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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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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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< 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" >
< h2 id = "background-information-on-included-data" > Background information on included data< a class = "anchor" aria-label = "anchor" href = "#background-information-on-included-data" > < / a > < / h2 >
< 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 >
2022-10-05 12:32:07 +02:00
< code > < a href = "AMR.html" > AMR< / a > < / code > < code > < a href = "AMR.html" > AMR-package< / a > < / code >
2022-08-21 16:59:35 +02:00
< / 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 >
2022-10-22 22:10:04 +02:00
< 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 >
2022-10-30 14:40:31 +01:00
< dd > Data Sets with 586 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 >
