2022-08-21 16:59:35 +02:00
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --> < html lang = "en" >
< head >
< meta http-equiv = "Content-Type" content = "text/html; charset=UTF-8" >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1, shrink-to-fit=no" >
< meta name = "description" content = "AMR" >
< title > How to work with WHONET data • AMR (for R)< / title >
<!-- favicons --> < link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" >
< link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "180x180" href = "../apple-touch-icon.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "120x120" href = "../apple-touch-icon-120x120.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "76x76" href = "../apple-touch-icon-76x76.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "60x60" href = "../apple-touch-icon-60x60.png" >
< script src = "../deps/jquery-3.6.0/jquery-3.6.0.min.js" > < / script > < meta name = "viewport" content = "width=device-width, initial-scale=1, shrink-to-fit=no" >
2022-12-20 16:22:22 +01:00
< link href = "../deps/bootstrap-5.2.2/bootstrap.min.css" rel = "stylesheet" >
< script src = "../deps/bootstrap-5.2.2/bootstrap.bundle.min.js" > < / script > < link href = "../deps/Fira_Code-0.4.4/font.css" rel = "stylesheet" >
2022-08-21 16:59:35 +02:00
<!-- Font Awesome icons --> < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity = "sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin = "anonymous" >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity = "sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin = "anonymous" >
2022-12-16 16:17:49 +01:00
<!-- bootstrap - toc --> < script src = "https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity = "sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin = "anonymous" > < / script > <!-- headroom.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity = "sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script > <!-- clipboard.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script > <!-- search --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity = "sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity = "sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity = "sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin = "anonymous" > < / script > <!-- pkgdown --> < script src = "../pkgdown.js" > < / script > < link href = "../extra.css" rel = "stylesheet" >
2022-08-21 16:59:35 +02:00
< script src = "../extra.js" > < / script > < meta property = "og:title" content = "How to work with WHONET data" >
< meta property = "og:description" content = "AMR" >
< meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" >
< meta name = "twitter:card" content = "summary_large_image" >
< meta name = "twitter:creator" content = "@msberends" >
2022-10-05 12:32:07 +02:00
< meta name = "twitter:site" content = "@msberends" >
2022-08-21 16:59:35 +02:00
<!-- mathjax --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity = "sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity = "sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin = "anonymous" > < / script > <!-- [if lt IE 9]>
< script src = "https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js" > < / script >
< script src = "https://oss.maxcdn.com/respond/1.4.2/respond.min.js" > < / script >
<![endif]-->
< / head >
< body >
< a href = "#main" class = "visually-hidden-focusable" > Skip to contents< / a >
< nav class = "navbar fixed-top navbar-dark navbar-expand-lg bg-primary" > < div class = "container" >
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
2023-01-12 23:23:33 +01:00
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 1.8.2.9091< / small >
2022-08-21 16:59:35 +02:00
< button class = "navbar-toggler" type = "button" data-bs-toggle = "collapse" data-bs-target = "#navbar" aria-controls = "navbar" aria-expanded = "false" aria-label = "Toggle navigation" >
< span class = "navbar-toggler-icon" > < / span >
< / button >
< div id = "navbar" class = "collapse navbar-collapse ms-3" >
< ul class = "navbar-nav me-auto" >
< li class = "nav-item" >
< a class = "nav-link" href = "../index.html" >
< span class = "fa fa-home" > < / span >
Home
< / a >
< / li >
< li class = "active nav-item dropdown" >
< a href = "#" class = "nav-link dropdown-toggle" data-bs-toggle = "dropdown" role = "button" aria-expanded = "false" aria-haspopup = "true" id = "dropdown--how-to" >
< span class = "fa fa-question-circle" > < / span >
How to
< / a >
< div class = "dropdown-menu" aria-labelledby = "dropdown--how-to" >
< a class = "dropdown-item" href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< a class = "dropdown-item" href = "../articles/resistance_predict.html" >
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< a class = "dropdown-item" href = "../articles/datasets.html" >
< span class = "fa fa-database" > < / span >
Data sets for download / own use
< / a >
< a class = "dropdown-item" href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
Conduct principal component analysis for AMR
< / a >
< a class = "dropdown-item" href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / a >
< a class = "dropdown-item" href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< a class = "dropdown-item" href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< a class = "dropdown-item" href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< a class = "dropdown-item" href = "../reference/mo_property.html" >
< span class = "fa fa-bug" > < / span >
