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(v0.7.0.9010) mo_synonyms, plot/barplot fixes

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dr. M.S. (Matthijs) Berends 2019-06-16 21:42:40 +02:00
parent 980be2b22d
commit 9c39c35f86
72 changed files with 595 additions and 802 deletions
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10
.gitlab-ci.yml
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@ -20,7 +20,7 @@
# ==================================================================== #
# to check with R-Hub:
# rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))
# chck <- rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))
stages:
- build
@ -124,18 +124,10 @@ coverage:
pages:
stage: deploy
when: always
#cache:
# key: "$CI_COMMIT_REF_SLUG"
# paths:
# - installed_deps/
only:
- master
script:
- mv docs public
# install missing and outdated packages
#- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
#- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
#- R -e "pkgdown::build_site(examples = FALSE, lazy = TRUE, override = list(destination = 'public'))"
artifacts:
paths:
- public

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.0.9009
Date: 2019-06-13
Version: 0.7.0.9010
Date: 2019-06-16
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

1
NAMESPACE
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@ -154,6 +154,7 @@ export(mo_renamed)
export(mo_shortname)
export(mo_species)
export(mo_subspecies)
export(mo_synonyms)
export(mo_taxonomy)
export(mo_type)
export(mo_uncertainties)

26
NEWS.md
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@ -1,7 +1,7 @@
# AMR 0.7.0.9009
# AMR 0.7.0.9010
#### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
```r
septic_patients %>%
select(AMX, CIP) %>%
@ -12,14 +12,31 @@
# 3 Ciprofloxacin SI 0.8381831 1181
# 4 Ciprofloxacin R 0.1618169 228
```
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are:
* AIEC (Adherent-Invasive *E. coli*)
* ATEC (Atypical Entero-pathogenic *E. coli*)
* DAEC (Diffusely Adhering *E. coli*)
* EAEC (Entero-Aggresive *E. coli*)
* EHEC (Entero-Haemorrhagic *E. coli*)
* EIEC (Entero-Invasive *E. coli*)
* EPEC (Entero-Pathogenic *E. coli*)
* ETEC (Entero-Toxigenic *E. coli*)
* NMEC (Neonatal Meningitis‐causing *E. coli*)
* STEC (Shiga-toxin producing *E. coli*)
* UPEC (Uropathogenic *E. coli*)
All these lead to the microbial ID of *E. coli*:
```r
as.mo("UPEC")
# B_ESCHR_COL
mo_fullname("UPEC")
mo_name("UPEC")
# "Escherichia coli"
mo_gramstain("EHEC")
# "Gram-negative"
```
* Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism
* Function `mo_synonyms()` to get all previously accepted taxonomic names of a microorganism
#### Changed
* Column names of output `count_df()` and `portion_df()` are now lowercase
@ -36,6 +53,7 @@
* Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
* Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()`
* Manually added *Trichomonas vaginalis* from the kingdom of Protozoa, which is missing from the Catalogue of Life
* Small improvements to `plot()` and `barplot()` for MIC and RSI classes
#### Other
* Fixed a note thrown by CRAN tests

2
R/count.R
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@ -33,7 +33,7 @@
#'
#' The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
#'
#' The function \code{rsi_df} works exactly like \code{count_df}, but add the percentage of S, I and R.
#' The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
#' @source Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
#' @seealso \code{\link{portion}_*} to calculate microbial resistance and susceptibility.
#' @keywords resistance susceptibility rsi antibiotics isolate isolates

