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AMR
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v1.2.0

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dr. M.S. (Matthijs) Berends 2020-05-28 16:48:55 +02:00
parent d9a4b0bcaf
commit b44e2c9202
82 changed files with 448 additions and 517 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.1.0.9021
Version: 1.2.0
Date: 2020-05-28
Title: Antimicrobial Resistance Analysis
Authors@R: c(

55
NAMESPACE
View File

@ -195,61 +195,6 @@ export(set_mo_source)
export(skewness)
export(susceptibility)
export(theme_rsi)
exportMethods("[.ab")
exportMethods("[.disk")
exportMethods("[.mic")
exportMethods("[.mo")
exportMethods("[<-.ab")
exportMethods("[<-.disk")
exportMethods("[<-.mic")
exportMethods("[<-.mo")
exportMethods("[<-.rsi")
exportMethods("[[.ab")
exportMethods("[[.disk")
exportMethods("[[.mic")
exportMethods("[[.mo")
exportMethods("[[<-.ab")
exportMethods("[[<-.disk")
exportMethods("[[<-.mic")
exportMethods("[[<-.mo")
exportMethods("[[<-.rsi")
exportMethods(as.data.frame.ab)
exportMethods(as.data.frame.mo)
exportMethods(as.double.mic)
exportMethods(as.integer.mic)
exportMethods(as.numeric.mic)
exportMethods(barplot.mic)
exportMethods(barplot.rsi)
exportMethods(c.ab)
exportMethods(c.disk)
exportMethods(c.mic)
exportMethods(c.mo)
exportMethods(c.rsi)
exportMethods(droplevels.mic)
exportMethods(droplevels.rsi)
exportMethods(format.bug_drug_combinations)
exportMethods(kurtosis)
exportMethods(kurtosis.data.frame)
exportMethods(kurtosis.default)
exportMethods(kurtosis.matrix)
exportMethods(plot.mic)
exportMethods(plot.rsi)
exportMethods(print.ab)
exportMethods(print.bug_drug_combinations)
exportMethods(print.catalogue_of_life_version)
exportMethods(print.disk)
exportMethods(print.mic)
exportMethods(print.mo)
exportMethods(print.mo_renamed)
exportMethods(print.mo_uncertainties)
exportMethods(print.rsi)
exportMethods(skewness)
exportMethods(skewness.data.frame)
exportMethods(skewness.default)
exportMethods(skewness.matrix)
exportMethods(summary.mic)
exportMethods(summary.mo)
exportMethods(summary.rsi)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,barplot)

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.1.0.9021
## <small>Last updated: 28-May-2020</small>
# AMR 1.2.0
### Breaking
* Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.

14
R/ab.R
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@ -343,7 +343,7 @@ is.ab <- function(x) {
inherits(x, "ab")
}
#' @exportMethod print.ab
#' @method print ab
#' @export
#' @noRd
print.ab <- function(x, ...) {
@ -351,7 +351,7 @@ print.ab <- function(x, ...) {
print(as.character(x), quote = FALSE)
}
#' @exportMethod as.data.frame.ab
#' @method as.data.frame ab
#' @export
#' @noRd
as.data.frame.ab <- function(x, ...) {
@ -362,7 +362,7 @@ as.data.frame.ab <- function(x, ...) {
as.data.frame.vector(as.ab(x), ...)
}
}
#' @exportMethod [.ab
#' @method [ ab
#' @export
#' @noRd
"[.ab" <- function(x, ...) {
@ -370,7 +370,7 @@ as.data.frame.ab <- function(x, ...) {
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[.ab
#' @method [[ ab
#' @export
#' @noRd
"[[.ab" <- function(x, ...) {
@ -378,7 +378,7 @@ as.data.frame.ab <- function(x, ...) {
attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.ab
#' @method [<- ab
#' @export
#' @noRd
"[<-.ab" <- function(i, j, ..., value) {
@ -386,7 +386,7 @@ as.data.frame.ab <- function(x, ...) {
attributes(y) <- attributes(i)
class_integrity_check(y, "antimicrobial code", antibiotics$ab)
}
#' @exportMethod [[<-.ab
#' @method [[<- ab
#' @export
#' @noRd
"[[<-.ab" <- function(i, j, ..., value) {
@ -394,7 +394,7 @@ as.data.frame.ab <- function(x, ...) {
attributes(y) <- attributes(i)
class_integrity_check(y, "antimicrobial code", antibiotics$ab)
}
#' @exportMethod c.ab
#' @method c ab
#' @export
#' @noRd
c.ab <- function(x, ...) {

4
R/bug_drug_combinations.R
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@ -107,7 +107,7 @@ bug_drug_combinations <- function(x,
structure(.Data = out, class = c("bug_drug_combinations", class(x)))
}
#' @exportMethod format.bug_drug_combinations
#' @method format bug_drug_combinations
#' @export
#' @rdname bug_drug_combinations
format.bug_drug_combinations <- function(x,
@ -218,7 +218,7 @@ format.bug_drug_combinations <- function(x,
y
}
#' @exportMethod print.bug_drug_combinations
#' @method print bug_drug_combinations
#' @export
print.bug_drug_combinations <- function(x, ...) {
print(as.data.frame(x, stringsAsFactors = FALSE))

