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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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Get properties of an antiviral agent
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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Function reference< / h1 >
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< div class = "section level2" >
< h2 id = "preparing-data-microorganisms" > Preparing data: microorganisms< a class = "anchor" aria-label = "anchor" href = "#preparing-data-microorganisms" > < / a > < / h2 >
< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
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< 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_uncertainties()< / a > < / code > < code > < a href = "as.mo.html" > mo_renamed()< / a > < / code > < code > < a href = "as.mo.html" > mo_failures()< / a > < / code > < code > < a href = "as.mo.html" > mo_reset_session()< / a > < / code > < code > < a href = "as.mo.html" > mo_cleaning_regex()< / a > < / code >
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< / dt >
< dd > Transform Input to a Microorganism Code< / dd >
< / dl > < dl > < dt >
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< 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_status()< / 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_gbif()< / 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_current()< / 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 >
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< / dt >
< dd > Get Properties of a Microorganism< / dd >
< / dl > < dl > < dt >
< code > < a href = "mo_source.html" > set_mo_source()< / a > < / code > < code > < a href = "mo_source.html" > get_mo_source()< / a > < / code >
< / dt >
< dd > User-Defined Reference Data Set for Microorganisms< / dd >
< / dl > < / div > < div class = "section level2" >
< h2 id = "preparing-data-antibiotics" > Preparing data: antibiotics< a class = "anchor" aria-label = "anchor" href = "#preparing-data-antibiotics" > < / a > < / h2 >
< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
< code > < a href = "as.ab.html" > as.ab()< / a > < / code > < code > < a href = "as.ab.html" > is.ab()< / a > < / code >
< / dt >
< dd > Transform Input to an Antibiotic ID< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Get Properties of an Antibiotic< / dd >
< / dl > < dl > < dt >
< code > < a href = "ab_from_text.html" > ab_from_text()< / a > < / code >
< / dt >
< dd > Retrieve Antimicrobial Drug Names and Doses from Clinical Text< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Get ATC Properties from WHOCC Website< / dd >
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< / dl > < dl > < dt >
< code > < a href = "add_custom_antimicrobials.html" > add_custom_antimicrobials()< / a > < / code > < code > < a href = "add_custom_antimicrobials.html" > clear_custom_antimicrobials()< / a > < / code >
< / dt >
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< dd > Add Custom Antimicrobials to This Package< / dd >
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< / dl > < / div > < div class = "section level2" >
< h2 id = "preparing-data-antimicrobial-resistance" > Preparing data: antimicrobial resistance< a class = "anchor" aria-label = "anchor" href = "#preparing-data-antimicrobial-resistance" > < / a > < / h2 >
< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
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< 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 > < code > < a href = "as.rsi.html" > rsi_interpretation_history()< / a > < / code >
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< / dt >
< dd > Interpret MIC and Disk Values, or Clean Raw R/SI Data< / dd >
< / dl > < dl > < dt >
< 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 > < code > < a href = "as.mic.html" > droplevels(< i > < mic> < / i > )< / a > < / code >
< / dt >
< dd > Transform Input to Minimum Inhibitory Concentrations (MIC)< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Transform Input to Disk Diffusion Diameters< / dd >
< / dl > < dl > < dt >
< code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > < code > < a href = "eucast_rules.html" > eucast_dosage()< / a > < / code >
< / dt >
< dd > Apply EUCAST Rules< / dd >
< / dl > < dl > < dt >
< code > < a href = "custom_eucast_rules.html" > custom_eucast_rules()< / a > < / code >
< / dt >
< dd > Define Custom EUCAST Rules< / dd >
< / dl > < / div > < div class = "section level2" >
< h2 id = "analysing-data-antimicrobial-resistance" > Analysing data: antimicrobial resistance< a class = "anchor" aria-label = "anchor" href = "#analysing-data-antimicrobial-resistance" > < / a > < / h2 >
< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
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< code > < a href = "proportion.html" > resistance()< / a > < / code > < code > < a href = "proportion.html" > susceptibility()< / a > < / code > < code > < a href = "proportion.html" > rsi_confidence_interval()< / 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 >
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< / dt >
< dd > Calculate Microbial Resistance< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Count Available Isolates< / dd >
