2023-05-24 16:03:18 +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 > Using AMR with other packages: AMR & dplyr/tidyverse • 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" >
2023-12-03 01:14:24 +01:00
< link href = "../deps/bootstrap-5.3.1/bootstrap.min.css" rel = "stylesheet" >
2024-04-05 16:58:51 +02:00
< script src = "../deps/bootstrap-5.3.1/bootstrap.bundle.min.js" > < / script > < link href = "../deps/Lato-0.4.9/font.css" rel = "stylesheet" >
< link href = "../deps/Fira_Code-0.4.9/font.css" rel = "stylesheet" >
2023-05-24 16:03:18 +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" >
2024-04-23 10:39:01 +02:00
<!-- 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/2.0.11/clipboard.min.js" integrity = "sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin = "anonymous" referrerpolicy = "no-referrer" > < / 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" >
2023-05-24 16:03:18 +02:00
< script src = "../extra.js" > < / script > < meta property = "og:title" content = "Using AMR with other packages: AMR & dplyr/tidyverse" >
< 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" >
< meta name = "twitter:site" content = "@msberends" >
<!-- 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 >
2024-04-19 10:24:46 +02:00
< nav class = "navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme = "dark" > < div class = "container" >
2023-05-24 16:03:18 +02:00
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
2024-04-23 10:39:01 +02:00
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9022< / small >
2023-05-24 16:03:18 +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 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 = "../reference/antibiogram.html" >
< span class = "fa fa-file-prescription" > < / span >
Generate Antibiogram (Trad./Syndromic/WISCA)
< / 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 >
Download Data Sets for Own Use
< / a >
< a class = "dropdown-item" href = "../reference/AMR-options.html" >
< span class = "fa fa-gear" > < / span >
Set User- Or Team-specific Package Settings
< / 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/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 >
Get Taxonomy of a Microorganism
< / a >
< a class = "dropdown-item" href = "../reference/ab_property.html" >
< span class = "fa fa-capsules" > < / span >
Get Properties of an Antibiotic Drug
< / a >
< a class = "dropdown-item" href = "../reference/av_property.html" >
< span class = "fa fa-capsules" > < / span >
Get Properties of an Antiviral Drug
< / a >
< / div >
< / 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--with-other-pkgs" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
With other pkgs
< / a >
< div class = "dropdown-menu" aria-labelledby = "dropdown--with-other-pkgs" >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & dplyr/tidyverse
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & data.table
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & tidymodels
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
2023-05-27 10:53:23 +02:00
< span class = "fa fa-layer-group" > < / span >
2023-05-24 16:03:18 +02:00
AMR & base R
< / a >
< / 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 >
< / 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 = "nav-link" href = "../news/index.html" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< 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 > Using AMR with other packages: AMR & dplyr/tidyverse< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/vignettes/other_pkg.Rmd" class = "external-link" > < code > vignettes/other_pkg.Rmd< / code > < / a > < / small >
< div class = "d-none name" > < code > other_pkg.Rmd< / code > < / div >
< / div >
< p > This page will be updated shortly, to give explicit examples of how
to work ideally with the < code > AMR< / code > package, for those who are
used to working in < code > dplyr< / code > or other tidyverse packages.< / p >
< / main >
< / div >
< footer > < div class = "pkgdown-footer-left" >
2024-04-23 10:39:01 +02:00
< 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 >
2023-05-24 16:03:18 +02:00
< / div >
< div class = "pkgdown-footer-right" >
2024-04-23 10:39:01 +02:00
< 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 >
2023-05-24 16:03:18 +02:00
< / div >
< / footer >
< / div >
< / body >
< / html >
