@ exec_as.mo <- function(x,
# all empty
if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
if (property == "mo") {
return(structure(rep(NA_character_, length(x_input)),
class = "mo"))
return(to_class_mo(rep(NA_character_, length(x_input))))
} else {
return(rep(NA_character_, length(x_input)))
}
@ -1455,7 +1458,7 @@ exec_as.mo <- function(x,
)
if (property == "mo") {
class(x) <- "mo"
x <- to_class_mo(x)
}
if (length(mo_renamed()) > 0) {
@ -1507,6 +1510,20 @@ print.mo <- function(x, ...) {
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
#' @importFrom dplyr n_distinct
#' @importFrom clean freq top_freq

3
R/mo_property.R
View File

@ -425,11 +425,10 @@ mo_validate <- function(x, property, ...) {
}
if (property == "mo") {
return(structure(x, class = "mo"))
return(to_class_mo(x))
} else if (property == "col_id") {
return(as.integer(x))
} else {
return(x)
}
}

10
R/resistance_predict.R
View File

@ -28,7 +28,7 @@
#' @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 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 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.
@ -112,7 +112,7 @@ resistance_predict <- function(x,
year_max = NULL,
year_every = 1,
minimum = 30,
model = 'binomial',
model = NULL,
I_as_S = TRUE,
preserve_measurements = TRUE,
info = TRUE,
@ -121,6 +121,10 @@ resistance_predict <- function(x,
if (nrow(x) == 0) {
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)) {
stop('Column ', col_ab, ' not found.')
@ -252,7 +256,7 @@ resistance_predict <- function(x,
se <- predictmodel$se.fit
} else {
stop('No valid model selected.')
stop('No valid model selected. See ?resistance_predict.')
}
# prepare the output dataframe

18
R/rsi.R
View File

@ -472,3 +472,21 @@ barplot.rsi <- function(height,
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)
}

115
docs/LICENSE-text.html
View File

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>
@ -224,17 +224,17 @@
<h1>License</h1>
</div>
<pre> GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
<pre>GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc., &lt;http://fsf.org/&gt;
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Copyright (C) 1989, 1991 Free Software Foundation, Inc., &lt;http://fsf.org/&gt;
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
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
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
@ -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
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.
GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
GNU GENERAL PUBLIC LICENSE
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
under the terms of this General Public License. The "Program", below,
refers to any such program or work, and a "work based on the Program"
means either the Program or any derivative work under copyright law:
that is to say, a work containing the Program or a portion of it,
that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another
language. (Hereinafter, translation is included without limitation in
the term "modification".) Each licensee is addressed as "you".
the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
@ -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).
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
conspicuously and appropriately publish on each copy an appropriate
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
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),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
@ -452,7 +452,7 @@ 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
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
@ -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
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
be similar in spirit to the present version, but may differ in detail to
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
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
to ask for permission. For software which is copyrighted by the Free
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 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
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
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,
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
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
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.
END OF TERMS AND CONDITIONS
</pre>
</div>