< / dl > < dl > < dt >
< code > < a href = "get_episode.html" > get_episode()< / a > < / code > < code > < a href = "get_episode.html" > is_new_episode()< / a > < / code >
< / dt >
< dd > Determine (New) Episodes for Patients< / dd >
< / dl > < dl > < dt >
< code > < a href = "first_isolate.html" > first_isolate()< / a > < / code > < code > < a href = "first_isolate.html" > filter_first_isolate()< / a > < / code >
< / dt >
< dd > Determine First Isolates< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > (Key) Antimicrobials for First Weighted Isolates< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Determine Multidrug-Resistant Organisms (MDRO)< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Plotting for Classes < code > rsi< / code > , < code > mic< / code > and < code > disk< / code > < / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > AMR Plots with < code > ggplot2< / code > < / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Determine Bug-Drug Combinations< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Antibiotic Selectors< / dd >
< / dl > < dl > < dt >
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< code > < a href = "mean_amr_distance.html" > mean_amr_distance()< / a > < / code > < code > < a href = "mean_amr_distance.html" > amr_distance_from_row()< / a > < / code >
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< / dt >
< dd > Mean AMR Distance< / dd >
< / dl > < dl > < dt >
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< 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 >
< / dt >
< dd > Predict Antimicrobial Resistance< / dd >
< / dl > < dl > < dt >
< code > < a href = "guess_ab_col.html" > guess_ab_col()< / a > < / code >
< / dt >
< dd > Guess Antibiotic Column< / dd >
< / dl > < / div > < div class = "section level2" >
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< h2 id = "other-antiviral-drugs" > Other: antiviral drugs< a class = "anchor" aria-label = "anchor" href = "#other-antiviral-drugs" > < / a > < / h2 >
< p class = "section-desc" > < / p > < p > This package also provides extensive support for antiviral agents, even though it is not the primary scope of this package. Working with data containing information about antiviral drugs was never easier. Use these functions to get valid properties of antiviral drugs 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/av_from_text.html" > av_from_text()< / a > < / code > .< / p >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
< code > < a href = "as.av.html" > as.av()< / a > < / code > < code > < a href = "as.av.html" > is.av()< / a > < / code >
< / dt >
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< dd > Transform Input to an Antiviral Drug ID< / dd >
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< / dl > < dl > < dt >
< code > < a href = "av_property.html" > av_name()< / a > < / code > < code > < a href = "av_property.html" > av_cid()< / a > < / code > < code > < a href = "av_property.html" > av_synonyms()< / a > < / code > < code > < a href = "av_property.html" > av_tradenames()< / a > < / code > < code > < a href = "av_property.html" > av_group()< / a > < / code > < code > < a href = "av_property.html" > av_atc()< / a > < / code > < code > < a href = "av_property.html" > av_loinc()< / a > < / code > < code > < a href = "av_property.html" > av_ddd()< / a > < / code > < code > < a href = "av_property.html" > av_ddd_units()< / a > < / code > < code > < a href = "av_property.html" > av_info()< / a > < / code > < code > < a href = "av_property.html" > av_url()< / a > < / code > < code > < a href = "av_property.html" > av_property()< / a > < / code >
< / dt >
2022-11-13 13:52:01 +01:00
< dd > Get Properties of an Antiviral Drug< / dd >
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< / dl > < dl > < dt >
< code > < a href = "av_from_text.html" > av_from_text()< / a > < / code >
< / dt >
< dd > Retrieve Antiviral Drug Names and Doses from Clinical Text< / dd >
< / dl > < / div > < div class = "section level2" >
< h2 id = "other-background-information-on-included-data" > Other: background information on included data< a class = "anchor" aria-label = "anchor" href = "#other-background-information-on-included-data" > < / a > < / h2 >
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< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
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< code > < a href = "AMR.html" > AMR< / a > < / code > < code > < a href = "AMR.html" > AMR-package< / a > < / code >
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< / dt >
< dd > The < code > AMR< / code > Package< / dd >
< / dl > < dl > < dt >
< code > < a href = "example_isolates.html" > example_isolates< / a > < / code >
< / dt >
< dd > Data Set with 2,000 Example Isolates< / dd >
< / dl > < dl > < dt >
< code > < a href = "microorganisms.html" > microorganisms< / a > < / code >
< / dt >
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< dd > Data Set with 48,883 Microorganisms< / dd >
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< / dl > < dl > < dt >
< code > < a href = "microorganisms.codes.html" > microorganisms.codes< / a > < / code >
< / dt >
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< dd > Data Set with 5,932 Common Microorganism Codes< / dd >