2022-12-30 13:10:58 +01:00
Get taxonomy of a microorganism
2022-08-21 16:59:35 +02:00
< / a >
< a class = "dropdown-item" href = "../reference/ab_property.html" >
< span class = "fa fa-capsules" > < / span >
2022-12-30 13:10:58 +01:00
Get properties of an antibiotic drug
2022-08-21 16:59:35 +02:00
< / a >
2022-11-13 08:54:32 +01:00
< a class = "dropdown-item" href = "../reference/av_property.html" >
< span class = "fa fa-capsules" > < / span >
2022-12-30 13:10:58 +01:00
Get properties of an antiviral drug
2022-11-13 08:54:32 +01:00
< / a >
2022-08-21 16:59:35 +02:00
< / div >
< / li >
< li class = "nav-item" >
< a class = "nav-link" href = "../reference/index.html" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
< / li >
< li class = "nav-item" >
< a class = "nav-link" href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
< li class = "nav-item" >
< a class = "nav-link" href = "../news/index.html" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< / ul >
< form class = "form-inline my-2 my-lg-0" role = "search" >
< input type = "search" class = "form-control me-sm-2" aria-label = "Toggle navigation" name = "search-input" data-search-index = "../search.json" id = "search-input" placeholder = "Search for" autocomplete = "off" >
< / form >
< ul class = "navbar-nav" >
< li class = "nav-item" >
< a class = "external-link nav-link" href = "https://github.com/msberends/AMR" >
< span class = "fab fa fab fa-github" > < / span >
Source Code
< / a >
< / li >
< / ul >
< / div >
< / div >
< / nav > < div class = "container template-article" >
< div class = "row" >
< main id = "main" class = "col-md-9" > < div class = "page-header" >
< img src = "../logo.svg" class = "logo" alt = "" > < h1 > How to work with WHONET data< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/vignettes/WHONET.Rmd" class = "external-link" > < code > vignettes/WHONET.Rmd< / code > < / a > < / small >
< div class = "d-none name" > < code > WHONET.Rmd< / code > < / div >
< / div >
< div class = "section level3" >
< h3 id = "import-of-data" > Import of data< a class = "anchor" aria-label = "anchor" href = "#import-of-data" > < / a >
< / h3 >
2022-10-29 14:24:08 +02:00
< p > This tutorial assumes you already imported the WHONET data with
e.g. < a href = "https://readxl.tidyverse.org/" class = "external-link" > < code > readxl< / code >
package< / a > . In RStudio, this can be done using the menu button ‘
Dataset’ ‘ ’ ‘ ’
select your exported file. Make sure date fields are imported
correctly.< / p >
2022-08-21 16:59:35 +02:00
< p > An example syntax could look like this:< / p >
< div class = "sourceCode" id = "cb1" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://readxl.tidyverse.org" class = "external-link" > readxl< / a > < / span > < span class = "op" > )< / span > < / span >
< span > < span class = "va" > data< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://readxl.tidyverse.org/reference/read_excel.html" class = "external-link" > read_excel< / a > < / span > < span class = "op" > (< / span > path < span class = "op" > =< / span > < span class = "st" > "path/to/your/file.xlsx"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
2022-10-29 14:24:08 +02:00
< p > This package comes with an < a href = "https://msberends.github.io/AMR/reference/WHONET.html" > example
data set < code > WHONET< / code > < / a > . We will use it for this analysis.< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "section level3" >
< h3 id = "preparation" > Preparation< a class = "anchor" aria-label = "anchor" href = "#preparation" > < / a >
< / h3 >
2022-10-29 14:24:08 +02:00
< p > First, load the relevant packages if you did not yet did this. I use
the tidyverse for all of my analyses. All of them. If you don’
yet, I suggest you read about it on their website: < a href = "https://www.tidyverse.org/" class = "external-link uri" > https://www.tidyverse.org/< / a > .< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb2" > < pre class = "downlit sourceCode r" >
2022-08-28 22:45:38 +02:00
< code class = "sourceCode R" > < span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > dplyr< / a > < / span > < span class = "op" > )< / span > < span class = "co" > # part of tidyverse< / span > < / span >
2022-08-21 16:59:35 +02:00
< span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://ggplot2.tidyverse.org" class = "external-link" > ggplot2< / a > < / span > < span class = "op" > )< / span > < span class = "co" > # part of tidyverse< / span > < / span >
2022-08-28 22:45:38 +02:00
< span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://msberends.github.io/AMR/" > AMR< / a > < / span > < span class = "op" > )< / span > < span class = "co" > # this package< / span > < / span >
2022-10-29 14:24:08 +02:00
< span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://msberends.github.io/cleaner/" class = "external-link" > cleaner< / a > < / span > < span class = "op" > )< / span > < span class = "co" > # to create frequency tables< / span > < / span > < / code > < / pre > < / div >
< p > We will have to transform some variables to simplify and automate the
analysis:< / p >
2022-08-21 16:59:35 +02:00
< ul >
2022-10-29 14:24:08 +02:00
< li > Microorganisms should be transformed to our own microorganism codes
(called an < code > mo< / code > ) using < a href = "https://msberends.github.io/AMR/reference/catalogue_of_life" > our
Catalogue of Life reference data set< / a > , which contains all ~70,000
microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa.
