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(v1.5.0.9031) math processing of MICs

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dr. M.S. (Matthijs) Berends 2021-03-05 15:36:39 +01:00
parent 0d29bde693
commit 91dd755cac
36 changed files with 310 additions and 52 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.5.0.9030
Version: 1.5.0.9031
Date: 2021-03-05
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

26
NAMESPACE
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@ -1,5 +1,17 @@
# Generated by roxygen2: do not edit by hand
S3method("!=",mic)
S3method("%%",mic)
S3method("%/%",mic)
S3method("*",mic)
S3method("+",mic)
S3method("-",mic)
S3method("/",mic)
S3method("<",mic)
S3method("<=",mic)
S3method("==",mic)
S3method(">",mic)
S3method(">=",mic)
S3method("[",ab)
S3method("[",disk)
S3method("[",isolate_identifier)
@ -22,7 +34,10 @@ S3method("[[<-",isolate_identifier)
S3method("[[<-",mic)
S3method("[[<-",mo)
S3method("[[<-",rsi)
S3method("^",mic)
S3method(all,mic)
S3method(all.equal,isolate_identifier)
S3method(any,mic)
S3method(as.data.frame,ab)
S3method(as.data.frame,mo)
S3method(as.double,mic)
@ -41,12 +56,19 @@ S3method(c,isolate_identifier)
S3method(c,mic)
S3method(c,mo)
S3method(c,rsi)
S3method(ceiling,mic)
S3method(droplevels,mic)
S3method(droplevels,rsi)
S3method(floor,mic)
S3method(format,bug_drug_combinations)
S3method(hist,mic)
S3method(kurtosis,data.frame)
S3method(kurtosis,default)
S3method(kurtosis,matrix)
S3method(max,mic)
S3method(mean,mic)
S3method(median,mic)
S3method(min,mic)
S3method(plot,disk)
S3method(plot,mic)
S3method(plot,resistance_predict)
@ -63,10 +85,14 @@ S3method(print,mo_renamed)
S3method(print,mo_uncertainties)
S3method(print,pca)
S3method(print,rsi)
S3method(quantile,mic)
S3method(range,mic)
S3method(rep,mo)
S3method(skewness,data.frame)
S3method(skewness,default)
S3method(skewness,matrix)
S3method(sort,mic)
S3method(sum,mic)
S3method(summary,mic)
S3method(summary,mo)
S3method(summary,pca)

5
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.5.0.9030
# AMR 1.5.0.9031
## <small>Last updated: 5 March 2021</small>
### New
@ -43,6 +43,7 @@
mo_type(c("Aspergillus", "Candida"), language = "es") # also supported: de, nl, fr, it, pt
#> [1] "Hongos" "Levaduras"
```
* Added Pretomanid (PMD, J04AK08) to the `antibiotics` data set
### Changed
* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
@ -56,8 +57,8 @@
* `is.rsi()` and `is.rsi.eligible()` now return a vector of `TRUE`/`FALSE` when the input is a data set, by iterating over all columns
* Using functions without setting a data set (e.g., `mo_is_gram_negative()`, `mo_is_gram_positive()`, `mo_is_intrinsic_resistant()`, `first_isolate()`, `mdro()`) now work with `dplyr`s `group_by()` again
* `first_isolate()` can be used with `group_by()` (also when using a dot `.` as input for the data) and now returns the names of the groups
* MIC values now allow for any mathematical processing, such as usage inside functions `min()`, `max()`, `range()`, and with binary operators (+, -, etc.). This also enables other functions, such as `fivenum()`.
* Updated the data set `microorganisms.codes` (which contains popular LIS and WHONET codes for microorganisms) for some species of *Mycobacterium* that previously incorrectly returned *M. africanum*
* Added Pretomanid (PMD, J04AK08) to the `antibiotics` data set
* WHONET code `"PNV"` will now correctly be interpreted as `PHN`, the antibiotic code for phenoxymethylpenicillin ('peni V')
* Fix for verbose output of `mdro(..., verbose = TRUE)` for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only *P. aeruginosa*)
* `is.rsi.eligible()` now detects if the column name resembles an antibiotic name or code and now returns `TRUE` immediately if the input contains any of the values "R", "S" or "I". This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.

2
R/amr.R
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@ -29,7 +29,7 @@
#' @details
#' `AMR` is a free, open-source and independent \R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
#'
#' After installing this package, \R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
#' After installing this package, \R knows `r format_included_data_number(microorganisms)` distinct microbial species and all `r format_included_data_number(rbind(antibiotics[, "atc", drop = FALSE], antivirals[, "atc", drop = FALSE]))` antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
#'
#' This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
#'

2
R/catalogue_of_life.R
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@ -44,7 +44,7 @@ format_included_data_number <- function(data) {
#' This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.