42
R/mic.R
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@ -242,34 +242,38 @@ summary.mic <- function(object, ...) {
#' @exportMethod plot.mic
#' @export
#' @importFrom dplyr %>% group_by summarise
#' @importFrom graphics plot text
#' @importFrom graphics barplot axis
#' @noRd
plot.mic <- function(x, ...) {
x_name <- deparse(substitute(x))
create_barplot_mic(x, x_name, ...)
plot.mic <- function(x,
main = paste('MIC values of', deparse(substitute(x))),
ylab = 'Frequency',
xlab = 'MIC value',
axes = FALSE,
...) {
barplot(table(droplevels.factor(x)),
ylab = ylab,
xlab = xlab,
axes = axes,
main = main,
...)
axis(2, seq(0, max(table(droplevels.factor(x)))))
}
#' @exportMethod barplot.mic
#' @export
#' @importFrom graphics barplot axis
#' @noRd
barplot.mic <- function(height, ...) {
x_name <- deparse(substitute(height))
create_barplot_mic(height, x_name, ...)
}
#' @importFrom graphics barplot axis
#' @importFrom dplyr %>% group_by summarise
create_barplot_mic <- function(x, x_name, ...) {
data <- data.frame(mic = droplevels(x), cnt = 1) %>%
group_by(mic) %>%
summarise(cnt = sum(cnt))
barplot(table(droplevels.factor(x)),
barplot.mic <- function(height,
main = paste('MIC values of', deparse(substitute(height))),
ylab = 'Frequency',
xlab = 'MIC value',
main = paste('MIC values of', x_name),
axes = FALSE,
...) {
barplot(table(droplevels.factor(height)),
ylab = ylab,
xlab = xlab,
axes = axes,
main = main,
...)
axis(2, seq(0, max(data$cnt)))
axis(2, seq(0, max(table(droplevels.factor(height)))))
}

11
R/misc.R
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@ -307,5 +307,14 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
}
"%or%" <- function(x, y) {
ifelse(!is.na(x), x, ifelse(!is.na(y), y, NA))
if (is.null(x) | is.null(y)) {
if (is.null(x)) {
return(y)
} else {
return(x)
}
}
ifelse(!is.na(x),
x,
ifelse(!is.na(y), y, NA))
}

15
R/mo_property.R
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@ -73,6 +73,7 @@
#' mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
#' mo_rank("E. coli") # "species"
#' mo_url("E. coli") # get the direct url to the online database entry
#' mo_synonyms("E. coli") # get previously accepted taxonomic names
#'
#' ## scientific reference
#' mo_ref("E. coli") # "Castellani et al., 1919"
@ -312,12 +313,24 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
subspecies = mo_subspecies(x, language = language))
}
#' @rdname mo_property
#' @export
mo_synonyms <- function(x, ...) {
x <- AMR::as.mo(x, ...)
col_id <- AMR::microorganisms[which(AMR::microorganisms$mo == x), "col_id"]
if (is.na(col_id) | !col_id %in% AMR::microorganisms.old$col_id_new) {
return(NULL)
}
sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
}
#' @rdname mo_property
#' @export
mo_info <- function(x, language = get_locale(), ...) {
x <- AMR::as.mo(x, ...)
c(mo_taxonomy(x, language = language),
list(url = unname(mo_url(x, open = FALSE)),
list(synonyms = mo_synonyms(x),
url = unname(mo_url(x, open = FALSE)),
ref = mo_ref(x)))
}

2
R/portion.R
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@ -40,7 +40,7 @@
#'
#' The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
#'
#' The function \code{rsi_df} works exactly like \code{portion_df}, but add the number of isolates.
#' The function \code{rsi_df} works exactly like \code{portion_df}, but adds the number of isolates.
#' \if{html}{
# (created with https://www.latex4technics.com/)
#' \cr\cr