2
R/catalogue_of_life.R
View File

@ -107,7 +107,7 @@ catalogue_of_life_version <- function() {
class = c("catalogue_of_life_version", "list"))
}
#' @exportMethod print.catalogue_of_life_version
#' @method print catalogue_of_life_version
#' @export
#' @noRd
print.catalogue_of_life_version <- function(x, ...) {

12
R/disk.R
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@ -95,7 +95,7 @@ is.disk <- function(x) {
inherits(x, "disk")
}
#' @exportMethod print.disk
#' @method print disk
#' @export
#' @noRd
print.disk <- function(x, ...) {
@ -103,7 +103,7 @@ print.disk <- function(x, ...) {
print(as.integer(x), quote = FALSE)
}
#' @exportMethod [.disk
#' @method [ disk
#' @export
#' @noRd
"[.disk" <- function(x, ...) {
@ -111,7 +111,7 @@ print.disk <- function(x, ...) {
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[.disk
#' @method [[ disk
#' @export
#' @noRd
"[[.disk" <- function(x, ...) {
@ -119,7 +119,7 @@ print.disk <- function(x, ...) {
attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.disk
#' @method [<- disk
#' @export
#' @noRd
"[<-.disk" <- function(i, j, ..., value) {
@ -128,7 +128,7 @@ print.disk <- function(x, ...) {
attributes(y) <- attributes(i)
y
}
#' @exportMethod [[<-.disk
#' @method [[<- disk
#' @export
#' @noRd
"[[<-.disk" <- function(i, j, ..., value) {
@ -137,7 +137,7 @@ print.disk <- function(x, ...) {
attributes(y) <- attributes(i)
y
}
#' @exportMethod c.disk
#' @method c disk
#' @export
#' @noRd
c.disk <- function(x, ...) {

7
R/kurtosis.R
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@ -25,7 +25,6 @@
#' @inheritSection lifecycle Questioning lifecycle
#' @param x a vector of values, a [`matrix`] or a [`data.frame`]
#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
#' @exportMethod kurtosis
#' @seealso [skewness()]
#' @rdname kurtosis
#' @inheritSection AMR Read more on our website!
@ -34,7 +33,7 @@ kurtosis <- function(x, na.rm = FALSE) {
UseMethod("kurtosis")
}
#' @exportMethod kurtosis.default
#' @method kurtosis default
#' @rdname kurtosis
#' @export
kurtosis.default <- function(x, na.rm = FALSE) {
@ -47,14 +46,14 @@ kurtosis.default <- function(x, na.rm = FALSE) {
(base::sum((x - base::mean(x, na.rm = na.rm))^2, na.rm = na.rm)^2)
}
#' @exportMethod kurtosis.matrix
#' @method kurtosis matrix
#' @rdname kurtosis
#' @export
kurtosis.matrix <- function(x, na.rm = FALSE) {
base::apply(x, 2, kurtosis.default, na.rm = na.rm)
}
#' @exportMethod kurtosis.data.frame
#' @method kurtosis data.frame
#' @rdname kurtosis
#' @export
kurtosis.data.frame <- function(x, na.rm = FALSE) {

26
R/mic.R
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@ -140,28 +140,28 @@ is.mic <- function(x) {
inherits(x, "mic")
}
#' @exportMethod as.double.mic
#' @method as.double mic
#' @export
#' @noRd
as.double.mic <- function(x, ...) {
as.double(gsub("(<|=|>)+", "", as.character(x)))
}
#' @exportMethod as.integer.mic
#' @method as.integer mic
#' @export
#' @noRd
as.integer.mic <- function(x, ...) {
as.integer(gsub("(<|=|>)+", "", as.character(x)))
}
#' @exportMethod as.numeric.mic
#' @method as.numeric mic
#' @export
#' @noRd
as.numeric.mic <- function(x, ...) {
as.numeric(gsub("(<|=|>)+", "", as.character(x)))
}
#' @exportMethod droplevels.mic
#' @method droplevels mic
#' @export
#' @noRd
droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) {
@ -170,7 +170,7 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...)
x
}
#' @exportMethod print.mic
#' @method print mic
#' @export
#' @noRd
print.mic <- function(x, ...) {
@ -178,7 +178,7 @@ print.mic <- function(x, ...) {
print(as.character(x), quote = FALSE)
}
#' @exportMethod summary.mic
#' @method summary mic
#' @export
#' @noRd
summary.mic <- function(object, ...) {
@ -194,7 +194,7 @@ summary.mic <- function(object, ...) {
)
}
#' @exportMethod plot.mic
#' @method plot mic
#' @export
#' @importFrom graphics barplot axis par
#' @noRd
@ -213,7 +213,7 @@ plot.mic <- function(x,
axis(2, seq(0, max(table(droplevels.factor(x)))))
}
#' @exportMethod barplot.mic
#' @method barplot mic
#' @export
#' @importFrom graphics barplot axis
#' @noRd
@ -232,7 +232,7 @@ barplot.mic <- function(height,
axis(2, seq(0, max(table(droplevels.factor(height)))))
}
#' @exportMethod [.mic
#' @method [ mic
#' @export
#' @noRd
"[.mic" <- function(x, ...) {
@ -240,7 +240,7 @@ barplot.mic <- function(height,
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[.mic
#' @method [[ mic
#' @export
#' @noRd
"[[.mic" <- function(x, ...) {
@ -248,7 +248,7 @@ barplot.mic <- function(height,
attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.mic
#' @method [<- mic
#' @export
#' @noRd
"[<-.mic" <- function(i, j, ..., value) {
@ -257,7 +257,7 @@ barplot.mic <- function(height,
attributes(y) <- attributes(i)
y
}
#' @exportMethod [[<-.mic
#' @method [[<- mic
#' @export
#' @noRd
"[[<-.mic" <- function(i, j, ..., value) {
@ -266,7 +266,7 @@ barplot.mic <- function(height,
attributes(y) <- attributes(i)
y
}
#' @exportMethod c.mic
#' @method c mic
#' @export
#' @noRd
c.mic <- function(x, ...) {