550
docs/articles/AMR.html
View File

@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to conduct AMR analysis</h1>
<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>
@ -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">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -210,21 +210,21 @@
</tr></thead>
<tbody>
<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">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<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">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<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">Escherichia coli</td>
<td align="center">R</td>
@ -320,71 +320,71 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-03-10</td>
<td align="center">Q5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2017-01-02</td>
<td align="center">V8</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-12-26</td>
<td align="center">G6</td>
<td align="center">Hospital C</td>
<td align="center">2013-05-08</td>
<td align="center">W2</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">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>
</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>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -406,8 +406,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,366 51.8% 10,366 51.8%
# 2 F 9,634 48.2% 20,000 100.0%</code></pre>
# 1 M 10,401 52.0% 10,401 52.0%
# 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>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 &lt;-<span class="st"> </span>data <span class="op">%&gt;%</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="cb15-5" 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="cb15-7" data-line-number="7"><span class="co"># Aerococcus sanguinicola (no new changes)</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="cb15-9" data-line-number="9"><span class="co"># Anaerobic Gram-negatives (no new changes)</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="cb15-11" data-line-number="11"><span class="co"># Campylobacter coli (no new changes)</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="cb15-13" data-line-number="13"><span class="co"># Enterobacteriales (Order) (no new changes)</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="cb15-15" data-line-number="15"><span class="co"># Haemophilus influenzae (no new changes)</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="cb15-17" data-line-number="17"><span class="co"># Moraxella catarrhalis (no new changes)</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="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (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 new changes)</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="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (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 values changed)</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 values changed)</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 values changed)</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 values changed)</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 values changed)</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 values changed)</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 values changed)</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 values changed)</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="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,329 new changes)</span></a>
<a class="sourceLine" id="cb15-26" 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="cb15-27" 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="cb15-28" 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="cb15-29" 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="cb15-30" 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="cb15-31" 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="cb15-32" data-line-number="32"><span class="co"># Table 12: Interpretive rules for aminoglycosides (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 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 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 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 (2,759 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 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 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 values changed)</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 values changed)</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="cb15-36" 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="cb15-37" 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="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
<a class="sourceLine" id="cb15-36" 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 (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 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 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 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 values changed)</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="cb15-44" 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"># =&gt; 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="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,908 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="cb15-49" data-line-number="49"><span class="co"># - 4,680 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="cb15-51" data-line-number="51"><span class="co"># - 326 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="cb15-53" data-line-number="53"><span class="co"># - 13 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; 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="cb15-49" 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"># * 1,119 test results changed from I to S</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"># * 1,664 test results changed from R to S</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="cb15-55" 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 id="adding-new-variables" class="section level1">
<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="cb17-4" 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="cb17-6" data-line-number="6"><span class="co"># =&gt; 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"># =&gt; 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>
<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 &lt;-<span class="st"> </span>data <span class="op">%&gt;%</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>
@ -508,7 +508,7 @@
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<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">
<thead><tr class="header">
<th align="center">isolate</th>
@ -524,21 +524,21 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-07-24</td>
<td align="center">C10</td>
<td align="center">2010-04-02</td>
<td align="center">M4</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-12-03</td>
<td align="center">C10</td>
<td align="center">2010-05-26</td>
<td align="center">M4</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>
@ -546,10 +546,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-12-19</td>
<td align="center">C10</td>
<td align="center">2010-07-15</td>
<td align="center">M4</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>
@ -557,10 +557,10 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2011-02-18</td>
<td align="center">C10</td>
<td align="center">2010-09-11</td>
<td align="center">M4</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>
@ -568,21 +568,21 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-06-26</td>
<td align="center">C10</td>
<td align="center">2010-11-13</td>
<td align="center">M4</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">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-06-28</td>
<td align="center">C10</td>
<td align="center">2010-11-16</td>
<td align="center">M4</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>
@ -590,43 +590,43 @@
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-06-30</td>
<td align="center">C10</td>
<td align="center">2011-01-03</td>
<td align="center">M4</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-08-29</td>
