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<!-- 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=1.0" > < title > Function reference • 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" > <!-- jquery --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script > <!-- Bootstrap --> < link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" > < script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity = "sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin = "anonymous" > < / script > <!-- bootstrap - toc --> < link rel = "stylesheet" href = "../bootstrap-toc.css" > < script src = "../bootstrap-toc.js" > < / script > <!-- 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" > <!-- 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 > <!-- 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 > <!-- pkgdown --> < link href = "../pkgdown.css" rel = "stylesheet" > < script src = "../pkgdown.js" > < / script > < link href = "../extra.css" rel = "stylesheet" > < script src = "../extra.js" > < / script > < meta property = "og:title" content = "Function reference" > < 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 = "@univgroningen" > <!-- 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]>
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< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Released version" > 1.8.1.9003< / span >
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How to
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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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Manual
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Source Code
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< h1 > Reference< / h1 >
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< table class = "ref-index" > < colgroup > < col class = "alias" > < col class = "title" > < / colgroup > < tbody > < tr > < th colspan = "2" >
< h2 id = "preparing-data-microorganisms" > Preparing data: microorganisms < a href = "#preparing-data-microorganisms" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
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< p class = "section-desc" > < / p > < p > These functions are meant to get taxonomically valid properties of microorganisms from any input. Use < code > < a href = "../reference/mo_source.html" > mo_source()< / a > < / code > to teach this package how to translate your own codes to valid microorganism codes.< / p >
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< / th >
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< / tr > < / tbody > < tbody > < tr > < td >
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< p > < code > < a href = "as.mo.html" > as.mo()< / a > < / code > < code > < a href = "as.mo.html" > is.mo()< / a > < / code > < code > < a href = "as.mo.html" > mo_failures()< / a > < / code > < code > < a href = "as.mo.html" > mo_uncertainties()< / a > < / code > < code > < a href = "as.mo.html" > mo_renamed()< / a > < / code > < / p >
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< / td >
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< td > < p > Transform Input to a Microorganism Code< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "mo_property.html" > mo_name()< / a > < / code > < code > < a href = "mo_property.html" > mo_fullname()< / a > < / code > < code > < a href = "mo_property.html" > mo_shortname()< / a > < / code > < code > < a href = "mo_property.html" > mo_subspecies()< / a > < / code > < code > < a href = "mo_property.html" > mo_species()< / a > < / code > < code > < a href = "mo_property.html" > mo_genus()< / a > < / code > < code > < a href = "mo_property.html" > mo_family()< / a > < / code > < code > < a href = "mo_property.html" > mo_order()< / a > < / code > < code > < a href = "mo_property.html" > mo_class()< / a > < / code > < code > < a href = "mo_property.html" > mo_phylum()< / a > < / code > < code > < a href = "mo_property.html" > mo_kingdom()< / a > < / code > < code > < a href = "mo_property.html" > mo_domain()< / a > < / code > < code > < a href = "mo_property.html" > mo_type()< / a > < / code > < code > < a href = "mo_property.html" > mo_gramstain()< / a > < / code > < code > < a href = "mo_property.html" > mo_is_gram_negative()< / a > < / code > < code > < a href = "mo_property.html" > mo_is_gram_positive()< / a > < / code > < code > < a href = "mo_property.html" > mo_is_yeast()< / a > < / code > < code > < a href = "mo_property.html" > mo_is_intrinsic_resistant()< / a > < / code > < code > < a href = "mo_property.html" > mo_snomed()< / a > < / code > < code > < a href = "mo_property.html" > mo_ref()< / a > < / code > < code > < a href = "mo_property.html" > mo_authors()< / a > < / code > < code > < a href = "mo_property.html" > mo_year()< / a > < / code > < code > < a href = "mo_property.html" > mo_lpsn()< / a > < / code > < code > < a href = "mo_property.html" > mo_rank()< / a > < / code > < code > < a href = "mo_property.html" > mo_taxonomy()< / a > < / code > < code > < a href = "mo_property.html" > mo_synonyms()< / a > < / code > < code > < a href = "mo_property.html" > mo_info()< / a > < / code > < code > < a href = "mo_property.html" > mo_url()< / a > < / code > < code > < a href = "mo_property.html" > mo_property()< / a > < / code > < / p >
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< / td >