20
R/mo.R
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@ -1566,7 +1566,7 @@ format_uncertainty_as_df <- function(uncertainty_level,
df
}
#' @exportMethod print.mo
#' @method print mo
#' @export
#' @noRd
print.mo <- function(x, ...) {
@ -1577,7 +1577,7 @@ print.mo <- function(x, ...) {
print.default(x, quote = FALSE)
}
#' @exportMethod summary.mo
#' @method summary mo
#' @export
#' @noRd
summary.mo <- function(object, ...) {
@ -1593,7 +1593,7 @@ summary.mo <- function(object, ...) {
"#3" = top_3[3])
}
#' @exportMethod as.data.frame.mo
#' @method as.data.frame mo
#' @export
#' @noRd
as.data.frame.mo <- function(x, ...) {
@ -1605,7 +1605,7 @@ as.data.frame.mo <- function(x, ...) {
}
}
#' @exportMethod [.mo
#' @method [ mo
#' @export
#' @noRd
"[.mo" <- function(x, ...) {
@ -1613,7 +1613,7 @@ as.data.frame.mo <- function(x, ...) {
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[.mo
#' @method [[ mo
#' @export
#' @noRd
"[[.mo" <- function(x, ...) {
@ -1621,7 +1621,7 @@ as.data.frame.mo <- function(x, ...) {
attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.mo
#' @method [<- mo
#' @export
#' @noRd
"[<-.mo" <- function(i, j, ..., value) {
@ -1631,7 +1631,7 @@ as.data.frame.mo <- function(x, ...) {
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
as.character(microorganisms.translation$mo_old)))
}
#' @exportMethod [[<-.mo
#' @method [[<- mo
#' @export
#' @noRd
"[[<-.mo" <- function(i, j, ..., value) {
@ -1641,7 +1641,7 @@ as.data.frame.mo <- function(x, ...) {
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
as.character(microorganisms.translation$mo_old)))
}
#' @exportMethod c.mo
#' @method c mo
#' @export
#' @noRd
c.mo <- function(x, ...) {
@ -1668,7 +1668,7 @@ mo_uncertainties <- function() {
class = c("mo_uncertainties", "data.frame"))
}
#' @exportMethod print.mo_uncertainties
#' @method print mo_uncertainties
#' @export
#' @noRd
print.mo_uncertainties <- function(x, ...) {
@ -1717,7 +1717,7 @@ mo_renamed <- function() {
class = c("mo_renamed", "data.frame"))
}
#' @exportMethod print.mo_renamed
#' @method print mo_renamed
#' @export
#' @noRd
print.mo_renamed <- function(x, ...) {

2
R/resistance_predict.R
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@ -302,7 +302,7 @@ resistance_predict <- function(x,
#' @export
rsi_predict <- resistance_predict
#' @exportMethod plot.mic
#' @method plot resistance_predict
#' @export
#' @importFrom graphics axis arrows points
#' @rdname resistance_predict