<td align="center">C10</td>
<td align="center">2011-03-16</td>
<td align="center">M4</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">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-10-03</td>
<td align="center">C10</td>
<td align="center">2011-04-21</td>
<td align="center">M4</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-12-30</td>
<td align="center">C10</td>
<td align="center">2011-04-24</td>
<td align="center">M4</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>
@ -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="cb20-8" 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="cb20-10" data-line-number="10"><span class="co"># =&gt; 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"># =&gt; Found 14,973 first weighted isolates (74.9% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -662,22 +662,22 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-07-24</td>
<td align="center">C10</td>
<td align="center">2010-04-02</td>
<td align="center">M4</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-12-03</td>
<td align="center">C10</td>
<td align="center">2010-05-26</td>
<td align="center">M4</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>
@ -686,10 +686,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-12-19</td>
<td align="center">C10</td>
<td align="center">2010-07-15</td>
<td align="center">M4</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>
@ -698,10 +698,10 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2011-02-18</td>
<td align="center">C10</td>
<td align="center">2010-09-11</td>
<td align="center">M4</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>
@ -710,83 +710,83 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-06-26</td>
<td align="center">C10</td>
<td align="center">2010-11-13</td>
<td align="center">M4</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">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-06-28</td>
<td align="center">C10</td>
<td align="center">2010-11-16</td>
<td align="center">M4</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-06-30</td>
<td align="center">C10</td>
<td align="center">2011-01-03</td>
<td align="center">M4</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">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>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-08-29</td>
<td align="center">C10</td>
<td align="center">2011-03-16</td>
<td align="center">M4</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">TRUE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-10-03</td>
<td align="center">C10</td>
<td align="center">2011-04-21</td>
<td align="center">M4</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-12-30</td>
<td align="center">C10</td>
<td align="center">2011-04-24</td>
<td align="center">M4</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</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>
<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 &lt;-<span class="st"> </span>data <span class="op">%&gt;%</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>
<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>
<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 &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</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>
@ -811,64 +811,64 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2017-03-10</td>
<td align="center">Q5</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">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>3</td>
<td align="center">2015-08-15</td>
<td align="center">R1</td>
<td align="center">Hospital B</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">M</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="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">
<td>6</td>
<td align="center">2017-06-20</td>
<td align="center">V2</td>
<td>4</td>
<td align="center">2012-01-09</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</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">Escherichia</td>
<td align="center">coli</td>
@ -876,34 +876,34 @@
</tr>
<tr class="odd">
<td>7</td>
<td align="center">2012-02-10</td>
<td align="center">D1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">2010-11-14</td>
<td align="center">W5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AUR</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">S</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>8</td>
<td align="center">2010-05-01</td>
<td align="center">E1</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">2010-12-25</td>
<td align="center">F4</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">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</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">%&gt;%</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>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>
<p>Shortest: 16<br>
Longest: 24</p>
@ -942,33 +942,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,456</td>
<td align="right">49.6%</td>
<td align="right">7,456</td>
<td align="right">49.6%</td>
<td align="right">7,385</td>
<td align="right">49.3%</td>
<td align="right">7,385</td>
<td align="right">49.3%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,709</td>
<td align="right">24.7%</td>
<td align="right">11,165</td>
<td align="right">74.3%</td>
<td align="right">24.8%</td>
<td align="right">11,094</td>
<td align="right">74.1%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,267</td>
<td align="right">15.1%</td>
<td align="right">13,432</td>
<td align="right">89.4%</td>
<td align="right">2,340</td>
<td align="right">15.6%</td>
<td align="right">13,434</td>
<td align="right">89.7%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,595</td>
<td align="right">10.6%</td>
<td align="right">15,027</td>
<td align="right">1,539</td>
<td align="right">10.3%</td>
<td align="right">14,973</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -979,7 +979,7 @@ Longest: 24</p>
<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>
<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">%&gt;%</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>
<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">%&gt;%</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">%&gt;%</span><span class="st"> </span></a>
@ -992,19 +992,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4574111</td>
<td align="center">0.4721851</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4789054</td>
<td align="center">0.4554570</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4639895</td>
<td align="center">0.4683715</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4705098</td>
<td align="center">0.4663838</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4574111</td>
<td align="center">4473</td>
<td align="center">0.4721851</td>
<td align="center">4494</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4789054</td>
<td align="center">5262</td>
<td align="center">0.4554570</td>
<td align="center">5186</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4639895</td>
<td align="center">2291</td>
<td align="center">0.4683715</td>
<td align="center">2229</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4705098</td>
<td align="center">3001</td>
<td align="center">0.4663838</td>
<td align="center">3064</td>
</tr>
</tbody>
</table>
@ -1058,27 +1058,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9244903</td>
<td align="center">0.8964592</td>
<td align="center">0.9936964</td>
<td align="center">0.9243060</td>
<td align="center">0.8958700</td>
<td align="center">0.9932295</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8244514</td>
<td align="center">0.9059561</td>
<td align="center">0.9811912</td>
<td align="center">0.8401559</td>
<td align="center">0.8992853</td>
<td align="center">0.9837557</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9266649</td>
<td align="center">0.9201941</td>
<td align="center">0.9935293</td>
<td align="center">0.9280129</td>
<td align="center">0.9263953</td>
<td align="center">0.9967646</td>
</tr>
<tr class="even">
<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">0.6060873</td>
<td align="center">0.6303419</td>
</tr>
</tbody>
</table>