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< td > < p > Get Properties of a Microorganism< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "mo_source.html" > set_mo_source()< / a > < / code > < code > < a href = "mo_source.html" > get_mo_source()< / a > < / code > < / p >
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< / td >
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< td > < p > User-Defined Reference Data Set for Microorganisms< / p > < / td >
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< / tr > < / tbody > < tbody > < tr > < th colspan = "2" >
< h2 id = "preparing-data-antibiotics" > Preparing data: antibiotics < a href = "#preparing-data-antibiotics" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
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< p class = "section-desc" > < / p > < p > Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using < code > < a href = "../reference/ab_from_text.html" > ab_from_text()< / a > < / code > .< / p >
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< / tr > < / tbody > < tbody > < tr > < td >
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< p > < code > < a href = "as.ab.html" > as.ab()< / a > < / code > < code > < a href = "as.ab.html" > is.ab()< / a > < / code > < / p >
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< / td >
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< td > < p > Transform Input to an Antibiotic ID< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "ab_property.html" > ab_name()< / a > < / code > < code > < a href = "ab_property.html" > ab_cid()< / a > < / code > < code > < a href = "ab_property.html" > ab_synonyms()< / a > < / code > < code > < a href = "ab_property.html" > ab_tradenames()< / a > < / code > < code > < a href = "ab_property.html" > ab_group()< / a > < / code > < code > < a href = "ab_property.html" > ab_atc()< / a > < / code > < code > < a href = "ab_property.html" > ab_atc_group1()< / a > < / code > < code > < a href = "ab_property.html" > ab_atc_group2()< / a > < / code > < code > < a href = "ab_property.html" > ab_loinc()< / a > < / code > < code > < a href = "ab_property.html" > ab_ddd()< / a > < / code > < code > < a href = "ab_property.html" > ab_ddd_units()< / a > < / code > < code > < a href = "ab_property.html" > ab_info()< / a > < / code > < code > < a href = "ab_property.html" > ab_url()< / a > < / code > < code > < a href = "ab_property.html" > ab_property()< / a > < / code > < code > < a href = "ab_property.html" > set_ab_names()< / a > < / code > < / p >
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< / td >
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< td > < p > Get Properties of an Antibiotic< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "ab_from_text.html" > ab_from_text()< / a > < / code > < / p >
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< / td >
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< td > < p > Retrieve Antimicrobial Drug Names and Doses from Clinical Text< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "atc_online.html" > atc_online_property()< / a > < / code > < code > < a href = "atc_online.html" > atc_online_groups()< / a > < / code > < code > < a href = "atc_online.html" > atc_online_ddd()< / a > < / code > < code > < a href = "atc_online.html" > atc_online_ddd_units()< / a > < / code > < / p >
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< / td >
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< td > < p > Get ATC Properties from WHOCC Website< / p > < / td >
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< / tr > < / tbody > < tbody > < tr > < th colspan = "2" >
< h2 id = "preparing-data-antimicrobial-resistance" > Preparing data: antimicrobial resistance < a href = "#preparing-data-antimicrobial-resistance" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
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< p class = "section-desc" > < / p > < p > With < code > < a href = "../reference/as.mic.html" > as.mic()< / a > < / code > and < code > < a href = "../reference/as.disk.html" > as.disk()< / a > < / code > you can transform your raw input to valid MIC or disk diffusion values. Use < code > < a href = "../reference/as.rsi.html" > as.rsi()< / a > < / code > for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying < a href = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class = "external-link" > EUCAST rules< / a > with < code > < a href = "../reference/eucast_rules.html" > eucast_rules()< / a > < / code > .< / p >
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< / th >
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< p > < code > < a href = "as.rsi.html" > as.rsi()< / a > < / code > < code > < a href = "as.rsi.html" > NA_rsi_< / a > < / code > < code > < a href = "as.rsi.html" > is.rsi()< / a > < / code > < code > < a href = "as.rsi.html" > is.rsi.eligible()< / a > < / code > < / p >
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< / td >
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< td > < p > Interpret MIC and Disk Values, or Clean Raw R/SI Data< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "as.mic.html" > as.mic()< / a > < / code > < code > < a href = "as.mic.html" > NA_mic_< / a > < / code > < code > < a href = "as.mic.html" > is.mic()< / a > < / code > < / p >
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< td > < p > Transform Input to Minimum Inhibitory Concentrations (MIC)< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-11-28 23:01:26 +01:00