16
R/rsi.R
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@ -529,7 +529,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
}
}
#' @exportMethod print.rsi
#' @method print rsi
#' @export
#' @noRd
print.rsi <- function(x, ...) {
@ -537,7 +537,7 @@ print.rsi <- function(x, ...) {
print(as.character(x), quote = FALSE)
}
#' @exportMethod droplevels.rsi
#' @method droplevels rsi
#' @export
#' @noRd
droplevels.rsi <- function(x, exclude = if (anyNA(levels(x))) NULL else NA, ...) {
@ -546,7 +546,7 @@ droplevels.rsi <- function(x, exclude = if (anyNA(levels(x))) NULL else NA, ...)
x
}
#' @exportMethod summary.rsi
#' @method summary rsi
#' @export
#' @noRd
summary.rsi <- function(object, ...) {
@ -561,7 +561,7 @@ summary.rsi <- function(object, ...) {
)
}
#' @exportMethod plot.rsi
#' @method plot rsi
#' @export
#' @importFrom graphics text axis
#' @noRd
@ -618,7 +618,7 @@ plot.rsi <- function(x,
}
#' @exportMethod barplot.rsi
#' @method barplot rsi
#' @export
#' @importFrom graphics barplot axis par
#' @noRd
@ -652,7 +652,7 @@ barplot.rsi <- function(height,
}
}
#' @exportMethod [<-.rsi
#' @method [<- rsi
#' @export
#' @noRd
"[<-.rsi" <- function(i, j, ..., value) {
@ -661,7 +661,7 @@ barplot.rsi <- function(height,
attributes(y) <- attributes(i)
y
}
#' @exportMethod [[<-.rsi
#' @method [[<- rsi
#' @export
#' @noRd
"[[<-.rsi" <- function(i, j, ..., value) {
@ -670,7 +670,7 @@ barplot.rsi <- function(height,
attributes(y) <- attributes(i)
y
}
#' @exportMethod c.rsi
#' @method c rsi
#' @export
#' @noRd
c.rsi <- function(x, ...) {

7
R/skewness.R
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@ -27,7 +27,6 @@
#' @inheritSection lifecycle Questioning lifecycle
#' @param x a vector of values, a [`matrix`] or a [`data.frame`]
#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
#' @exportMethod skewness
#' @seealso [kurtosis()]
#' @rdname skewness
#' @inheritSection AMR Read more on our website!
@ -36,7 +35,7 @@ skewness <- function(x, na.rm = FALSE) {
UseMethod("skewness")
}
#' @exportMethod skewness.default
#' @method skewness default
#' @rdname skewness
#' @export
skewness.default <- function(x, na.rm = FALSE) {
@ -48,14 +47,14 @@ skewness.default <- function(x, na.rm = FALSE) {
(base::sum((x - base::mean(x))^3) / n) / (base::sum((x - base::mean(x)) ^ 2) / n) ^ (3 / 2)
}
#' @exportMethod skewness.matrix
#' @method skewness matrix
#' @rdname skewness
#' @export
skewness.matrix <- function(x, na.rm = FALSE) {
base::apply(x, 2, skewness.default, na.rm = na.rm)
}
#' @exportMethod skewness.data.frame
#' @method skewness data.frame
#' @rdname skewness
#' @export
skewness.data.frame <- function(x, na.rm = FALSE) {

4
cran-comments.md
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@ -1,5 +1,3 @@
* Although the previous release (1.0.1) is from 2020-02-23, this updates provides support for the upcoming dplyr 1.0.0 which is used (and relied upon) by probably all our users.
* For this specific version, otherwise nothing to mention.
* For this specific version, nothing to mention.
* Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