60
R/rsi.R
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@ -387,9 +387,14 @@ summary.rsi <- function(object, ...) {
#' @importFrom dplyr %>% group_by summarise filter mutate if_else n_distinct
#' @importFrom graphics plot text
#' @noRd
plot.rsi <- function(x, ...) {
x_name <- deparse(substitute(x))
plot.rsi <- function(x,
lwd = 2,
ylim = NULL,
ylab = 'Percentage',
xlab = 'Antimicrobial Interpretation',
main = paste('Susceptibility Analysis of', deparse(substitute(x))),
axes = FALSE,
...) {
suppressWarnings(
data <- data.frame(x = x,
y = 1,
@ -415,13 +420,12 @@ plot.rsi <- function(x, ...) {
plot(x = data$x,
y = data$s,
lwd = 2,
col = c('green', 'orange', 'red'),
lwd = lwd,
ylim = c(0, ymax),
ylab = 'Percentage',
xlab = 'Antimicrobial Interpretation',
main = paste('Susceptibility Analysis of', x_name),
axes = FALSE,
ylab = ylab,
xlab = xlab,
main = main,
axes = axes,
...)
# x axis
axis(side = 1, at = 1:n_distinct(data$x), labels = levels(data$x), lwd = 0)
@ -439,24 +443,32 @@ plot.rsi <- function(x, ...) {
#' @importFrom dplyr %>% group_by summarise
#' @importFrom graphics barplot axis
#' @noRd
barplot.rsi <- function(height, ...) {
x <- height
x_name <- deparse(substitute(height))
suppressWarnings(
data <- data.frame(rsi = x, cnt = 1) %>%
group_by(rsi) %>%
summarise(cnt = sum(cnt)) %>%
droplevels()
)
barplot(table(x),
barplot.rsi <- function(height,
col = c('green3', 'orange2', 'red3'),
xlab = 'Antimicrobial Interpretation',
main = paste('Susceptibility Analysis of', x_name),
xlab = ifelse(beside, 'Antimicrobial Interpretation', ''),
main = paste('Susceptibility Analysis of', deparse(substitute(height))),
ylab = 'Frequency',
beside = TRUE,
axes = beside,
...) {
if (axes == TRUE) {
par(mar = c(5, 4, 4, 2) + 0.1)
} else {
par(mar = c(2, 4, 4, 2) + 0.1)
}
barplot(as.matrix(table(height)),
col = col,
xlab = xlab,
main = main,
ylab = ylab,
beside = beside,
axes = FALSE,
...)
# y axis, 0-100%
axis(side = 2, at = seq(0, max(data$cnt) + max(data$cnt) * 1.1, by = 25))
axis(side = 2, at = seq(0, max(table(height)) + max(table(height)) * 1.1, by = 25))
if (axes == TRUE && beside == TRUE) {
axis(side = 1, labels = levels(height), at = c(1, 2, 3) + 0.5, lwd = 0)
}
}

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
</span>
</div>

659
docs/articles/AMR.html
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docs/articles/index.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
</span>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
</span>
</div>

36
docs/news/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
</span>
</div>
@ -232,16 +232,16 @@
</div>
<div id="amr-0709009" class="section level1">
<div id="amr-0709010" class="section level1">
<h1 class="page-header">
<a href="#amr-0709009" class="anchor"></a>AMR 0.7.0.9009<small> Unreleased </small>
<a href="#amr-0709010" class="anchor"></a>AMR 0.7.0.9010<small> Unreleased </small>
</h1>
<div id="new" class="section level4">
<h4 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h4>
<ul>
<li>
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb1-2" title="2"><span class="st"> </span><span class="kw">select</span>(AMX, CIP) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb1-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
@ -252,13 +252,30 @@
<a class="sourceLine" id="cb1-8" title="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
</li>
<li>
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are: AIEC (Adherent-Invasive <em>E. coli</em>), ATEC (Atypical Entero-pathogenic <em>E. coli</em>), DAEC (Diffusely Adhering <em>E. coli</em>), EAEC (Entero-Aggresive <em>E. coli</em>), EHEC (Entero-Haemorrhagic <em>E. coli</em>), EIEC (Entero-Invasive <em>E. coli</em>), EPEC (Entero-Pathogenic <em>E. coli</em>), ETEC (Entero-Toxigenic <em>E. coli</em>), NMEC (Neonatal Meningitis‐causing <em>E. coli</em>), STEC (Shiga-toxin producing <em>E. coli</em>) and UPEC (Uropathogenic <em>E. coli</em>). All these lead to the microbial ID of <em>E. coli</em>:</p>
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are:</p>
<ul>
<li>AIEC (Adherent-Invasive <em>E. coli</em>)</li>
<li>ATEC (Atypical Entero-pathogenic <em>E. coli</em>)</li>
<li>DAEC (Diffusely Adhering <em>E. coli</em>)</li>
<li>EAEC (Entero-Aggresive <em>E. coli</em>)</li>
<li>EHEC (Entero-Haemorrhagic <em>E. coli</em>)</li>
<li>EIEC (Entero-Invasive <em>E. coli</em>)</li>
<li>EPEC (Entero-Pathogenic <em>E. coli</em>)</li>
<li>ETEC (Entero-Toxigenic <em>E. coli</em>)</li>
<li>NMEC (Neonatal Meningitis‐causing <em>E. coli</em>)</li>
<li>STEC (Shiga-toxin producing <em>E. coli</em>)</li>
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
</ul>
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb2-2" title="2"><span class="co"># B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a></code></pre></div>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a>
<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
<a class="sourceLine" id="cb2-6" title="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
</ul>
</div>
<div id="changed" class="section level4">
@ -283,6 +300,7 @@
<li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
<li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
</ul>
</div>
<div id="other" class="section level4">
@ -1121,7 +1139,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0709009">0.7.0.9009</a></li>
<li><a href="#amr-0709010">0.7.0.9010</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>