< p > < code > < a href = "as.disk.html" > as.disk()< / a > < / code > < code > < a href = "as.disk.html" > NA_disk_< / a > < / code > < code > < a href = "as.disk.html" > is.disk()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Transform Input to Disk Diffusion Diameters< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-01-12 22:08:04 +01:00
< p > < code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > < code > < a href = "eucast_rules.html" > eucast_dosage()< / a > < / code > < / p >
2019-05-10 16:44:59 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Apply EUCAST Rules< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-04-07 08:37:42 +02:00
< p > < code > < a href = "custom_eucast_rules.html" > custom_eucast_rules()< / a > < / code > < / p >
< / td >
2021-04-20 10:46:17 +02:00
< td > < p > Define Custom EUCAST Rules< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < tbody > < tr > < th colspan = "2" >
< h2 id = "analysing-data-antimicrobial-resistance" > Analysing data: antimicrobial resistance < a href = "#analysing-data-antimicrobial-resistance" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
2022-03-27 09:37:55 +02:00
< p class = "section-desc" > < / p > < p > Use these function for the analysis part. You can use < code > < a href = "../reference/proportion.html" > susceptibility()< / a > < / code > or < code > < a href = "../reference/proportion.html" > resistance()< / a > < / code > on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using < code > < a href = "../reference/first_isolate.html" > first_isolate()< / a > < / code > or < code > < a href = "../reference/get_episode.html" > is_new_episode()< / a > < / code > . You can also filter your data on certain resistance in certain antibiotic classes (< code > < a href = "../reference/antibiotic_class_selectors.html" > carbapenems()< / a > < / code > , < code > < a href = "../reference/antibiotic_class_selectors.html" > aminoglycosides()< / a > < / code > ), or determine multi-drug resistant microorganisms (MDRO, < code > < a href = "../reference/mdro.html" > mdro()< / a > < / code > ).< / p >
2018-12-29 22:24:19 +01:00
< / th >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < tbody > < tr > < td >
2020-03-07 21:48:21 +01:00
< p > < code > < a href = "proportion.html" > resistance()< / a > < / code > < code > < a href = "proportion.html" > susceptibility()< / a > < / code > < code > < a href = "proportion.html" > proportion_R()< / a > < / code > < code > < a href = "proportion.html" > proportion_IR()< / a > < / code > < code > < a href = "proportion.html" > proportion_I()< / a > < / code > < code > < a href = "proportion.html" > proportion_SI()< / a > < / code > < code > < a href = "proportion.html" > proportion_S()< / a > < / code > < code > < a href = "proportion.html" > proportion_df()< / a > < / code > < code > < a href = "proportion.html" > rsi_df()< / a > < / code > < / p >
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Calculate Microbial Resistance< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-03-07 21:48:21 +01:00
< p > < code > < a href = "count.html" > count_resistant()< / a > < / code > < code > < a href = "count.html" > count_susceptible()< / a > < / code > < code > < a href = "count.html" > count_R()< / a > < / code > < code > < a href = "count.html" > count_IR()< / a > < / code > < code > < a href = "count.html" > count_I()< / a > < / code > < code > < a href = "count.html" > count_SI()< / a > < / code > < code > < a href = "count.html" > count_S()< / a > < / code > < code > < a href = "count.html" > count_all()< / a > < / code > < code > < a href = "count.html" > n_rsi()< / a > < / code > < code > < a href = "count.html" > count_df()< / a > < / code > < / p >
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Count Available Isolates< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-12-27 00:07:00 +01:00
< p > < code > < a href = "get_episode.html" > get_episode()< / a > < / code > < code > < a href = "get_episode.html" > is_new_episode()< / a > < / code > < / p >
2020-11-23 21:50:27 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Determine (New) Episodes for Patients< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-04-29 17:16:30 +02:00
< p > < code > < a href = "first_isolate.html" > first_isolate()< / a > < / code > < code > < a href = "first_isolate.html" > filter_first_isolate()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-08-30 14:07:46 +02:00
< td > < p > Determine First Isolates< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-04-27 10:27:13 +02:00
< p > < code > < a href = "key_antimicrobials.html" > key_antimicrobials()< / a > < / code > < code > < a href = "key_antimicrobials.html" > all_antimicrobials()< / a > < / code > < code > < a href = "key_antimicrobials.html" > antimicrobials_equal()< / a > < / code > < / p >
2020-03-07 21:48:21 +01:00
< / td >
2021-04-27 10:27:13 +02:00
< td > < p > (Key) Antimicrobials for First Weighted Isolates< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-01-17 00:26:48 +01:00
< p > < code > < a href = "mdro.html" > mdro()< / a > < / code > < code > < a href = "mdro.html" > custom_mdro_guideline()< / a > < / code > < code > < a href = "mdro.html" > brmo()< / a > < / code > < code > < a href = "mdro.html" > mrgn()< / a > < / code > < code > < a href = "mdro.html" > mdr_tb()< / a > < / code > < code > < a href = "mdro.html" > mdr_cmi2012()< / a > < / code > < code > < a href = "mdro.html" > eucast_exceptional_phenotypes()< / a > < / code > < / p >
