2019-01-21 15:53:01 +01:00
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
< html lang = "en" >
< head >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
< title > Use predefined reference data set — mo_source • 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" / >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<!-- jquery -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity = "sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin = "anonymous" > < / script >
<!-- Bootstrap -->
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity = "sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin = "anonymous" > < / script >
<!-- Font Awesome icons -->
2019-10-13 09:31:58 +02:00
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity = "sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin = "anonymous" / >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity = "sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin = "anonymous" / >
2019-01-21 15:53:01 +01:00
<!-- clipboard.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity = "sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin = "anonymous" > < / script >
2019-10-13 09:31:58 +02:00
<!-- headroom.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity = "sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin = "anonymous" > < / script >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script >
2019-01-21 15:53:01 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
<!-- docsearch -->
< script src = "../docsearch.js" > < / script >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity = "sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin = "anonymous" / >
< link href = "../docsearch.css" rel = "stylesheet" >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity = "sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin = "anonymous" > < / script >
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2019-10-13 09:31:58 +02:00
< meta property = "og:title" content = "Use predefined reference data set — mo_source" / >
2019-11-28 22:32:17 +01:00
< meta property = "og:description" content = "These functions can be used to predefine your own reference to be used in as . mo ( ) and consequently all mo_ * functions like mo_genus ( ) and mo_gramstain ( ) .
2019-02-28 13:56:28 +01:00
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
2019-01-21 15:53:01 +01:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.png" / >
< meta name = "twitter:card" content = "summary" / >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
<!-- 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]-->
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< / head >
< body >
< div class = "container template-reference-topic" >
< header >
< div class = "navbar navbar-default navbar-fixed-top" role = "navigation" >
< div class = "container" >
< div class = "navbar-header" >
< button type = "button" class = "navbar-toggle collapsed" data-toggle = "collapse" data-target = "#navbar" aria-expanded = "false" >
< span class = "sr-only" > Toggle navigation< / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< / button >
< span class = "navbar-brand" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2019-11-29 19:43:23 +01:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 0.9.0< / span >
2019-01-21 15:53:01 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
< span class = "fa fa-home" > < / span >
Home
< / a >
< / li >
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
< span class = "fa fa-question-circle" > < / span >
How to
< span class = "caret" > < / span >
< / a >
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../articles/resistance_predict.html" >
2019-01-21 15:53:01 +01:00
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
2019-05-28 16:50:40 +02:00
< li >
< a href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / a >
< / li >
2019-01-29 00:06:50 +01:00
< li >
< a href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< / li >
2019-02-14 15:18:17 +01:00
< li >
< a href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< / li >
2019-01-21 15:53:01 +01:00
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../reference/mo_property.html" >
2019-01-21 15:53:01 +01:00
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
2019-05-16 21:20:00 +02:00
< a href = "../reference/ab_property.html" >
2019-01-21 15:53:01 +01:00
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
< li >
< a href = "../articles/benchmarks.html" >
< span class = "fa fa-shipping-fast" > < / span >
Other: benchmarks
< / a >
< / li >
< / ul >
< / li >
< li >
< a href = "../reference/" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
< / li >
< li >
< a href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
< li >
< a href = "../news/" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
< a href = "https://gitlab.com/msberends/AMR" >
< span class = "fab fa fab fa-gitlab" > < / span >
Source Code
< / a >
< / li >
< li >
< a href = "../LICENSE-text.html" >
< span class = "fa fa-book" > < / span >
Licence
< / a >
< / li >
< / ul >
2019-10-13 09:31:58 +02:00
< form class = "navbar-form navbar-right hidden-xs hidden-sm" role = "search" >
2019-01-21 15:53:01 +01:00
< div class = "form-group" >
< input type = "search" class = "form-control" name = "search-input" id = "search-input" placeholder = "Search..." aria-label = "Search for..." autocomplete = "off" >
< / div >
< / form >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Use predefined reference data set< / h1 >
< div class = "hidden name" > < code > mo_source.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2019-11-28 22:32:17 +01:00
< p > These functions can be used to predefine your own reference to be used in < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > and consequently all < code > mo_*< / code > functions like < code > < a href = 'mo_property.html' > mo_genus()< / a > < / code > and < code > < a href = 'mo_property.html' > mo_gramstain()< / a > < / code > .< / p >
2019-02-28 13:56:28 +01:00
< p > This is < strong > the fastest way< / strong > to have your organisation (or analysis) specific codes picked up and translated by this package.< / p >
2019-01-21 15:53:01 +01:00
< / div >