We do the tranformation with < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > . This function also
recognises almost all WHONET abbreviations of microorganisms.< / li >
< li > Antimicrobial results or interpretations have to be clean and valid.
In other words, they should only contain values < code > "S"< / code > ,
< code > "I"< / code > or < code > "R"< / code > . That is exactly where the
< code > < a href = "../reference/as.rsi.html" > as.rsi()< / a > < / code > function is for.< / li >
2022-08-21 16:59:35 +02:00
< / ul >
< div class = "sourceCode" id = "cb3" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # transform variables< / span > < / span >
< span > < span class = "va" > data< / span > < span class = "op" > < -< / span > < span class = "va" > WHONET< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "co" > # get microbial ID based on given organism< / span > < / span >
2022-08-28 22:45:38 +02:00
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > mo < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "va" > Organism< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span > < span class = "co" > # transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class< / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP_ND10< / span > < span class = "op" > :< / span > < span class = "va" > CIP_EE< / span > < span class = "op" > )< / span > , < span class = "va" > as.rsi< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > No errors or warnings, so all values are transformed succesfully.< / p >
2022-10-29 14:24:08 +02:00
< p > We also created a package dedicated to data cleaning and checking,
called the < code > cleaner< / code > package. Its < code > < a href = "https://msberends.github.io/cleaner/reference/freq.html" class = "external-link" > freq()< / a > < / code >
function can be used to create frequency tables.< / p >
2022-08-21 16:59:35 +02:00
< p > So let’ < / p >
< div class = "sourceCode" id = "cb4" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # our newly created `mo` variable, put in the mo_name() function< / span > < / span >
2022-10-29 14:24:08 +02:00
< span > < span class = "va" > data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://msberends.github.io/cleaner/reference/freq.html" class = "external-link" > freq< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > < span class = "op" > )< / span > , nmax < span class = "op" > =< / span > < span class = "fl" > 10< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
2022-08-21 16:59:35 +02:00
< p > < strong > Frequency table< / strong > < / p >
< p > Class: character< br >
Length: 500< br >
2022-10-29 14:24:08 +02:00
Available: 500 (100%, NA: 0 = 0%)< br >
2022-10-22 22:10:04 +02:00
Unique: 38< / p >
2022-08-21 16:59:35 +02:00
< p > Shortest: 11< br >
Longest: 40< / p >
< table class = "table" >
2022-10-29 14:24:08 +02:00
< colgroup >
< col width = "4%" >
< col width = "47%" >
< col width = "7%" >
< col width = "10%" >
< col width = "13%" >
< col width = "15%" >
< / colgroup >
2022-08-21 16:59:35 +02:00
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > Escherichia coli< / td >
< td align = "right" > 245< / td >
< td align = "right" > 49.0%< / td >
< td align = "right" > 245< / td >
< td align = "right" > 49.0%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > Coagulase-negative Staphylococcus (CoNS)< / td >
< td align = "right" > 74< / td >
< td align = "right" > 14.8%< / td >
< td align = "right" > 319< / td >
< td align = "right" > 63.8%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > Staphylococcus epidermidis< / td >
< td align = "right" > 38< / td >
< td align = "right" > 7.6%< / td >
< td align = "right" > 357< / td >
< td align = "right" > 71.4%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > Streptococcus pneumoniae< / td >
< td align = "right" > 31< / td >
< td align = "right" > 6.2%< / td >
< td align = "right" > 388< / td >
< td align = "right" > 77.6%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 5< / td >
2022-10-22 22:10:04 +02:00
< td align = "left" > Staphylococcus hominis hominis< / td >
2022-08-21 16:59:35 +02:00
< td align = "right" > 21< / td >
< td align = "right" > 4.2%< / td >
< td align = "right" > 409< / td >
< td align = "right" > 81.8%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 6< / td >
< td align = "left" > Proteus mirabilis< / td >
< td align = "right" > 9< / td >
< td align = "right" > 1.8%< / td >
< td align = "right" > 418< / td >
