(v1.0.0.9004) add example_isolaten_unclean

v1.8.2
parent bb3728f023
commit 47fe8b7820
  1. 2
      DESCRIPTION
  2. 2
      NEWS.md
  3. 12
      R/data.R
  4. 94
      data-raw/reproduction_of_example_isolates_unclean.R
  5. BIN
      data/example_isolates_unclean.rda
  6. 2
      docs/404.html
  7. 2
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  8. 2
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  9. 2
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  10. 2
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  11. 8
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  12. 276
      docs/reference/example_isolates_unclean.html
  13. 2
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  15. 26
      man/example_isolates_unclean.Rd
  16. 2
      tests/testthat/test-rsi.R

@ -1,5 +1,5 @@
Package: AMR
Version: 1.0.0.9003
Version: 1.0.0.9004
Date: 2020-02-21
Title: Antimicrobial Resistance Analysis
Authors@R: c(

@ -1,4 +1,4 @@
# AMR 1.0.0.9003
# AMR 1.0.0.9004
## <small>Last updated: 21-Feb-2020</small>
### Changed

@ -161,6 +161,18 @@ catalogue_of_life <- list(
#' @inheritSection AMR Read more on our website!
"example_isolates"
#' Data set with unclean data
#'
#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.
#' @format A [`data.frame`] with 3,000 observations and 8 variables:
#' - `patient_id`\cr ID of the patient
#' - `date`\cr date of receipt at the laboratory
#' - `hospital`\cr ID of the hospital, from A to C
#' - `bacteria`\cr info about microorganism that can be transformed with [as.mo()], see also [microorganisms]
#' - `AMX:GEN`\cr 4 different antibiotics that have to be transformed with [as.rsi()]
#' @inheritSection AMR Read more on our website!
"example_isolates_unclean"
#' Data set with 500 isolates - WHONET example
#'
#' This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our [example_isolates] data set.

@ -0,0 +1,94 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
patients <- unlist(lapply(LETTERS, paste0, 1:10))
patients_table <- data.frame(patient_id = patients,
gender = c(rep("M", 135),
rep("F", 125)))
dates <- seq(as.Date("2011-01-01"), as.Date("2020-01-01"), by = "day")
bacteria_a <- c("E. coli", "S. aureus",
"S. pneumoniae", "K. pneumoniae")
bacteria_b <- c("esccol", "staaur", "strpne", "klepne")
bacteria_c <- c("Escherichia coli", "Staphylococcus aureus",
"Streptococcus pneumoniae", "Klebsiella pneumoniae")
ab_interpretations <- c("S", "I", "R")
ab_interpretations_messy = c("R", "< 0.5 S", "I")
sample_size <- 1000
data_a <- data.frame(date = sample(dates, size = sample_size, replace = TRUE),
hospital = "A",
bacteria = sample(bacteria_a, size = sample_size, replace = TRUE,
prob = c(0.50, 0.25, 0.15, 0.10)),
AMX = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.60, 0.05, 0.35)),
AMC = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.75, 0.10, 0.15)),
CIP = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.80, 0.00, 0.20)),
GEN = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.92, 0.00, 0.08)))
data_b <- data.frame(date = sample(dates, size = sample_size, replace = TRUE),
hospital = "B",
bacteria = sample(bacteria_b, size = sample_size, replace = TRUE,
prob = c(0.50, 0.25, 0.15, 0.10)),
AMX = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
prob = c(0.60, 0.05, 0.35)),
AMC = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
prob = c(0.75, 0.10, 0.15)),
CIP = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
prob = c(0.80, 0.00, 0.20)),
GEN = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
prob = c(0.92, 0.00, 0.08)))
data_c <- data.frame(date = sample(dates, size = sample_size, replace = TRUE),
hospital = "C",
bacteria = sample(bacteria_c, size = sample_size, replace = TRUE,
prob = c(0.50, 0.25, 0.15, 0.10)),
AMX = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.60, 0.05, 0.35)),
AMC = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.75, 0.10, 0.15)),
CIP = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.80, 0.00, 0.20)),
GEN = sample(ab_interpretations, size = sample_size, replace = TRUE,
prob = c(0.92, 0.00, 0.08)))
example_isolates_unclean <- data_a %>%
bind_rows(data_b, data_c)
example_isolates_unclean$patient_id <- sample(patients, size = nrow(example_isolates_unclean), replace = TRUE)
example_isolates_unclean <- example_isolates_unclean %>%
select(patient_id, hospital, date, bacteria, everything())
usethis::use_data(example_isolates_unclean, overwrite = TRUE)