< pre class = "usage" > < span class = 'fu' > set_mo_source< / span > (< span class = 'no' > path< / span > )
< span class = 'fu' > get_mo_source< / span > ()< / pre >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > path< / th >
< td > < p > location of your reference file, see Details< / p > < / td >
< / tr >
< / table >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2019-02-27 11:36:12 +01:00
< p > The reference file can be a text file seperated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the < code > readxl< / code > package installed.< / p >
2019-11-28 22:32:17 +01:00
< p > < code > set_mo_source()< / code > will check the file for validity: it must be a < code > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / code > , must have a column named < code > "mo"< / code > which contains values from < code > < a href = 'microorganisms.html' > microorganisms$mo< / a > < / code > and must have a reference column with your own defined values. If all tests pass, < code > set_mo_source()< / code > will read the file into R and export it to < code > "~/.mo_source.rds"< / code > . This compressed data file will then be used at default for MO determination (function < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > and consequently all < code > mo_*< / code > functions like < code > < a href = 'mo_property.html' > mo_genus()< / a > < / code > and < code > < a href = 'mo_property.html' > mo_gramstain()< / a > < / code > ). The location of the original file will be saved as option with < code > < a href = 'https://rdrr.io/r/base/options.html' > options(mo_source = path)< / a > < / code > . Its timestamp will be saved with < code > < a href = 'https://rdrr.io/r/base/options.html' > options(mo_source_datetime = ...)< / a > < / code > .< / p >
< p > < code > get_mo_source()< / code > will return the data set by reading < code > "~/.mo_source.rds"< / code > with < code > < a href = 'https://rdrr.io/r/base/readRDS.html' > readRDS()< / a > < / code > . If the original file has changed (the file defined with < code > path< / code > ), it will call < code > set_mo_source()< / code > to update the data file automatically.< / p >
< p > Reading an Excel file (< code > .xlsx< / code > ) with only one row has a size of 8-9 kB. The compressed file used by this package will have a size of 0.1 kB and can be read by < code > get_mo_source()< / code > in only a couple of microseconds (a millionth of a second).< / p > < h3 > How it works< / h3 >
2019-02-28 13:56:28 +01:00
2019-10-13 09:31:58 +02:00
2019-11-30 12:01:50 +01:00
< p > Imagine this data on a sheet of an Excel file (mo codes were looked up in the < code > microorganisms< / code > data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:< / p > < pre > | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
4 | | |
2019-02-28 13:56:28 +01:00
< / pre >
2019-10-13 09:31:58 +02:00
2019-11-28 22:32:17 +01:00
< p > We save it as < code > "home/me/ourcodes.xlsx"< / code > . Now we have to set it as a source:< / p > < pre > set_mo_source("home/me/ourcodes.xlsx")
2019-02-28 13:56:28 +01:00
# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
< / pre >
2019-10-13 09:31:58 +02:00
2019-11-28 22:32:17 +01:00
< p > It has now created a file < code > "~/.mo_source.rds"< / code > with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.< / p >
< p > And now we can use it in our functions:< / p > < pre > as.mo("lab_mo_ecoli")
2019-11-30 12:01:50 +01:00
[1] B_ESCHR_COLI
2019-10-13 09:31:58 +02:00
mo_genus("lab_mo_kpneumoniae")
2019-03-01 09:34:04 +01:00
[1] "Klebsiella"
2019-10-13 09:31:58 +02:00
# other input values still work too
2019-03-01 09:34:04 +01:00
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
2019-11-28 22:32:17 +01:00
[1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
2019-02-28 13:56:28 +01:00
< / pre >
2019-10-13 09:31:58 +02:00
2019-11-30 12:01:50 +01:00
< p > If we edit the Excel file to, let's say, by adding row 4 like this:< / p > < pre > | A | B |
2019-11-28 22:32:17 +01:00
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
4 | lab_Staph_aureus | B_STPHY_AURS |
5 | | |
2019-02-28 13:56:28 +01:00
< / pre >
2019-10-13 09:31:58 +02:00
2019-11-30 12:01:50 +01:00
< p > ...any new usage of an MO function in this package will update your data file:< / p > < pre > as.mo("lab_mo_ecoli")
2019-02-28 13:56:28 +01:00
# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
2019-11-28 22:32:17 +01:00
[1] B_ESCHR_COLI
2019-10-13 09:31:58 +02:00
mo_genus("lab_Staph_aureus")
2019-03-01 09:34:04 +01:00
[1] "Staphylococcus"
2019-02-28 13:56:28 +01:00
< / pre >
2019-10-13 09:31:58 +02:00
2019-11-30 12:01:50 +01:00
< p > To remove the reference data file completely, just use < code > ""< / code > or < code > NULL< / code > as input for < code > [set_mo_source()]< / code > :< / p > < pre > set_mo_source(NULL)
2019-02-28 13:56:28 +01:00
# Removed mo_source file '~/.mo_source.rds'.
< / pre >
2019-10-13 09:31:58 +02:00
2019-11-28 22:32:17 +01:00
2019-01-21 15:53:01 +01:00
< 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 >
2019-10-13 09:31:58 +02:00
< 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 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 >
2019-01-21 15:53:01 +01:00
< / 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 = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
2019-10-13 09:31:58 +02:00
< / ul >
2019-01-21 15:53:01 +01:00
< / div >
< / div >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< footer >
< div class = "copyright" >
2019-10-13 09:31:58 +02:00
< 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/' > Alex 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 >
2019-01-21 15:53:01 +01:00
< / div >
< div class = "pkgdown" >
2019-10-13 09:31:58 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
2019-01-21 15:53:01 +01:00
< / div >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< / footer >
< / div >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity = "sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin = "anonymous" > < / script >
< script >
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
});
}
});
< / script >
2019-10-13 09:31:58 +02:00
2019-01-21 15:53:01 +01:00
< / body >
< / html >
2019-10-13 09:31:58 +02:00