9
docs/reference/AMR-deprecated.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/AMR.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/WHOCC.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/WHONET.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/ab_property.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/age.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/age_groups.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

2
docs/reference/antibiotics.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>

9
docs/reference/as.ab.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/as.atc.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/as.disk.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/as.mic.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/as.mo.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/as.rsi.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/atc_online.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/availability.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

2
docs/reference/catalogue_of_life.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>

2
docs/reference/count.html
View File

@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>

9
docs/reference/eucast_rules.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/extended-functions.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/filter_ab_class.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/first_isolate.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/freq.html
View File

@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -166,13 +166,6 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

9
docs/reference/g.test.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

2
docs/reference/ggplot_rsi.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>

9
docs/reference/guess_ab_col.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>

4
docs/reference/index.html
View File

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
</span>
</div>
@ -373,7 +373,7 @@
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>

9
docs/reference/join.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
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docs/reference/key_antibiotics.html
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@ -80,7 +80,7 @@
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docs/reference/kurtosis.html
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@ -80,7 +80,7 @@
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@ -80,7 +80,7 @@
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@ -80,7 +80,7 @@
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docs/reference/microorganisms.codes.html
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@ -80,7 +80,7 @@
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docs/reference/microorganisms.html
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@ -80,7 +80,7 @@
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docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
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docs/reference/mo_property.html
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@ -80,7 +80,7 @@
</button>
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</span>
</div>
@ -277,6 +277,8 @@
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_synonyms</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
@ -377,6 +379,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
<span class='fu'>mo_synonyms</span>(<span class='st'>"E. coli"</span>) <span class='co'># get previously accepted taxonomic names</span>
<span class='co'>## scientific reference</span>
<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al., 1919"</span>

9
docs/reference/mo_source.html
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@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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</span>
</div>
@ -166,13 +166,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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docs/reference/p.symbol.html
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@ -80,7 +80,7 @@
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</span>
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@ -165,13 +165,6 @@
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docs/reference/portion.html
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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docs/reference/read.4D.html
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@ -80,7 +80,7 @@
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docs/reference/resistance_predict.html
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@ -80,7 +80,7 @@
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docs/reference/rsi_translation.html
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@ -80,7 +80,7 @@
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docs/reference/septic_patients.html
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@ -80,7 +80,7 @@
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docs/reference/skewness.html
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@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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@ -166,13 +166,6 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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@ -80,7 +80,7 @@
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git_merge.sh
View File

@ -13,15 +13,15 @@
git add .
git commit -a -m "website update" --quiet
git checkout master --quiet
echo "changed branch to master"
echo "• changed branch to master"
# import everything from premaster
git merge premaster --quiet
# and send it to git
git push --quiet
echo "pushed changes to master"
echo "• pushed changes to master"
# return to premaster
git checkout premaster --quiet
echo "changed branch back to premaster"
echo "• changed branch back to premaster"
git status --short