479
docs/articles/AMR.html
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@ -39,7 +39,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -336,54 +336,32 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-07-23</td>
<td align="center">Z5</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">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-01-21</td>
<td align="center">D6</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</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">2014-05-20</td>
<td align="center">Y10</td>
<td align="center">2013-12-18</td>
<td align="center">P10</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-11-02</td>
<td align="center">M10</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2010-07-10</td>
<td align="center">K6</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2014-08-26</td>
<td align="center">B4</td>
<td align="center">2014-12-14</td>
<td align="center">F6</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -391,11 +369,33 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-05-29</td>
<td align="center">R3</td>
<td align="center">2010-12-31</td>
<td align="center">N8</td>
<td align="center">Hospital D</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">F</td>
</tr>
<tr class="odd">
<td align="center">2010-11-24</td>
<td align="center">M5</td>
<td align="center">Hospital B</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">2010-10-07</td>
<td align="center">Z8</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
@ -432,16 +432,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,518</td>
<td align="right">52.59%</td>
<td align="right">10,518</td>
<td align="right">52.59%</td>
<td align="right">10,397</td>
<td align="right">51.99%</td>
<td align="right">10,397</td>
<td align="right">51.99%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,482</td>
<td align="right">47.41%</td>
<td align="right">9,603</td>
<td align="right">48.02%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -491,7 +491,7 @@ Longest: 1</p>
<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 P10, 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 U2, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -507,10 +507,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-22</td>
<td align="center">P10</td>
<td align="center">2010-03-30</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -518,43 +518,43 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-24</td>
<td align="center">P10</td>
<td align="center">2010-07-30</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-03-10</td>
<td align="center">P10</td>
<td align="center">2010-10-14</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-03-25</td>
<td align="center">P10</td>
<td align="center">2010-12-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-04-30</td>
<td align="center">P10</td>
<td align="center">2011-02-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</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>
@ -562,62 +562,62 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-05-05</td>
<td align="center">P10</td>
<td align="center">2011-03-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-05-19</td>
<td align="center">P10</td>
<td align="center">2011-06-10</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-05-27</td>
<td align="center">P10</td>
<td align="center">2011-07-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-01</td>
<td align="center">P10</td>
<td align="center">2011-08-08</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-19</td>
<td align="center">P10</td>
<td align="center">2011-08-21</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb18"><html><body><pre class="r"><span class="no">data</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">keyab</span> <span class="kw">=</span> <span class="fu"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(<span class="no">.</span>)) <span class="kw">%&gt;%</span>
@ -643,10 +643,10 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-22</td>
<td align="center">P10</td>
<td align="center">2010-03-30</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -655,46 +655,46 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-24</td>
<td align="center">P10</td>
<td align="center">2010-07-30</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-03-10</td>
<td align="center">P10</td>
<td align="center">2010-10-14</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_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">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-03-25</td>
<td align="center">P10</td>
<td align="center">2010-12-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-04-30</td>
<td align="center">P10</td>
<td align="center">2011-02-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</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>
@ -703,71 +703,71 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-05-05</td>
<td align="center">P10</td>
<td align="center">2011-03-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</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">2010-05-19</td>
<td align="center">P10</td>
<td align="center">2011-06-10</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-05-27</td>
<td align="center">P10</td>
<td align="center">2011-07-17</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-01</td>
<td align="center">P10</td>
<td align="center">B_ESCHR_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">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-19</td>
<td align="center">P10</td>
<td align="center">2011-08-08</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-08-21</td>
<td align="center">U2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 1, now 9 isolates are flagged. In total, 78.3% of all isolates are marked ‘first weighted’ - 49.8% 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 6 isolates are flagged. In total, 78.7% of all isolates are marked ‘first weighted’ - 50.2% 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="cb19"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</pre></body></html></div>
<p>So we end up with 15,654 isolates for analysis.</p>
<p>So we end up with 15,741 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">first</span>, <span class="no">keyab</span>))</pre></body></html></div>
@ -775,7 +775,6 @@ Longest: 1</p>
<div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">data_1st</span>)</pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -792,79 +791,14 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2015-07-23</td>
<td align="center">Z5</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</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>2</td>
<td align="center">2017-01-21</td>
<td align="center">D6</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>4</td>
<td align="center">2017-11-02</td>
<td align="center">M10</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</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="even">
<td>5</td>
<td align="center">2014-08-26</td>
<td align="center">B4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2013-05-29</td>
<td align="center">R3</td>
<td align="center">Hospital B</td>
<td align="center">2013-12-18</td>
<td align="center">P10</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -872,15 +806,74 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2013-12-10</td>
<td align="center">T3</td>
<td align="center">2010-07-10</td>
<td align="center">K6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_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>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-12-14</td>
<td align="center">F6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_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>
<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 align="center">2010-12-31</td>
<td align="center">N8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_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">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="odd">
<td align="center">2010-11-24</td>
<td align="center">M5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_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>
<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 align="center">2010-10-07</td>
<td align="center">Z8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -906,8 +899,8 @@ Longest: 1</p>
<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>, <span class="no">species</span>)</pre></body></html></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,654<br>
Available: 15,654 (100%, NA: 0 = 0%)<br>
Length: 15,741<br>
Available: 15,741 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -924,33 +917,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,778</td>
<td align="right">49.69%</td>
<td align="right">7,778</td>
<td align="right">49.69%</td>
<td align="right">7,943</td>
<td align="right">50.46%</td>
<td align="right">7,943</td>
<td align="right">50.46%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,999</td>
<td align="right">25.55%</td>
<td align="right">11,777</td>
<td align="right">75.23%</td>
<td align="right">3,978</td>
<td align="right">25.27%</td>
<td align="right">11,921</td>
<td align="right">75.73%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,300</td>
<td align="right">14.69%</td>
<td align="right">14,077</td>
<td align="right">89.93%</td>
<td align="right">2,248</td>
<td align="right">14.28%</td>
<td align="right">14,169</td>
<td align="right">90.01%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,577</td>
<td align="right">10.07%</td>
<td align="right">15,654</td>
<td align="right">1,572</td>
<td align="right">9.99%</td>
<td align="right">15,741</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -962,7 +955,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>)
<span class="co"># [1] 0.4435288</span></pre></body></html></div>
<span class="co"># [1] 0.4476209</span></pre></body></html></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="cb25"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital</span>) <span class="kw">%&gt;%</span>
@ -975,19 +968,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4461239</td>
<td align="center">0.4402730</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4404762</td>
<td align="center">0.4607609</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4549763</td>
<td align="center">0.4437526</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4366688</td>
<td align="center">0.4389635</td>
</tr>
</tbody>
</table>
@ -1005,23 +998,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4461239</td>
<td align="center">4631</td>
<td align="center">0.4402730</td>
<td align="center">4688</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4404762</td>
<td align="center">5544</td>
<td align="center">0.4607609</td>
<td align="center">5441</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4549763</td>
<td align="center">2321</td>
<td align="center">0.4437526</td>
<td align="center">2409</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4366688</td>
<td align="center">3158</td>
<td align="center">0.4389635</td>
<td align="center">3203</td>
</tr>
</tbody>
</table>
@ -1041,27 +1034,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8215480</td>
<td align="center">0.8976601</td>
<td align="center">0.9835433</td>
<td align="center">0.8296613</td>
<td align="center">0.8992824</td>
<td align="center">0.9862772</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8300571</td>
<td align="center">0.8972733</td>
<td align="center">0.9866836</td>
<td align="center">0.8250636</td>
<td align="center">0.9083969</td>
<td align="center">0.9840967</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8202051</td>
<td align="center">0.9229807</td>
<td align="center">0.9832458</td>
<td align="center">0.8245349</td>
<td align="center">0.9263449</td>
<td align="center">0.9891905</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6204348</td>
<td align="center">0.6107651</td>
<td align="center">0.0000000</td>
<td align="center">0.6204348</td>
<td align="center">0.6107651</td>
</tr>
</tbody>
</table>

