mirror of https://github.com/msberends/AMR.git
(v1.0.0.9004) add example_isolaten_unclean
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Package: AMR
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Version: 1.0.0.9003
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Version: 1.0.0.9004
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Date: 2020-02-21
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.0.0.9003
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# AMR 1.0.0.9004
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## <small>Last updated: 21-Feb-2020</small>
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### Changed
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12
R/data.R
12
R/data.R
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@ -161,6 +161,18 @@ catalogue_of_life <- list(
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#' @inheritSection AMR Read more on our website!
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"example_isolates"
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#' Data set with unclean data
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#'
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#' 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.
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#' @format A [`data.frame`] with 3,000 observations and 8 variables:
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#' - `patient_id`\cr ID of the patient
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#' - `date`\cr date of receipt at the laboratory
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#' - `hospital`\cr ID of the hospital, from A to C
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#' - `bacteria`\cr info about microorganism that can be transformed with [as.mo()], see also [microorganisms]
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#' - `AMX:GEN`\cr 4 different antibiotics that have to be transformed with [as.rsi()]
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#' @inheritSection AMR Read more on our website!
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"example_isolates_unclean"
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#' Data set with 500 isolates - WHONET example
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#'
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#' 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.
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@ -0,0 +1,94 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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patients <- unlist(lapply(LETTERS, paste0, 1:10))
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patients_table <- data.frame(patient_id = patients,
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gender = c(rep("M", 135),
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rep("F", 125)))
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dates <- seq(as.Date("2011-01-01"), as.Date("2020-01-01"), by = "day")
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bacteria_a <- c("E. coli", "S. aureus",
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"S. pneumoniae", "K. pneumoniae")
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bacteria_b <- c("esccol", "staaur", "strpne", "klepne")
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bacteria_c <- c("Escherichia coli", "Staphylococcus aureus",
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"Streptococcus pneumoniae", "Klebsiella pneumoniae")
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ab_interpretations <- c("S", "I", "R")
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ab_interpretations_messy = c("R", "< 0.5 S", "I")
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sample_size <- 1000
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data_a <- data.frame(date = sample(dates, size = sample_size, replace = TRUE),
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hospital = "A",
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bacteria = sample(bacteria_a, size = sample_size, replace = TRUE,
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prob = c(0.50, 0.25, 0.15, 0.10)),
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AMX = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.60, 0.05, 0.35)),
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AMC = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.75, 0.10, 0.15)),
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CIP = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.80, 0.00, 0.20)),
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GEN = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.92, 0.00, 0.08)))
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data_b <- data.frame(date = sample(dates, size = sample_size, replace = TRUE),
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hospital = "B",
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bacteria = sample(bacteria_b, size = sample_size, replace = TRUE,
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prob = c(0.50, 0.25, 0.15, 0.10)),
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AMX = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
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prob = c(0.60, 0.05, 0.35)),
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AMC = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
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prob = c(0.75, 0.10, 0.15)),
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CIP = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
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prob = c(0.80, 0.00, 0.20)),
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GEN = sample(ab_interpretations_messy, size = sample_size, replace = TRUE,
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prob = c(0.92, 0.00, 0.08)))
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data_c <- data.frame(date = sample(dates, size = sample_size, replace = TRUE),
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hospital = "C",
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bacteria = sample(bacteria_c, size = sample_size, replace = TRUE,
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prob = c(0.50, 0.25, 0.15, 0.10)),
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AMX = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.60, 0.05, 0.35)),
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AMC = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.75, 0.10, 0.15)),
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CIP = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.80, 0.00, 0.20)),
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GEN = sample(ab_interpretations, size = sample_size, replace = TRUE,
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prob = c(0.92, 0.00, 0.08)))
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example_isolates_unclean <- data_a %>%
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bind_rows(data_b, data_c)
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example_isolates_unclean$patient_id <- sample(patients, size = nrow(example_isolates_unclean), replace = TRUE)
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example_isolates_unclean <- example_isolates_unclean %>%
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select(patient_id, hospital, date, bacteria, everything())
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usethis::use_data(example_isolates_unclean, overwrite = TRUE)
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Binary file not shown.
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<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>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<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>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<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>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
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<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>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9004</span>
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</span>
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</div>
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@ -219,9 +219,9 @@
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</div>
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<div id="amr-1009003" class="section level1">
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<div id="amr-1009004" class="section level1">
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<h1 class="page-header">
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<a href="#amr-1009003" class="anchor"></a>AMR 1.0.0.9003<small> Unreleased </small>
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<a href="#amr-1009004" class="anchor"></a>AMR 1.0.0.9004<small> Unreleased </small>
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</h1>
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<div id="last-updated-21-feb-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -1473,7 +1473,7 @@
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-1009003">1.0.0.9003</a></li>
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<li><a href="#amr-1009004">1.0.0.9004</a></li>
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<li><a href="#amr-100">1.0.0</a></li>
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<li><a href="#amr-090">0.9.0</a></li>
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<li><a href="#amr-080">0.8.0</a></li>
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|
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@ -0,0 +1,276 @@
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<title>Data set with unclean data — example_isolates_unclean • AMR (for R)</title>
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<meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
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<meta property="og:description" content="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." />
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Conduct AMR analysis
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||||
<a href="../reference/">
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Manual
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Authors
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<span class="far fa far fa-newspaper"></span>
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<ul class="nav navbar-nav navbar-right">
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<a href="https://gitlab.com/msberends/AMR">
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<span class="fab fa fab fa-gitlab"></span>
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Source Code
|
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<a href="../LICENSE-text.html">
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</div><!--/.nav-collapse -->
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</div><!--/.container -->
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</header>
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|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<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>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<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>
|
||||
</ul>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
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</div>
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</footer>
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</div>
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||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
|
||||
|
|
@ -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)))
|
||||
|
|
|
|||
Loading…
Reference in New Issue