2
man/count.Rd
View File

@ -62,7 +62,7 @@ The function \code{n_rsi} is an alias of \code{count_all}. They can be used to c
The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
The function \code{rsi_df} works exactly like \code{count_df}, but add the percentage of S, I and R.
The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
}
\section{Interpretation of S, I and R}{

4
man/mo_property.Rd
View File

@ -20,6 +20,7 @@
\alias{mo_year}
\alias{mo_rank}
\alias{mo_taxonomy}
\alias{mo_synonyms}
\alias{mo_info}
\alias{mo_url}
\title{Property of a microorganism}
@ -60,6 +61,8 @@ mo_rank(x, ...)
mo_taxonomy(x, language = get_locale(), ...)
mo_synonyms(x, ...)
mo_info(x, language = get_locale(), ...)
mo_url(x, open = FALSE, ...)
@ -147,6 +150,7 @@ mo_gramstain("E. coli") # "Gram-negative"
mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
mo_rank("E. coli") # "species"
mo_url("E. coli") # get the direct url to the online database entry
mo_synonyms("E. coli") # get previously accepted taxonomic names
## scientific reference
mo_ref("E. coli") # "Castellani et al., 1919"

2
man/portion.Rd
View File

@ -73,7 +73,7 @@ These functions are not meant to count isolates, but to calculate the portion of
The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
The function \code{rsi_df} works exactly like \code{portion_df}, but add the number of isolates.
The function \code{rsi_df} works exactly like \code{portion_df}, but adds the number of isolates.
\if{html}{
\cr\cr
To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula:

92
tests/testthat/test-mo_property.R
View File

@ -22,34 +22,37 @@
context("mo_property.R")
test_that("mo_property works", {
expect_equal(mo_kingdom("E. coli"), "Bacteria")
expect_equal(mo_phylum("E. coli"), "Proteobacteria")
expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
expect_equal(mo_order("E. coli"), "Enterobacteriales")
expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
expect_equal(mo_genus("E. coli"), "Escherichia")
expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), "")
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
expect_equal(mo_name("E. coli"), "Escherichia coli")
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram-negative")
expect_equal(class(mo_taxonomy("E. coli")), "list")
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacteriales")
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
expect_equal(mo_genus("Escherichia coli"), "Escherichia")
expect_equal(mo_species("Escherichia coli"), "coli")
expect_equal(mo_subspecies("Escherichia coli"), "")
expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
expect_equal(class(mo_taxonomy("Escherichia coli")), "list")
expect_equal(names(mo_taxonomy("Escherichia coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies"))
expect_equal(names(mo_info("E. coli")), c("kingdom", "phylum", "class", "order",
expect_equal(mo_synonyms("Escherichia coli"), NULL)
expect_gt(length(mo_synonyms("C. albicans")), 1)
expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"url", "ref"))
"synonyms", "url", "ref"))
expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
expect_equal(mo_authors("E. coli"), "Castellani et al.")
expect_equal(mo_year("E. coli"), 1919)
expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
expect_equal(mo_year("Escherichia coli"), 1919)
expect_equal(mo_shortname("MRSA"), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
expect_equal(mo_shortname("Escherichia coli"), "E. coli")
expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
@ -58,28 +61,28 @@ test_that("mo_property works", {
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
# check languages
expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("E. coli", language = "nl"), "Gram-negatief")
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
expect_output(print(mo_gramstain("E. coli", language = "en")))
expect_output(print(mo_gramstain("E. coli", language = "de")))
expect_output(print(mo_gramstain("E. coli", language = "nl")))
expect_output(print(mo_gramstain("E. coli", language = "es")))
expect_output(print(mo_gramstain("E. coli", language = "pt")))
expect_output(print(mo_gramstain("E. coli", language = "it")))
expect_output(print(mo_gramstain("E. coli", language = "fr")))
expect_output(print(mo_gramstain("Escherichia coli", language = "en")))
expect_output(print(mo_gramstain("Escherichia coli", language = "de")))
expect_output(print(mo_gramstain("Escherichia coli", language = "nl")))
expect_output(print(mo_gramstain("Escherichia coli", language = "es")))
expect_output(print(mo_gramstain("Escherichia coli", language = "pt")))
expect_output(print(mo_gramstain("Escherichia coli", language = "it")))
expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
expect_error(mo_gramstain("E. coli", language = "UNKNOWN"))
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
# manual property function
expect_error(mo_property("E. coli", property = c("tsn", "fullname")))
expect_error(mo_property("E. coli", property = "UNKNOWN"))
expect_identical(mo_property("E. coli", property = "fullname"),
mo_fullname("E. coli"))
expect_identical(mo_property("E. coli", property = "genus"),
mo_genus("E. coli"))
expect_identical(mo_property("E. coli", property = "species"),
mo_species("E. coli"))
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
expect_identical(mo_property("Escherichia coli", property = "fullname"),
mo_fullname("Escherichia coli"))
expect_identical(mo_property("Escherichia coli", property = "genus"),
mo_genus("Escherichia coli"))
expect_identical(mo_property("Escherichia coli", property = "species"),
mo_species("Escherichia coli"))
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
@ -87,14 +90,13 @@ test_that("mo_property works", {
# outcome of mo_fullname must always return the fullname from the data set
library(dplyr)
a <- microorganisms %>%
x <- microorganisms %>%
transmute(mo,
# fullname from the original data:
f1 = fullname,
# newly created fullname based on MO code:
f2 = mo_fullname(mo, language = "en")) %>%
filter(f1 != f2)
expect_equal(nrow(a), 0)
expect_equal(nrow(x), 0)
})