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docs/articles/EUCAST.html
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@ -39,7 +39,7 @@
</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">1.1.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">21 May 2020</h4>
<h4 class="date">28 May 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div>
@ -301,6 +301,8 @@
</tbody>
</table>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>)</pre></body></html></div>
<pre><code># Warning: Not all columns with antimicrobial results are of class &lt;rsi&gt;.
# Transform eligible columns to class &lt;rsi&gt; on beforehand: your_data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></pre>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>

56
docs/articles/MDR.html
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@ -39,7 +39,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -302,19 +302,19 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 R S R I I S</span>
<span class="co"># 2 S R S I R I</span>
<span class="co"># 3 S S I S R R</span>
<span class="co"># 4 I R S S I S</span>
<span class="co"># 5 S S R R R S</span>
<span class="co"># 6 I R R R R S</span>
<span class="co"># 1 S R R S R R</span>
<span class="co"># 2 R S R S R S</span>
<span class="co"># 3 R R S S R S</span>
<span class="co"># 4 S S S S R S</span>
<span class="co"># 5 S R S S R S</span>
<span class="co"># 6 R S R S S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 I</span>
<span class="co"># 2 I</span>
<span class="co"># 3 R</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
<span class="co"># 6 I</span></pre></body></html></div>
<span class="co"># 6 S</span></pre></body></html></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="no">my_TB_data</span>, <span class="kw">guideline</span> <span class="kw">=</span> <span class="st">"TB"</span>)</pre></body></html></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -343,40 +343,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
<td align="right">3245</td>
<td align="right">64.90%</td>
<td align="right">3245</td>
<td align="right">64.90%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">667</td>
<td align="right">13.34%</td>
<td align="right">3859</td>
<td align="right">77.18%</td>
<td align="right">678</td>
<td align="right">13.56%</td>
<td align="right">3923</td>
<td align="right">78.46%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">637</td>
<td align="right">12.74%</td>
<td align="right">4496</td>
<td align="right">89.92%</td>
<td align="right">607</td>
<td align="right">12.14%</td>
<td align="right">4530</td>
<td align="right">90.60%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">287</td>
<td align="right">5.74%</td>
<td align="right">4783</td>
<td align="right">95.66%</td>
<td align="right">262</td>
<td align="right">5.24%</td>
<td align="right">4792</td>
<td align="right">95.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">217</td>
<td align="right">4.34%</td>
<td align="right">208</td>
<td align="right">4.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
docs/articles/PCA.html
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@ -39,7 +39,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

10
docs/articles/SPSS.html
View File

@ -39,7 +39,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">15 April 2020</h4>
<h4 class="date">28 May 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -242,10 +242,10 @@
<p>To demonstrate the first point:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="co"># not all values are valid MIC values:</span>
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)
<span class="co"># Class 'mic'</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 0.125</span>
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="st">"testvalue"</span>)
<span class="co"># Class 'mic'</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] &lt;NA&gt;</span>
<span class="co"># the Gram stain is avaiable for all bacteria:</span>
@ -398,7 +398,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

18
docs/articles/WHONET.html
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@ -39,7 +39,7 @@
</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">1.1.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2020</h4>
<h4 class="date">28 May 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -232,7 +232,7 @@
<p>Class: character<br>
Length: 500<br>
Available: 500 (100%, NA: 0 = 0%)<br>
Unique: 39</p>
Unique: 37</p>
<p>Shortest: 11<br>
Longest: 40</p>
<table class="table">
@ -319,15 +319,15 @@ Longest: 40</p>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">Enterococcus columbae</td>
<td align="right">4</td>
<td align="right">0.8%</td>
<td align="right">443</td>
<td align="right">88.6%</td>
<td align="left">Streptococcus anginosus</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">444</td>
<td align="right">88.8%</td>
</tr>
</tbody>
</table>
<p>(omitted 29 entries, n = 57 [11.40%])</p>
<p>(omitted 27 entries, n = 56 [11.20%])</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="co"># our transformed antibiotic columns</span>
<span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
<span class="no">data</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">AMC_ND2</span>)</pre></body></html></div>