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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<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>
@ -228,16 +228,16 @@
<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>
<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="cb3-4" data-line-number="4"><span class="co"># 2 R R S R S S</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="cb3-6" data-line-number="6"><span class="co"># 4 R I S R R 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="cb3-8" data-line-number="8"><span class="co"># 6 R R R S I 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 S S S R R 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 S S S R S R</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 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="cb3-10" data-line-number="10"><span class="co"># 1 I</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 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 R</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="cb3-14" 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>
@ -272,39 +272,39 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3264</td>
<td align="right">65.3%</td>
<td align="right">3264</td>
<td align="right">65.3%</td>
<td align="right">3271</td>
<td align="right">65.4%</td>
<td align="right">3271</td>
<td align="right">65.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">627</td>
<td align="right">12.5%</td>
<td align="right">3891</td>
<td align="right">77.8%</td>
<td align="right">643</td>
<td align="right">12.9%</td>
<td align="right">3914</td>
<td align="right">78.3%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">607</td>
<td align="right">12.1%</td>
<td align="right">4498</td>
<td align="right">90.0%</td>
<td align="right">582</td>
<td align="right">11.6%</td>
<td align="right">4496</td>
<td align="right">89.9%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">288</td>
<td align="right">5.8%</td>
<td align="right">4786</td>
<td align="right">287</td>
<td align="right">5.7%</td>
<td align="right">4783</td>
<td align="right">95.7%</td>
</tr>
<tr class="odd">
<td align="left">5</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">5000</td>
<td align="right">100.0%</td>