2020-06-17 15:14:37 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Determine Multidrug-Resistant Organisms (MDRO)< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-11-01 13:51:13 +01:00
< p > < code > < a href = "plot.html" > plot(< i > < mic> < / i > )< / a > < / code > < code > < a href = "plot.html" > autoplot(< i > < mic> < / i > )< / a > < / code > < code > < a href = "plot.html" > fortify(< i > < mic> < / i > )< / a > < / code > < code > < a href = "plot.html" > plot(< i > < disk> < / i > )< / a > < / code > < code > < a href = "plot.html" > autoplot(< i > < disk> < / i > )< / a > < / code > < code > < a href = "plot.html" > fortify(< i > < disk> < / i > )< / a > < / code > < code > < a href = "plot.html" > plot(< i > < rsi> < / i > )< / a > < / code > < code > < a href = "plot.html" > autoplot(< i > < rsi> < / i > )< / a > < / code > < code > < a href = "plot.html" > fortify(< i > < rsi> < / i > )< / a > < / code > < / p >
2021-03-04 23:28:32 +01:00
< / td >
< td > < p > Plotting for Classes < code > rsi< / code > , < code > mic< / code > and < code > disk< / code > < / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "ggplot_rsi.html" > ggplot_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > geom_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > facet_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > scale_y_percent()< / a > < / code > < code > < a href = "ggplot_rsi.html" > scale_rsi_colours()< / a > < / code > < code > < a href = "ggplot_rsi.html" > theme_rsi()< / a > < / code > < code > < a href = "ggplot_rsi.html" > labels_rsi_count()< / a > < / code > < / p >
2019-03-06 14:39:02 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > AMR Plots with < code > ggplot2< / code > < / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "bug_drug_combinations.html" > bug_drug_combinations()< / a > < / code > < code > < a href = "bug_drug_combinations.html" > format(< i > < bug_drug_combinations> < / i > )< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Determine Bug-Drug Combinations< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-12-09 10:48:25 +01:00
< p > < code > < a href = "antibiotic_class_selectors.html" > ab_class()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > ab_selector()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > aminoglycosides()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > aminopenicillins()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > antifungals()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > antimycobacterials()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > betalactams()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > carbapenems()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > cephalosporins()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > cephalosporins_1st()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > cephalosporins_2nd()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > cephalosporins_3rd()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > cephalosporins_4th()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > cephalosporins_5th()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > fluoroquinolones()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > glycopeptides()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > lincosamides()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > lipoglycopeptides()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > macrolides()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > oxazolidinones()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > penicillins()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > polymyxins()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > streptogramins()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > quinolones()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > tetracyclines()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > trimethoprims()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > ureidopenicillins()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > administrable_per_os()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > administrable_iv()< / a > < / code > < code > < a href = "antibiotic_class_selectors.html" > not_intrinsic_resistant()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-08-16 21:54:34 +02:00
< td > < p > Antibiotic Selectors< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-07-12 20:24:49 +02:00
< p > < code > < a href = "resistance_predict.html" > resistance_predict()< / a > < / code > < code > < a href = "resistance_predict.html" > rsi_predict()< / a > < / code > < code > < a href = "resistance_predict.html" > plot(< i > < resistance_predict> < / i > )< / a > < / code > < code > < a href = "resistance_predict.html" > ggplot_rsi_predict()< / a > < / code > < code > < a href = "resistance_predict.html" > autoplot(< i > < resistance_predict> < / i > )< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-07-12 20:24:49 +02:00
< td > < p > Predict Antimicrobial Resistance< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "guess_ab_col.html" > guess_ab_col()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Guess Antibiotic Column< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < tbody > < tr > < th colspan = "2" >
< h2 id = "background-information-on-included-data" > Background information on included data < a href = "#background-information-on-included-data" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
2022-03-27 09:37:55 +02:00