#' @section Catalogue of Life:
#' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
#' This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
#' This package contains the complete taxonomic tree of almost all microorganisms (`r format_included_data_number(microorganisms)` species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
#'
#' [Click here][catalogue_of_life] for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with [catalogue_of_life_version()].
#' @section Included Taxa:

221
R/mic.R
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@ -42,6 +42,11 @@
#'
#' # this can also coerce combined MIC/RSI values:
#' as.mic("<=0.002; S") # will return <=0.002
#'
#' # mathematical processing treats MICs as numeric values
#' fivenum(mic_data)
#' quantile(mic_data)
#' all(mic_data < 512)
#'
#' # interpret MIC values
#' as.rsi(x = as.mic(2),
@ -276,6 +281,222 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
y
}
#' @method range mic
#' @export
#' @noRd
range.mic <- function(..., na.rm = FALSE) {
rng <- sort(c(...))
if (na.rm == TRUE) {
rng <- rng[!is.na(rng)]
}
out <- c(as.character(rng[1]), as.character(rng[length(rng)]))
as.double(as.mic(out))
}
#' @method min mic
#' @export
#' @noRd
min.mic <- function(..., na.rm = FALSE) {
rng <- sort(c(...))
if (na.rm == TRUE) {
rng <- rng[!is.na(rng)]
}
as.double(as.mic(as.character(rng[1])))
}
#' @method max mic
#' @export
#' @noRd
max.mic <- function(..., na.rm = FALSE) {
rng <- sort(c(...))
if (na.rm == TRUE) {
rng <- rng[!is.na(rng)]
}
as.double(as.mic(as.character(rng[length(rng)])))
}
#' @method sum mic
#' @export
#' @noRd
sum.mic <- function(..., na.rm = FALSE) {
rng <- sort(c(...))
if (na.rm == TRUE) {
rng <- rng[!is.na(rng)]
}
sum(as.double(rng))
}
#' @method all mic
#' @export
#' @noRd
all.mic <- function(..., na.rm = FALSE) {
rng <- sort(c(...))
if (na.rm == TRUE) {
rng <- rng[!is.na(rng)]
}
all(as.double(rng))
}
#' @method any mic
#' @export
#' @noRd
any.mic <- function(..., na.rm = FALSE) {
rng <- sort(c(...))
if (na.rm == TRUE) {
rng <- rng[!is.na(rng)]
}
any(as.double(rng))
}
#' @method mean mic
#' @export
#' @noRd
mean.mic <- function(x, na.rm = FALSE, ...) {
mean(as.double(x), na.rm = na.rm, ...)
}
#' @method median mic
#' @export
#' @noRd
median.mic <- function(x, na.rm = FALSE, ...) {
median(as.double(x), na.rm = na.rm, ...)
}
#' @method quantile mic
#' @export
#' @noRd
quantile.mic <- function(x, probs = seq(0, 1, 0.25), na.rm = FALSE,
names = TRUE, type = 7, ...) {
quantile(as.double(x), props = props, na.rm = na.rm, names = names, type = type, ...)
}
#' @method floor mic
#' @export
#' @noRd
floor.mic <- function(x) {
floor(as.double(x))
}
#' @method ceiling mic
#' @export
#' @noRd
ceiling.mic <- function(x) {
ceiling(as.double(x))
}
#' @method + mic
#' @export
#' @noRd
`+.mic` <- function(e1, e2) {
as.double(e1) + as.double(e2)
}
#' @method - mic
#' @export
#' @noRd
`-.mic` <- function(e1, e2) {
as.double(e1) - as.double(e2)
}
#' @method * mic
#' @export
#' @noRd
`*.mic` <- function(e1, e2) {
as.double(e1) * as.double(e2)
}
#' @method / mic
#' @export
#' @noRd
`/.mic` <- function(e1, e2) {
as.double(e1) / as.double(e2)
}
#' @method ^ mic
#' @export
#' @noRd
`^.mic` <- function(e1, e2) {
as.double(e1) ^ as.double(e2)
}
#' @method %% mic
#' @export
#' @noRd
`%%.mic` <- function(e1, e2) {
as.double(e1) %% as.double(e2)
}
#' @method %/% mic
#' @export
#' @noRd
`%/%.mic` <- function(e1, e2) {
as.double(e1) %/% as.double(e2)
}
#' @method == mic
#' @export
#' @noRd
`==.mic` <- function(e1, e2) {
as.double(e1) == as.double(e2)
}
#' @method != mic
#' @export
#' @noRd
`!=.mic` <- function(e1, e2) {
as.double(e1) != as.double(e2)
}
#' @method < mic
#' @export
#' @noRd
`<.mic` <- function(e1, e2) {
as.double(e1) < as.double(e2)
}
#' @method <= mic
#' @export
#' @noRd
`<=.mic` <- function(e1, e2) {
as.double(e1) <= as.double(e2)
}
#' @method >= mic
#' @export
#' @noRd
`>=.mic` <- function(e1, e2) {
as.double(e1) >= as.double(e2)
}
#' @method > mic
#' @export
#' @noRd
`>.mic` <- function(e1, e2) {
as.double(e1) > as.double(e2)
}
#' @method sort mic
#' @export
#' @noRd
sort.mic <- function(x, decreasing = FALSE, ...) {
if (decreasing == TRUE) {
ord <- order(-as.double(x))
} else {
ord <- order(as.double(x))
}
x[ord]
}
#' @method hist mic
#' @export
#' @noRd
hist.mic <- function(x, ...) {
warning_("Use `plot()` or `ggplot()` for plotting MIC values", call = FALSE)
hist(as.double(x), ...)