4
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to work with WHONET data</h1>
<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>

2
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

292
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>
@ -225,9 +225,9 @@
</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">
<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>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -273,7 +273,18 @@
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<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>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>
@ -294,6 +305,7 @@
<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>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>
</div>
</div>
@ -307,14 +319,14 @@
<ul>
<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>
<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">%&gt;%</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">%&gt;%</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="cb2-4" 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="cb2-6" 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="cb2-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
<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">%&gt;%</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">%&gt;%</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="cb3-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</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="cb3-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</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="cb3-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
</li>
<li>
<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>
</ul>
<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>
<a class="sourceLine" id="cb3-2" 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="cb3-4" 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="cb3-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
<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="cb4-2" data-line-number="2"><span class="co"># B_ESCHR_COL</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="cb4-4" data-line-number="4"><span class="co"># "Escherichia coli"</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="cb4-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
</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>
@ -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>
<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">%&gt;%</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">%&gt;%</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="cb4-4" 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">%&gt;%</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">%&gt;%</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">%&gt;%</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>
<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">%&gt;%</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">%&gt;%</span><span class="st"> </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="cb5-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5">septic_patients <span class="op">%&gt;%</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">%&gt;%</span><span class="st"> </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">%&gt;%</span></a>
<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>
</ul>
</li>
@ -528,32 +540,32 @@ This data is updated annually - check the included version with the new function
</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>
<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>
<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="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="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="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="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="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="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="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="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="cb5-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
<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="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="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="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="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="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="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="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="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="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="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>
<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">%&gt;%</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="cb6-3" data-line-number="3">septic_patients <span class="op">%&gt;%</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>
<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">%&gt;%</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="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="cb7-3" data-line-number="3">septic_patients <span class="op">%&gt;%</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="cb7-4" 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>
<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 -&gt;<span class="st"> </span><span class="kw">atc_property</span>()</a>
<a class="sourceLine" id="cb7-2" data-line-number="2">ab_name -&gt;<span class="st"> </span><span class="kw">atc_name</span>()</a>
<a class="sourceLine" id="cb7-3" data-line-number="3">ab_official -&gt;<span class="st"> </span><span class="kw">atc_official</span>()</a>
<a class="sourceLine" id="cb7-4" data-line-number="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
<a class="sourceLine" id="cb7-5" data-line-number="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
<a class="sourceLine" id="cb7-6" data-line-number="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
<a class="sourceLine" id="cb7-7" data-line-number="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
<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 -&gt;<span class="st"> </span><span class="kw">atc_property</span>()</a>
<a class="sourceLine" id="cb8-2" data-line-number="2">ab_name -&gt;<span class="st"> </span><span class="kw">atc_name</span>()</a>
<a class="sourceLine" id="cb8-3" data-line-number="3">ab_official -&gt;<span class="st"> </span><span class="kw">atc_official</span>()</a>
<a class="sourceLine" id="cb8-4" data-line-number="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
<a class="sourceLine" id="cb8-5" data-line-number="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
<a class="sourceLine" id="cb8-6" data-line-number="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
<a class="sourceLine" id="cb8-7" data-line-number="7">ab_tradenames -&gt;<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>
<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>
@ -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>
<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 &lt;-<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="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>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">x &lt;-<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="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="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>
<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">%&gt;%</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="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>
<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">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># or</span></a>
<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>
<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">%&gt;%</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">%&gt;%</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">%&gt;%</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>
<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">%&gt;%</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">%&gt;%</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">%&gt;%</span></a>
<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>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>
@ -607,33 +619,33 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
<ul>
<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>
<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>
<a class="sourceLine" id="cb11-2" 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="cb11-4" data-line-number="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
<a class="sourceLine" id="cb11-5" 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="cb11-7" data-line-number="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
<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="cb12-2" data-line-number="2"></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="cb12-4" data-line-number="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
<a class="sourceLine" id="cb12-5" data-line-number="5"></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="cb12-7" data-line-number="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
</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>
<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>
<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="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="cb12-4" 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="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="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>
<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="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="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="cb13-4" data-line-number="4"></a>
<a class="sourceLine" id="cb13-5" data-line-number="5"><span class="co"># also equal:</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="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>
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
</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>
<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>
<a class="sourceLine" id="cb13-2" 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="cb13-4" data-line-number="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
<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="cb14-2" data-line-number="2"><span class="co"># Warning: </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="cb14-4" data-line-number="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
</li>
<li>Fix for vector containing only empty values</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>
<li>
<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>
<a class="sourceLine" id="cb14-2" 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">%&gt;%</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">%&gt;%</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="cb14-6" 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">%&gt;%</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="cb14-9" 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="cb14-11" data-line-number="11">septic_patients <span class="op">%&gt;%</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">%&gt;%</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>
<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="cb15-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb15-3" data-line-number="3">septic_patients <span class="op">%&gt;%</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">%&gt;%</span></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="cb15-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb15-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></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="cb15-9" data-line-number="9"></a>
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb15-11" data-line-number="11">septic_patients <span class="op">%&gt;%</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">%&gt;%</span><span class="st"> </span></a>
<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>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>
@ -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>
<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>
<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="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="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>
<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="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="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="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>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>
@ -782,15 +794,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul>
<li>
<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">%&gt;%</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">%&gt;%</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>
<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">%&gt;%</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">%&gt;%</span><span class="st"> </span></a>
<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>
<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">%&gt;%</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">%&gt;%</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>
<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">%&gt;%</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">%&gt;%</span><span class="st"> </span></a>
<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>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/Deprecated">hms::is.hms</a></code>
</li>
@ -870,18 +882,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
</ul>
<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>
<a class="sourceLine" id="cb18-2" 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="cb18-4" 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="cb18-6" 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="cb18-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<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="cb19-2" data-line-number="2"><span class="co"># [1] "Gram negative"</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="cb19-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</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="cb19-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</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="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>
<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>
<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="cb19-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
<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="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="cb20-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</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
<ul>
@ -892,18 +904,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</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>
<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>
<a class="sourceLine" id="cb20-2" 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="cb20-4" 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="cb20-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<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="cb21-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</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="cb21-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</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="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>
<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 &lt;-<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="cb21-3" 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="cb21-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
<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 &lt;-<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="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="cb22-3" data-line-number="3"><span class="co"># Unit: seconds</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="cb22-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</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:
@ -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>
<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>
<a class="sourceLine" id="cb22-2" 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="cb22-4" 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="cb22-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
<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="cb23-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</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="cb23-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</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="cb23-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</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>
@ -947,13 +959,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</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>
<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">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</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="cb23-3" data-line-number="3">septic_patients <span class="op">%&gt;%</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="cb23-5" data-line-number="5">septic_patients <span class="op">%&gt;%</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">%&gt;%</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">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
<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">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></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="cb24-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb24-4" data-line-number="4"></a>
<a class="sourceLine" id="cb24-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb24-6" data-line-number="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb24-7" data-line-number="7">septic_patients <span class="op">%&gt;%</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>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>
@ -967,12 +979,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>
<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>
<a class="sourceLine" id="cb24-2" data-line-number="2"><span class="kw">freq</span>(my_matrix)</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">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="cb25-2" data-line-number="2"><span class="kw">freq</span>(my_matrix)</a></code></pre></div>
<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">$</span>gender)</a>
<a class="sourceLine" id="cb25-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">freq</span>(age)</a>
<a class="sourceLine" id="cb25-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb26-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">freq</span>(age)</a>
<a class="sourceLine" id="cb26-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">freq</span>(gender)</a></code></pre></div>
</li>
</ul>
</div>
@ -1206,7 +1218,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9026">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-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