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< / dl > < dl > < dt >
< code > < a href = "antibiotics.html" > antibiotics< / a > < / code > < code > < a href = "antibiotics.html" > antivirals< / a > < / code >
< / dt >
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< dd > Data Sets with 603 Antimicrobial Drugs< / dd >
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< / dl > < dl > < dt >
< code > < a href = "intrinsic_resistant.html" > intrinsic_resistant< / a > < / code >
< / dt >
< dd > Data Set with Bacterial Intrinsic Resistance< / dd >
< / dl > < dl > < dt >
< code > < a href = "dosage.html" > dosage< / a > < / code >
< / dt >
< dd > Data Set with Treatment Dosages as Defined by EUCAST< / dd >
< / dl > < dl > < dt >
< code > < a href = "WHOCC.html" > WHOCC< / a > < / code >
< / dt >
< dd > WHOCC: WHO Collaborating Centre for Drug Statistics Methodology< / dd >
< / dl > < dl > < dt >
< code > < a href = "example_isolates_unclean.html" > example_isolates_unclean< / a > < / code >
< / dt >
< dd > Data Set with Unclean Data< / dd >
< / dl > < dl > < dt >
< code > < a href = "rsi_translation.html" > rsi_translation< / a > < / code >
< / dt >
< dd > Data Set for R/SI Interpretation< / dd >
< / dl > < dl > < dt >
< code > < a href = "WHONET.html" > WHONET< / a > < / code >
< / dt >
< dd > Data Set with 500 Isolates - WHONET Example< / dd >
< / dl > < / div > < div class = "section level2" >
< h2 id = "other-miscellaneous-functions" > Other: miscellaneous functions< a class = "anchor" aria-label = "anchor" href = "#other-miscellaneous-functions" > < / a > < / h2 >
< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
< code > < a href = "age_groups.html" > age_groups()< / a > < / code >
< / dt >
< dd > Split Ages into Age Groups< / dd >
< / dl > < dl > < dt >
< code > < a href = "age.html" > age()< / a > < / code >
< / dt >
< dd > Age in Years of Individuals< / dd >
< / dl > < dl > < dt >
< code > < a href = "availability.html" > availability()< / a > < / code >
< / dt >
< dd > Check Availability of Columns< / dd >
< / dl > < dl > < dt >
< code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > < code > < a href = "translate.html" > set_AMR_locale()< / a > < / code > < code > < a href = "translate.html" > reset_AMR_locale()< / a > < / code > < code > < a href = "translate.html" > translate_AMR()< / a > < / code >
< / dt >
< dd > Translate Strings from the AMR Package< / dd >
< / dl > < dl > < dt >
< code > < a href = "ggplot_pca.html" > ggplot_pca()< / a > < / code >
< / dt >
< dd > PCA Biplot with < code > ggplot2< / code > < / dd >
< / dl > < dl > < dt >
< code > < a href = "italicise_taxonomy.html" > italicise_taxonomy()< / a > < / code > < code > < a href = "italicise_taxonomy.html" > italicize_taxonomy()< / a > < / code >
< / dt >
< dd > Italicise Taxonomic Families, Genera, Species, Subspecies< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Join microorganisms to a Data Set< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Vectorised Pattern Matching with Keyboard Shortcut< / dd >
< / dl > < dl > < dt >
< code > < a href = "mo_matching_score.html" > mo_matching_score()< / a > < / code >
< / dt >
< dd > Calculate the Matching Score for Microorganisms< / dd >
< / dl > < dl > < dt >
< code > < a href = "pca.html" > pca()< / a > < / code >
< / dt >
< dd > Principal Component Analysis (for AMR)< / dd >
< / dl > < dl > < dt >
< 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 >
< / dt >
< dd > Random MIC Values/Disk Zones/RSI Generation< / dd >
< / dl > < / div > < div class = "section level2" >
< h2 id = "other-statistical-tests" > Other: statistical tests< a class = "anchor" aria-label = "anchor" href = "#other-statistical-tests" > < / a > < / h2 >
< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
< code > < a href = "g.test.html" > g.test()< / a > < / code >
< / dt >
< dd > < em > G< / em > -test for Count Data< / dd >
< / dl > < dl > < dt >
< code > < a href = "kurtosis.html" > kurtosis()< / a > < / code >
< / dt >
< dd > Kurtosis of the Sample< / dd >
< / dl > < dl > < dt >
< code > < a href = "skewness.html" > skewness()< / a > < / code >
< / dt >
< dd > Skewness of the Sample< / dd >
< / dl > < / div > < div class = "section level2" >
< h2 id = "other-deprecated-functions" > Other: deprecated functions< a class = "anchor" aria-label = "anchor" href = "#other-deprecated-functions" > < / a > < / h2 >
< 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 >
< / div > < div id = "" class = "section level2" >
< dl > < dt >
< code > < a href = "AMR-deprecated.html" > AMR-deprecated< / a > < / code >
< / dt >
< dd > Deprecated Functions< / dd >
< / dl > < / 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 > < p > < code > AMR< / code > (for R). Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > in collaboration with non-profit organisations< br > < a target = "_blank" href = "https://www.certe.nl" class = "external-link" > Certe Medical Diagnostics and Advice Foundation< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > .< / p >
< / div >
< div class = "pkgdown-footer-right" >
2022-10-05 12:32:07 +02:00
< p > < / p > < 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 > < / p >
2022-08-21 16:59:35 +02:00
< / div >
< / footer > < / div >
< / body > < / html >