< td align = "right" > 83.6%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 7< / td >
< td align = "left" > Enterococcus faecium< / td >
< td align = "right" > 8< / td >
< td align = "right" > 1.6%< / td >
< td align = "right" > 426< / td >
< td align = "right" > 85.2%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 8< / td >
< td align = "left" > Staphylococcus capitis< / td >
< td align = "right" > 8< / td >
< td align = "right" > 1.6%< / td >
< td align = "right" > 434< / td >
< td align = "right" > 86.8%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 9< / td >
< td align = "left" > Enterobacter cloacae< / td >
< td align = "right" > 5< / td >
< td align = "right" > 1.0%< / td >
< td align = "right" > 439< / td >
< td align = "right" > 87.8%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 10< / td >
2022-10-22 22:10:04 +02:00
< td align = "left" > Enterococcus columbae< / td >
< td align = "right" > 4< / td >
< td align = "right" > 0.8%< / td >
< td align = "right" > 443< / td >
< td align = "right" > 88.6%< / td >
2022-08-21 16:59:35 +02:00
< / tr >
< / tbody >
< / table >
2022-10-29 14:24:08 +02:00
< p > (omitted 28 entries, n = 57 [11.4%])< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb5" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # our transformed antibiotic columns< / span > < / span >
< span > < span class = "co" > # amoxicillin/clavulanic acid (J01CR02) as an example< / span > < / span >
2022-10-29 14:24:08 +02:00
< span > < span class = "va" > data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://msberends.github.io/cleaner/reference/freq.html" class = "external-link" > freq< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMC_ND2< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
2022-08-21 16:59:35 +02:00
< p > < strong > Frequency table< / strong > < / p >
< p > Class: factor > ordered > rsi (numeric)< br >
Length: 500< br >
Levels: 3: S < I < R< br >
Available: 481 (96.2%, NA: 19 = 3.8%)< br >
Unique: 3< / p >
< p > Drug: Amoxicillin/clavulanic acid (AMC, J01CR02)< br >
Drug group: Beta-lactams/penicillins< br >
%SI: 78.59%< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > S< / td >
< td align = "right" > 356< / td >
< td align = "right" > 74.01%< / td >
< td align = "right" > 356< / td >
< td align = "right" > 74.01%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > R< / td >
< td align = "right" > 103< / td >
< td align = "right" > 21.41%< / td >
< td align = "right" > 459< / td >
< td align = "right" > 95.43%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > I< / td >
< td align = "right" > 22< / td >
< td align = "right" > 4.57%< / td >
< td align = "right" > 481< / td >
< td align = "right" > 100.00%< / td >
< / tr >
< / tbody >
< / table >
< / div >
< div class = "section level3" >
< h3 id = "a-first-glimpse-at-results" > A first glimpse at results< a class = "anchor" aria-label = "anchor" href = "#a-first-glimpse-at-results" > < / a >
< / h3 >
2022-10-29 14:24:08 +02:00
< p > An easy < code > ggplot< / code > will already give a lot of information,
using the included < code > < a href = "../reference/ggplot_rsi.html" > ggplot_rsi()< / a > < / code > function:< / p >
2022-08-21 16:59:35 +02:00
< div class = "sourceCode" id = "cb6" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > Country< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > Country< / span > , < span class = "va" > AMP_ND2< / span > , < span class = "va" > AMC_ED20< / span > , < span class = "va" > CAZ_ED10< / span > , < span class = "va" > CIP_ED5< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span > < span class = "fu" > < a href = "../reference/ggplot_rsi.html" > ggplot_rsi< / a > < / span > < span class = "op" > (< / span > translate_ab < span class = "op" > =< / span > < span class = "st" > "ab"< / span > , facet < span class = "op" > =< / span > < span class = "st" > "Country"< / span > , datalabels < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
2022-08-21 16:59:35 +02:00
< p > < img src = "WHONET_files/figure-html/unnamed-chunk-7-1.png" width = "720" > < / p >
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
< / nav > < / aside >
< / div >
< footer > < div class = "pkgdown-footer-left" >
< p > < / p >
2022-12-11 11:50:34 +01:00
< p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "pkgdown-footer-right" >
< p > < / p >
2022-12-11 11:50:34 +01:00
< p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
2022-08-21 16:59:35 +02:00
< / div >
< / footer >
< / div >
< / body >
< / html >