86
docs/articles/benchmarks.html
View File

@ -39,7 +39,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -221,21 +221,21 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">2</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 8.2 9.7 22.0 14.0 38.0 43</span>
<span class="co"># as.mo("stau") 130.0 130.0 160.0 170.0 170.0 190</span>
<span class="co"># as.mo("STAU") 120.0 130.0 150.0 150.0 180.0 190</span>
<span class="co"># as.mo("staaur") 8.3 9.1 13.0 9.4 10.0 40</span>
<span class="co"># as.mo("STAAUR") 8.0 9.3 15.0 10.0 13.0 35</span>
<span class="co"># as.mo("S. aureus") 9.3 11.0 26.0 14.0 15.0 120</span>
<span class="co"># as.mo("S aureus") 10.0 12.0 22.0 13.0 38.0 49</span>
<span class="co"># as.mo("Staphylococcus aureus") 6.6 7.7 8.5 8.6 9.1 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 820.0 860.0 890.0 880.0 930.0 1000</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 350.0 350.0 370.0 370.0 370.0 380</span>
<span class="co"># as.mo("MRSA") 7.8 9.1 13.0 10.0 11.0 42</span>
<span class="co"># as.mo("VISA") 11.0 12.0 19.0 13.0 15.0 47</span>
<span class="co"># as.mo("VRSA") 11.0 12.0 21.0 14.0 39.0 42</span>
<span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 150.0 190</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 8.5 11.0 17.0 12.0 12.0 43.0</span>
<span class="co"># as.mo("stau") 120.0 130.0 150.0 140.0 160.0 180.0</span>
<span class="co"># as.mo("STAU") 130.0 140.0 150.0 150.0 160.0 170.0</span>
<span class="co"># as.mo("staaur") 7.7 9.1 13.0 11.0 12.0 38.0</span>
<span class="co"># as.mo("STAAUR") 8.3 9.3 15.0 10.0 11.0 37.0</span>
<span class="co"># as.mo("S. aureus") 11.0 12.0 18.0 13.0 14.0 41.0</span>
<span class="co"># as.mo("S aureus") 8.8 11.0 17.0 12.0 13.0 41.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 6.4 6.6 7.4 7.6 7.8 9.1</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 810.0 870.0 890.0 890.0 900.0 1000.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 320.0 340.0 370.0 350.0 400.0 490.0</span>
<span class="co"># as.mo("MRSA") 9.2 10.0 13.0 11.0 12.0 37.0</span>
<span class="co"># as.mo("VISA") 12.0 12.0 22.0 13.0 43.0 44.0</span>
<span class="co"># as.mo("VRSA") 11.0 13.0 21.0 14.0 38.0 41.0</span>
<span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 170.0 200.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -262,12 +262,12 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 135.600 143.500 157.800 153.400 175.70 191.40</span>
<span class="co"># as.mo("METSEM") 139.700 140.800 158.100 148.300 176.10 188.50</span>
<span class="co"># as.mo("M. semesiae") 9.010 9.317 13.280 9.802 12.51 40.46</span>
<span class="co"># as.mo("M. semesiae") 9.155 9.321 9.665 9.557 10.07 10.37</span>
<span class="co"># as.mo("Methanosarcina semesiae") 6.737 7.160 16.020 8.413 33.21 37.10</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 143.400 146.300 156.10 155.400 164.900 176.40</span>
<span class="co"># as.mo("METSEM") 141.600 146.900 167.00 170.700 185.000 188.00</span>
<span class="co"># as.mo("M. semesiae") 9.665 9.879 16.50 10.090 11.960 44.29</span>
<span class="co"># as.mo("M. semesiae") 10.000 10.080 14.46 11.660 13.140 42.01</span>
<span class="co"># as.mo("Methanosarcina semesiae") 7.161 7.389 10.40 7.542 9.294 33.00</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -307,7 +307,7 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 1670 1740 1800 1790 1880 1900 10</span></pre></body></html></div>
<span class="co"># mo_name(x) 1650 1730 1790 1790 1840 1900 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.79 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
@ -320,10 +320,10 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 5.630 5.900 6.420 6.480 6.910 7.120 10</span>
<span class="co"># B 9.940 11.300 15.000 11.800 12.300 45.300 10</span>
<span class="co"># C 0.247 0.277 0.315 0.295 0.358 0.386 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 5.680 5.820 9.61 6.36 6.850 39.500 10</span>
<span class="co"># B 9.790 10.000 10.60 10.40 10.900 11.900 10</span>
<span class="co"># C 0.229 0.259 0.27 0.27 0.286 0.311 10</span></pre></body></html></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0003 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
@ -337,14 +337,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.207 0.214 0.241 0.218 0.240 0.412 10</span>
<span class="co"># B 0.178 0.207 0.215 0.211 0.219 0.272 10</span>
<span class="co"># C 0.218 0.221 0.234 0.233 0.240 0.264 10</span>
<span class="co"># D 0.203 0.211 0.221 0.214 0.218 0.290 10</span>
<span class="co"># E 0.208 0.209 0.223 0.214 0.227 0.279 10</span>
<span class="co"># F 0.172 0.203 0.222 0.212 0.222 0.302 10</span>
<span class="co"># G 0.200 0.202 0.212 0.208 0.213 0.253 10</span>
<span class="co"># H 0.193 0.194 0.208 0.200 0.215 0.261 10</span></pre></body></html></div>
<span class="co"># A 0.209 0.221 0.236 0.225 0.244 0.311 10</span>
<span class="co"># B 0.197 0.201 0.215 0.212 0.222 0.266 10</span>
<span class="co"># C 0.205 0.224 0.243 0.229 0.242 0.383 10</span>
<span class="co"># D 0.199 0.207 0.216 0.211 0.214 0.270 10</span>
<span class="co"># E 0.196 0.206 0.218 0.215 0.221 0.270 10</span>
<span class="co"># F 0.188 0.197 0.212 0.210 0.216 0.269 10</span>
<span class="co"># G 0.195 0.198 0.213 0.203 0.215 0.299 10</span>
<span class="co"># H 0.184 0.193 0.205 0.201 0.207 0.252 10</span></pre></body></html></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -370,14 +370,14 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 11.24 11.97 16.09 13.31 13.71 48.40 100</span>
<span class="co"># de 12.18 12.84 19.63 14.33 15.00 55.14 100</span>
<span class="co"># nl 16.24 17.07 24.36 18.61 19.83 55.70 100</span>
<span class="co"># es 12.23 12.77 17.38 13.71 14.72 51.57 100</span>
<span class="co"># it 12.15 13.01 18.55 14.03 14.81 146.90 100</span>
<span class="co"># fr 12.23 13.08 16.81 14.30 14.86 49.30 100</span>
<span class="co"># pt 12.30 12.85 18.13 14.24 14.88 49.70 100</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 9.303 11.59 14.90 12.40 13.63 45.92 100</span>
<span class="co"># de 10.080 12.39 15.77 13.11 14.45 46.27 100</span>
<span class="co"># nl 13.200 16.26 20.88 17.80 19.52 49.93 100</span>
<span class="co"># es 9.957 12.23 15.57 13.12 14.59 51.99 100</span>
<span class="co"># it 10.210 12.44 19.02 13.34 14.74 52.96 100</span>
<span class="co"># fr 10.040 12.40 18.90 13.26 15.07 54.40 100</span>
<span class="co"># pt 10.450 12.67 16.91 13.46 14.68 51.47 100</span></pre></body></html></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/articles/resistance_predict.html
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@ -39,7 +39,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