}
# will be exported using s3_register() in R/zzz.R
get_skimmers.mic <- function(column) {
skimr::sfl(

4
R/mo.R
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@ -1474,8 +1474,8 @@ exec_as.mo <- function(x,
if (length(uncertainties$input) > 1) {
plural <- c("s", "them", "were")
}
msg <- paste0("Translation to ", nr2char(length(uncertainties$input)), " microorganism", plural[1],
" was guessed with uncertainty. Use `mo_uncertainties()` to review ", plural[2], ".")
msg <- paste0("Translation is uncertain of ", nr2char(length(uncertainties$input)), " microorganism", plural[1],
". Use `mo_uncertainties()` to review ", plural[2], ".")
message_(msg)
}
x[already_known] <- x_known

1
R/plot.R
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@ -261,7 +261,6 @@ ggplot.mic <- function(data,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method plot disk
#' @export
#' @importFrom graphics barplot axis mtext legend

6
R/random.R
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@ -51,9 +51,9 @@
#' random_mic(100, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#' random_mic(100, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#'
#' random_disk(100, "Klebsiella pneumoniae") # range 11-50
#' random_disk(100, "Klebsiella pneumoniae", "ampicillin") # range 6-14
#' random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 16-22
#' random_disk(100, "Klebsiella pneumoniae") # range 8-50
#' random_disk(100, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#' random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#' }
random_mic <- function(size, mo = NULL, ab = NULL, ...) {
random_exec("MIC", size = size, mo = mo, ab = ab)

BIN
data-raw/AMR_latest.tar.gz
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docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

10
docs/articles/datasets.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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>
@ -211,7 +211,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>class</em>, <em>family</em>, <em>fullname</em>, <em>genus</em>, <em>kingdom</em>, <em>mo</em>, <em>order</em>, <em>phylum</em>, <em>prevalence</em>, <em>rank</em>, <em>ref</em>, <em>snomed</em>, <em>source</em>, <em>species</em>, <em>species_id</em> and <em>subspecies</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 5 March 2021 09:32:45 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 5 March 2021 10:46:55 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
@ -430,7 +430,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 14,100 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>prevalence</em> and <em>ref</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 4 March 2021 22:23:58 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 5 March 2021 10:46:55 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.2 MB)<br>
@ -790,7 +790,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>antibiotic</em> and <em>microorganism</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 4 March 2021 22:25:17 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 5 March 2021 10:46:55 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 kB)<br>
@ -1005,7 +1005,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>ab</em>, <em>breakpoint_R</em>, <em>breakpoint_S</em>, <em>disk_dose</em>, <em>guideline</em>, <em>method</em>, <em>mo</em>, <em>ref_tbl</em>, <em>site</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 4 March 2021 22:24:46 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 5 March 2021 10:46:55 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (34 kB)<br>

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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

15
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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1509030" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9030">
<a href="#amr-1509030" class="anchor"></a>AMR 1.5.0.9030<small> Unreleased </small>
<div id="amr-1509031" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9031">
<a href="#amr-1509031" class="anchor"></a>AMR 1.5.0.9031<small> Unreleased </small>
</h1>
<div id="last-updated-5-march-2021" class="section level2">
<h2 class="hasAnchor">
@ -280,7 +280,7 @@
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p>Function <code><a href="../reference/isolate_identifier.html">isolate_identifier()</a></code>, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
@ -302,6 +302,7 @@
<span class="fu"><a href="../reference/mo_property.html">mo_type</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># also supported: de, nl, fr, it, pt</span>
<span class="co">#&gt; [1] "Hongos" "Levaduras"</span></code></pre></div>
</li>
<li><p>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</p></li>
</ul>
</div>
<div id="changed" class="section level3">
@ -320,7 +321,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>
@ -328,9 +329,9 @@
<li>Using functions without setting a data set (e.g., <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>) now work with <code>dplyr</code>s <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> again</li>
<li>
<code><a href="../reference/first_isolate.html">first_isolate()</a></code> can be used with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> (also when using a dot <code>.</code> as input for the data) and now returns the names of the groups</li>
<li>MIC values now allow for any mathematical processing, such as usage inside functions <code><a href="https://rdrr.io/r/base/Extremes.html">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html">range()</a></code>, and with binary operators (+, -, etc.). This also enables other functions, such as <code><a href="https://rdrr.io/r/stats/fivenum.html">fivenum()</a></code>.</li>
<li>Updated the data set <code>microorganisms.codes</code> (which contains popular LIS and WHONET codes for microorganisms) for some species of <em>Mycobacterium</em> that previously incorrectly returned <em>M. africanum</em>
</li>
<li>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</li>