60
vignettes/AMR.Rmd
View File

@ -78,7 +78,7 @@ patients_table <- data.frame(patient_id = patients,
The first 135 patient IDs are now male, the other 125 are female.
## Dates
Let's pretend that our data consists of blood cultures isolates from 1 January 2010 until 1 January 2018.
Let's pretend that our data consists of blood cultures isolates from between 1 January 2010 and 1 January 2018.
```{r create dates}
dates <- seq(as.Date("2010-01-01"), as.Date("2018-01-01"), by = "day")
@ -131,7 +131,7 @@ Using the `left_join()` function from the `dplyr` package, we can 'map' the gend
data <- data %>% left_join(patients_table)
```
The resulting data set contains 5,000 blood culture isolates. With the `head()` function we can preview the first 6 values of this data set:
The resulting data set contains `r format(nrow(data), big.mark = ",")` blood culture isolates. With the `head()` function we can preview the first 6 values of this data set:
```{r preview data set 1, eval = FALSE}
head(data)
@ -154,7 +154,7 @@ data %>% freq(gender) # this would be the same: freq(data$gender)
data %>% freq(gender, markdown = FALSE, header = TRUE)
```
So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values `M` and `F`. From a researcher perspective: there are slightly more men. Nothing we didn't already know.
So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values `M` and `F`. From a researchers perspective: there are slightly more men. Nothing we didn't already know.
The data is already quite clean, but we still need to transform some variables. The `bacteria` column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The `mutate()` function of the `dplyr` package makes this really easy:
@ -219,7 +219,6 @@ data_1st <- data %>%
```
## First *weighted* isolates
We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Imagine this data, sorted on date:
```{r, echo = FALSE, message = FALSE, warning = FALSE, results = 'asis'}
weighted_df <- data %>%
@ -232,7 +231,11 @@ weighted_df <- data %>%
.[1:min(10, nrow(.)),] %>%
mutate(isolate = row_number()) %>%
select(isolate, everything())
```
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 `r as.data.frame(weighted_df[1, 'patient_id'])`, sorted on date:
```{r, echo = FALSE, message = FALSE, warning = FALSE, results = 'asis'}
weighted_df %>%
knitr::kable(align = "c")
```
@ -378,10 +381,10 @@ data_1st %>%
summarise("1. Amoxi/clav" = portion_SI(AMC),
"2. Gentamicin" = portion_SI(GEN),
"3. Amoxi/clav + genta" = portion_SI(AMC, GEN)) %>%
tidyr::gather("Antibiotic", "S", -genus) %>%
tidyr::gather("antibiotic", "S", -genus) %>%
ggplot(aes(x = genus,
y = S,
fill = Antibiotic)) +
fill = antibiotic)) +
geom_col(position = "dodge2")
```
@ -410,7 +413,7 @@ ggplot(data_1st) +
geom_rsi(translate_ab = FALSE)
```
Omit the `translate_ab = FALSE` to have the antibiotic codes (AMX, AMC, CIP, GEN) translated to official WHO names (amoxicillin, amoxicillin and betalactamase inhibitor, ciprofloxacin, gentamicin).