< p class = "section-desc" > < / p > < p > Some pages about our package and its external sources. Be sure to read our < a href = "./../articles/index.html" > How To’ < / a > for more information about how to work with functions in this package.< / p >
2021-08-18 23:19:38 +02:00
< / th >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < tbody > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "AMR.html" > AMR< / a > < / code > < / p >
< / td >
< td > < p > The < code > AMR< / code > Package< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "example_isolates.html" > example_isolates< / a > < / code > < / p >
< / td >
< td > < p > Data Set with 2,000 Example Isolates< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "microorganisms.html" > microorganisms< / a > < / code > < / p >
< / td >
2021-11-29 11:55:18 +01:00
< td > < p > Data Set with 70,760 Microorganisms< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "microorganisms.codes.html" > microorganisms.codes< / a > < / code > < / p >
< / td >
2021-10-05 14:00:35 +02:00
< td > < p > Data Set with 5,604 Common Microorganism Codes< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "microorganisms.old.html" > microorganisms.old< / a > < / code > < / p >
< / td >
< td > < p > Data Set with Previously Accepted Taxonomic Names< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "antibiotics.html" > antibiotics< / a > < / code > < code > < a href = "antibiotics.html" > antivirals< / a > < / code > < / p >
< / td >
2021-12-13 10:18:28 +01:00
< td > < p > Data Sets with 566 Antimicrobial Drugs< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "intrinsic_resistant.html" > intrinsic_resistant< / a > < / code > < / p >
< / td >
< td > < p > Data Set with Bacterial Intrinsic Resistance< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "dosage.html" > dosage< / a > < / code > < / p >
< / td >
< td > < p > Data Set with Treatment Dosages as Defined by EUCAST< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "catalogue_of_life.html" > catalogue_of_life< / a > < / code > < / p >
< / td >
< td > < p > The Catalogue of Life< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "catalogue_of_life_version.html" > catalogue_of_life_version()< / a > < / code > < / p >
< / td >
< td > < p > Version info of included Catalogue of Life< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "WHOCC.html" > WHOCC< / a > < / code > < / p >
< / td >
< td > < p > WHOCC: WHO Collaborating Centre for Drug Statistics Methodology< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "lifecycle.html" > lifecycle< / a > < / code > < / p >
< / td >
< td > < p > Lifecycles of Functions in the < code > AMR< / code > Package< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "example_isolates_unclean.html" > example_isolates_unclean< / a > < / code > < / p >
< / td >
< td > < p > Data Set with Unclean Data< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "rsi_translation.html" > rsi_translation< / a > < / code > < / p >
< / td >
< td > < p > Data Set for R/SI Interpretation< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "WHONET.html" > WHONET< / a > < / code > < / p >
< / td >
< td > < p > Data Set with 500 Isolates - WHONET Example< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < tbody > < tr > < th colspan = "2" >
< h2 id = "other-miscellaneous-functions" > Other: miscellaneous functions < a href = "#other-miscellaneous-functions" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
2022-03-27 09:37:55 +02:00
< p class = "section-desc" > < / p > < p > These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘ ’ < code > if (x %like% y) {...}< / code > .< / p >
2018-12-29 22:24:19 +01:00
< / th >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < tbody > < tr > < td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "age_groups.html" > age_groups()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Split Ages into Age Groups< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "age.html" > age()< / a > < / code > < / p >
2020-08-15 12:54:47 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Age in Years of Individuals< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "availability.html" > availability()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Check Availability of Columns< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-12-12 09:42:03 +01:00
< p > < code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > < / p >
2020-02-21 21:13:38 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Translate Strings from AMR Package< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-09-18 16:05:53 +02:00
< p > < code > < a href = "ggplot_pca.html" > ggplot_pca()< / a > < / code > < / p >
2019-11-18 12:10:47 +01:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > PCA Biplot with < code > ggplot2< / code > < / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2021-05-03 13:06:43 +02:00
< p > < code > < a href = "italicise_taxonomy.html" > italicise_taxonomy()< / a > < / code > < code > < a href = "italicise_taxonomy.html" > italicize_taxonomy()< / a > < / code > < / p >
< / td >
< td > < p > Italicise Taxonomic Families, Genera, Species, Subspecies< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
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< p > < code > < a href = "join.html" > inner_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > left_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > right_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > full_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > semi_join_microorganisms()< / a > < / code > < code > < a href = "join.html" > anti_join_microorganisms()< / a > < / code > < / p >