2
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</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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2
docs/reference/antibiotics.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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2
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@ -80,7 +80,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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2
docs/reference/as.mic.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</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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2
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@ -80,7 +80,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/extended-functions.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/like.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/mdro.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/microorganisms.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

2
docs/reference/microorganisms.old.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>

14
docs/reference/resistance_predict.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
</span>
</div>
@ -235,14 +235,12 @@
</div>
<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'>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'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</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'>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='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'>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'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</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'>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='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>,
@ -284,7 +282,7 @@
</tr>
<tr>
<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>
<th>I_as_S</th>

12
man/resistance_predict.Rd
View File

@ -8,14 +8,12 @@
\title{Predict antimicrobial resistance}
\usage{
resistance_predict(x, col_ab, col_date = NULL, year_min = NULL,
year_max = NULL, year_every = 1, minimum = 30,
model = "binomial", I_as_S = TRUE, preserve_measurements = TRUE,
info = TRUE, ...)
year_max = NULL, year_every = 1, minimum = 30, model = NULL,
I_as_S = TRUE, preserve_measurements = TRUE, info = TRUE, ...)
rsi_predict(x, col_ab, col_date = NULL, year_min = NULL,
year_max = NULL, year_every = 1, minimum = 30,
model = "binomial", I_as_S = TRUE, preserve_measurements = TRUE,
info = TRUE, ...)
year_max = NULL, year_every = 1, minimum = 30, model = NULL,
I_as_S = TRUE, preserve_measurements = TRUE, info = TRUE, ...)
\method{plot}{resistance_predict}(x,
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{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})}

2
tests/testthat/test-eucast_rules.R
View File

@ -34,6 +34,8 @@ test_that("EUCAST rules work", {
expect_error(eucast_rules(x = "text"))
expect_error(eucast_rules(data.frame(a = "test")))
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),
colnames(suppressWarnings(eucast_rules(septic_patients))))

5
tests/testthat/test-portion.R
View File

@ -115,6 +115,7 @@ test_that("portions works", {
septic_patients$AMX %>% portion_I(),
septic_patients$AMX %>% portion_R())
)
expect_error(portion_df(c("A", "B", "C")))
expect_error(portion_df(septic_patients[,"date"]))
})

16
tests/testthat/test-resistance_predict.R
View File

@ -32,7 +32,7 @@ test_that("prediction of rsi works", {
# # AMX resistance will increase according to data set `septic_patients`
# 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)
ggplot_rsi_predict(x)
expect_error(ggplot_rsi_predict(septic_patients))
@ -61,19 +61,27 @@ test_that("prediction of rsi works", {
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
col_ab = "AMX",
col_date = "date",
info = TRUE))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "MEM",
col_date = "date",
info = TRUE))
expect_error(portion_df(c("A", "B", "C")))
expect_error(portion_df(septic_patients[,"date"]))
})