Omit the `translate_ab = FALSE` to have the antibiotic codes (AMX, AMC, CIP, GEN) translated to official WHO names (amoxicillin, amoxicillin/clavulanic acid, ciprofloxacin, gentamicin).
If we group on e.g. the `genus` column and add some additional functions from our package, we can create this:
@ -422,7 +425,7 @@ ggplot(data_1st %>% group_by(genus)) +
# of which we have 4 (earlier created with `as.rsi`)
geom_rsi(x = "genus") +
# split plots on antibiotic
facet_rsi(facet = "Antibiotic") +
facet_rsi(facet = "antibiotic") +
# make R red, I yellow and S green
scale_rsi_colours() +
# show percentages on y axis
@ -443,7 +446,7 @@ To simplify this, we also created the `ggplot_rsi()` function, which combines al
data_1st %>%
group_by(genus) %>%
ggplot_rsi(x = "genus",
facet = "Antibiotic",
facet = "antibiotic",
breaks = 0:4 * 25,
datalabels = FALSE) +
coord_flip()
@ -453,33 +456,26 @@ data_1st %>%
The next example uses the included `septic_patients`, which is an anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This `data.frame` can be used to practice AMR analysis.
We will compare the resistance to fosfomycin (column `FOS`) in hospital A and D. The input for the final `fisher.test()` will be this:
We will compare the resistance to fosfomycin (column `FOS`) in hospital A and D. The input for the `fisher.test()` can be retrieved with a transformation like this:
```{r, echo = FALSE, results = 'asis'}
septic_patients %>%
filter(hospital_id %in% c("A", "D")) %>%
select(hospital_id, FOS) %>%
group_by(hospital_id) %>%
count_df(combine_IR = TRUE) %>%
tidyr::spread(hospital_id, Value) %>%
select(A, D) %>%
bind_cols(tibble(" " = c("IR", "S")), .) %>%
as.matrix() %>%
knitr::kable()
```
We can transform the data and apply the test in only a couple of lines:
```{r}
septic_patients %>%
```{r, results = 'markup'}
check_FOS <- septic_patients %>%
filter(hospital_id %in% c("A", "D")) %>% # filter on only hospitals A and D
select(hospital_id, FOS) %>% # select the hospitals and fosfomycin
group_by(hospital_id) %>% # group on the hospitals
count_df(combine_IR = TRUE) %>% # count all isolates per group (hospital_id)
tidyr::spread(hospital_id, Value) %>% # transform output so A and D are columns
count_df(combine_SI = TRUE) %>% # count all isolates per group (hospital_id)
tidyr::spread(hospital_id, value) %>% # transform output so A and D are columns
select(A, D) %>% # and select these only
as.matrix() %>% # transform to good old matrix for fisher.test()
fisher.test() # do Fisher's Exact Test
as.matrix() # transform to good old matrix for fisher.test()
check_FOS
```
As can be seen, the p value is 0.03, which means that the fosfomycin resistances found in hospital A and D are really different.
We can apply the test now with:
```{r}
# do Fisher's Exact Test
fisher.test(check_FOS)
```
As can be seen, the p value is `r round(fisher.test(check_FOS)$p.value, 3)`, which means that the fosfomycin resistances found in hospital A and D are really different.