Binary file not shown.

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
</span>
</div>

@ -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">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
</span>
</div>

@ -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">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
</span>
</div>

@ -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">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
</span>
</div>

@ -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">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
</span>
</div>

@ -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">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
</span>
</div>
@ -219,9 +219,9 @@
</div>
<div id="amr-1009003" class="section level1">
<div id="amr-1009004" class="section level1">
<h1 class="page-header">
<a href="#amr-1009003" class="anchor"></a>AMR 1.0.0.9003<small> Unreleased </small>
<a href="#amr-1009004" class="anchor"></a>AMR 1.0.0.9004<small> Unreleased </small>
</h1>
<div id="last-updated-21-feb-2020" class="section level2">
<h2 class="hasAnchor">
@ -1473,7 +1473,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-1009003">1.0.0.9003</a></li>
<li><a href="#amr-1009004">1.0.0.9004</a></li>
<li><a href="#amr-100">1.0.0</a></li>
<li><a href="#amr-090">0.9.0</a></li>
<li><a href="#amr-080">0.8.0</a></li>

@ -0,0 +1,276 @@
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<h1>Data set with unclean data</h1>
<div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.</p>
</div>
<pre class="usage"><span class='no'>example_isolates_unclean</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 3,000 observations and 8 variables:</p><ul>
<li><p><code>patient_id</code><br /> ID of the patient</p></li>
<li><p><code>date</code><br /> date of receipt at the laboratory</p></li>
<li><p><code>hospital</code><br /> ID of the hospital, from A to C</p></li>
<li><p><code>bacteria</code><br /> info about microorganism that can be transformed with <code><a href='as.mo.html'>as.mo()</a></code>, see also <a href='microorganisms.html'>microorganisms</a></p></li>
<li><p><code>AMX:GEN</code><br /> 4 different antibiotics that have to be transformed with <code><a href='as.rsi.html'>as.rsi()</a></code></p></li>
</ul>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#format">Format</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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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">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
</span>
</div>

@ -66,6 +66,9 @@
<url>
<loc>https://msberends.gitlab.io/AMR/reference/example_isolates.html</loc>
</url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/example_isolates_unclean.html</loc>
</url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/extended-functions.html</loc>
</url>

@ -0,0 +1,26 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{example_isolates_unclean}
\alias{example_isolates_unclean}
\title{Data set with unclean data}
\format{A \code{\link{data.frame}} with 3,000 observations and 8 variables:
\itemize{
\item \code{patient_id}\cr ID of the patient
\item \code{date}\cr date of receipt at the laboratory
\item \code{hospital}\cr ID of the hospital, from A to C
\item \code{bacteria}\cr info about microorganism that can be transformed with \code{\link[=as.mo]{as.mo()}}, see also \link{microorganisms}
\item \code{AMX:GEN}\cr 4 different antibiotics that have to be transformed with \code{\link[=as.rsi]{as.rsi()}}
}}
\usage{
example_isolates_unclean
}
\description{
A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.
}
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\keyword{datasets}

@ -58,7 +58,7 @@ test_that("rsi works", {
sum(),
40)
expect_output(tibble(ab = as.rsi("S")))
expect_output(print(tibble(ab = as.rsi("S"))))
expect_error(as.rsi.mic(as.mic(16)))
expect_error(as.rsi.disk(as.disk(16)))

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