13
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -229,14 +229,10 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1-1-0-9021" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0.9021">
<a href="#amr-1-1-0-9021" class="anchor"></a>AMR 1.1.0.9021<small> Unreleased </small>
<div id="amr-1-2-0" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0">
<a href="#amr-1-2-0" class="anchor"></a>AMR 1.2.0<small> Unreleased </small>
</h1>
<div id="last-updated-28-may-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-28-may-2020" class="anchor"></a><small>Last updated: 28-May-2020</small>
</h2>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -296,7 +292,6 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Removed function <code>read.4d()</code>, that was only useful for reading data from an old test database.</li>
</ul>
</div>
</div>
</div>
<div id="amr-1-1-0" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-05-28T08:48Z
last_built: 2020-05-28T10:26Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

2
docs/reference/AMR-deprecated.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

4
docs/reference/AMR.html
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@ -82,7 +82,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -293,7 +293,7 @@ The Netherlands</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

4
docs/reference/WHOCC.html
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@ -82,7 +82,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -272,7 +272,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

4
docs/reference/WHONET.html
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@ -82,7 +82,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -290,7 +290,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

2
docs/reference/ab_property.html
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@ -82,7 +82,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/age.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/age_groups.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/antibiotics.html
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@ -82,7 +82,7 @@
</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">1.1.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/as.ab.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/as.disk.html
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@ -82,7 +82,7 @@
</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">1.1.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/as.mic.html
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@ -82,7 +82,7 @@
</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">1.1.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/as.rsi.html
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@ -82,7 +82,7 @@
</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">1.1.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/atc_online.html
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@ -83,7 +83,7 @@ This function requires an internet connection." />
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/availability.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html
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@ -82,7 +82,7 @@
</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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
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@ -82,7 +82,7 @@
</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">1.1.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/count.html
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@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

2
docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>

4
docs/reference/example_isolates.html
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@ -82,7 +82,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -274,7 +274,7 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

4
docs/reference/example_isolates_unclean.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
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@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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