<li>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</li>
<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only <em>P. aeruginosa</em>)</li>
<li>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-03-05T09:15Z
last_built: 2021-03-05T14:27Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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">1.5.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>
@ -247,7 +247,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><code>AMR</code> is a free, open-source and independent <span style="R">R</span> package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, <span style="R">R</span> knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>After installing this package, <span style="R">R</span> knows ~70,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other <span style="R">R</span> package and works on Windows, macOS and Linux with all versions of <span style="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <span style="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>

7
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">1.5.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>
@ -288,6 +288,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># this can also coerce combined MIC/RSI values:</span>
<span class='fu'>as.mic</span><span class='op'>(</span><span class='st'>"&lt;=0.002; S"</span><span class='op'>)</span> <span class='co'># will return &lt;=0.002</span>
<span class='co'># mathematical processing treats MICs as numeric values</span>
<span class='fu'><a href='https://rdrr.io/r/stats/fivenum.html'>fivenum</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/quantile.html'>quantile</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/all.html'>all</a></span><span class='op'>(</span><span class='va'>mic_data</span> <span class='op'>&lt;</span> <span class='fl'>512</span><span class='op'>)</span>
<span class='co'># interpret MIC values</span>
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.mic</span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span>,
mo <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"S. pneumoniae"</span><span class='op'>)</span>,

2
docs/reference/as.mo.html
View File

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html
View File

@ -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">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
View File

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
View File

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/reference/index.html
View File

@ -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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

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

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/reference/microorganisms.html
View File

@ -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">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

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

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/reference/mo_property.html
View File

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/reference/plot.html
View File

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

8
docs/reference/random.html
View File

@ -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">1.5.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>
@ -303,9 +303,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span>, <span class='st'>"meropenem"</span><span class='op'>)</span> <span class='co'># range 0.0625-16</span>
<span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Streptococcus pneumoniae"</span>, <span class='st'>"meropenem"</span><span class='op'>)</span> <span class='co'># range 0.0625-4</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span><span class='op'>)</span> <span class='co'># range 11-50</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 6-14</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Streptococcus pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 16-22</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span><span class='op'>)</span> <span class='co'># range 8-50</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Klebsiella pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 11-17</span>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span>, <span class='st'>"Streptococcus pneumoniae"</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># range 12-27</span>
<span class='co'># }</span>
</pre>
</div>

2
docs/reference/rsi_translation.html
View File

@ -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">1.5.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
docs/survey.html
View File

@ -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">1.5.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
</span>
</div>

2
man/AMR.Rd
View File

@ -9,7 +9,7 @@ Welcome to the \code{AMR} package.
\details{
\code{AMR} is a free, open-source and independent \R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, \R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, \R knows ~70,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.

5
man/as.mic.Rd
View File

@ -44,6 +44,11 @@ is.mic(mic_data)
# this can also coerce combined MIC/RSI values:
as.mic("<=0.002; S") # will return <=0.002
# mathematical processing treats MICs as numeric values
fivenum(mic_data)
quantile(mic_data)
all(mic_data < 512)
# interpret MIC values
as.rsi(x = as.mic(2),
mo = as.mo("S. pneumoniae"),

6
man/random.Rd
View File

@ -57,8 +57,8 @@ random_mic(100, "Klebsiella pneumoniae") # range 0.0625-64
random_mic(100, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
random_mic(100, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
random_disk(100, "Klebsiella pneumoniae") # range 11-50
random_disk(100, "Klebsiella pneumoniae", "ampicillin") # range 6-14
random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 16-22
random_disk(100, "Klebsiella pneumoniae") # range 8-50
random_disk(100, "Klebsiella pneumoniae", "ampicillin") # range 11-17
random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 12-27
}
}