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< / td >
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< td > < p > Join microorganisms to a Data Set< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "like.html" > like()< / a > < / code > < code > < a href = "like.html" > `%like%`< / a > < / code > < code > < a href = "like.html" > `%unlike%`< / a > < / code > < code > < a href = "like.html" > `%like_case%`< / a > < / code > < code > < a href = "like.html" > `%unlike_case%`< / a > < / code > < / p >
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< / td >
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< td > < p > Vectorised Pattern Matching with Keyboard Shortcut< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
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< p > < code > < a href = "mo_matching_score.html" > mo_matching_score()< / a > < / code > < / p >
< / td >
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< td > < p > Calculate the Matching Score for Microorganisms< / p > < / td >
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< / tr > < tr > < td >
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< p > < code > < a href = "pca.html" > pca()< / a > < / code > < / p >
2019-01-29 20:20:09 +01:00
< / td >
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< td > < p > Principal Component Analysis (for AMR)< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < tr > < td >
2020-12-12 23:17:29 +01:00
< p > < code > < a href = "random.html" > random_mic()< / a > < / code > < code > < a href = "random.html" > random_disk()< / a > < / code > < code > < a href = "random.html" > random_rsi()< / a > < / code > < / p >
< / td >
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< td > < p > Random MIC Values/Disk Zones/RSI Generation< / p > < / td >
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< / tr > < / tbody > < tbody > < tr > < th colspan = "2" >
< h2 id = "other-statistical-tests" > Other: statistical tests < a href = "#other-statistical-tests" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
2022-03-27 09:37:55 +02:00
< p class = "section-desc" > < / p > < p > Some statistical tests or methods are not part of base R and were added to this package for convenience.< / p >
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< / th >
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< / tr > < / tbody > < tbody > < tr > < td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "g.test.html" > g.test()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
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< td > < p > < em > G< / em > -test for Count Data< / p > < / td >
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< / tr > < tr > < td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "kurtosis.html" > kurtosis()< / a > < / code > < / p >
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< / td >
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< td > < p > Kurtosis of the Sample< / p > < / td >
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< / tr > < tr > < td >
2020-09-03 12:31:48 +02:00
< p > < code > < a href = "skewness.html" > skewness()< / a > < / code > < / p >
2018-12-23 21:26:21 +01:00
< / td >
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< td > < p > Skewness of the Sample< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < tbody > < tr > < th colspan = "2" >
< h2 id = "other-deprecated-functions" > Other: deprecated functions < a href = "#other-deprecated-functions" class = "anchor" aria-hidden = "true" > < / a > < / h2 >
2022-03-27 09:37:55 +02:00
< p class = "section-desc" > < / p > < p > These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.< / p >
2020-11-23 21:50:27 +01:00
< / th >
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< / tr > < / tbody > < tbody > < tr > < td >
2021-08-18 23:19:38 +02:00
< p > < code > < a href = "AMR-deprecated.html" > AMR-deprecated< / a > < / code > < / p >
2019-06-09 08:57:54 +02:00
< / td >
2021-01-18 16:57:56 +01:00
< td > < p > Deprecated Functions< / p > < / td >
2021-12-05 22:06:45 +01:00
< / tr > < / tbody > < / table > < / div >
2018-12-23 21:26:21 +01:00
2020-04-13 21:09:56 +02:00
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
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< nav id = "toc" data-toggle = "toc" class = "sticky-top" > < h2 data-toc-skip > Contents< / h2 >
< / nav > < / div >
2018-12-23 21:26:21 +01:00
< / div >
2019-09-25 15:43:22 +02:00
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< footer > < div class = "copyright" >
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< p > < / p > < p > Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.< / p >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "pkgdown" >
2022-05-09 17:08:40 +02:00
< p > < / p > < p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a > 2.0.3.< / p >
2018-12-23 21:26:21 +01:00
< / div >
2019-09-25 15:43:22 +02:00
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< / footer > < / div >
2018-12-23 21:26:21 +01:00
2019-09-25 15:43:22 +02:00
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2018-12-23 21:26:21 +01:00
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< / body > < / html >
2019-09-25 15:43:22 +02:00
