Antimicrobial Resistance Data Analysis
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Documentation for package ‘AMR’ version 2.1.1
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A B C D E F G I J K L M N O P Q R S T U W X misc
-- A --
| ab | Transform Input to an Antibiotic ID |
| ab_atc | Get Properties of an Antibiotic |
| ab_atc_group1 | Get Properties of an Antibiotic |
| ab_atc_group2 | Get Properties of an Antibiotic |
| ab_cid | Get Properties of an Antibiotic |
| ab_class | Antibiotic Selectors |
| ab_ddd | Get Properties of an Antibiotic |
| ab_ddd_units | Get Properties of an Antibiotic |
| ab_from_text | Retrieve Antimicrobial Drug Names and Doses from Clinical Text |
| ab_group | Get Properties of an Antibiotic |
| ab_info | Get Properties of an Antibiotic |
| ab_loinc | Get Properties of an Antibiotic |
| ab_name | Get Properties of an Antibiotic |
| ab_property | Get Properties of an Antibiotic |
| ab_selector | Antibiotic Selectors |
| ab_synonyms | Get Properties of an Antibiotic |
| ab_tradenames | Get Properties of an Antibiotic |
| ab_url | Get Properties of an Antibiotic |
| add_custom_antimicrobials | Add Custom Antimicrobials |
| add_custom_microorganisms | Add Custom Microorganisms |
| administrable_iv | Antibiotic Selectors |
| administrable_per_os | Antibiotic Selectors |
| age | Age in Years of Individuals |
| age_groups | Split Ages into Age Groups |
| all_antimicrobials | (Key) Antimicrobials for First Weighted Isolates |
| aminoglycosides | Antibiotic Selectors |
| aminopenicillins | Antibiotic Selectors |
| amr_distance_from_row | Calculate the Mean AMR Distance |
| antibiogram | Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) |
| antibiotics | Data Sets with 603 Antimicrobial Drugs |
| antibiotic_class_selectors | Antibiotic Selectors |
| antifungals | Antibiotic Selectors |
| antimicrobials_equal | (Key) Antimicrobials for First Weighted Isolates |
| antimycobacterials | Antibiotic Selectors |
| antivirals | Data Sets with 603 Antimicrobial Drugs |
| anti_join_microorganisms | Join microorganisms to a Data Set |
| as.ab | Transform Input to an Antibiotic ID |
| as.av | Transform Input to an Antiviral Drug ID |
| as.disk | Transform Input to Disk Diffusion Diameters |
| as.mic | Transform Input to Minimum Inhibitory Concentrations (MIC) |
| as.mo | Transform Arbitrary Input to Valid Microbial Taxonomy |
| as.sir | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| as.sir.data.frame | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| as.sir.disk | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| as.sir.mic | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| ATC | Get Properties of an Antibiotic |
| atc_online_ddd | Get ATC Properties from WHOCC Website |
| atc_online_ddd_units | Get ATC Properties from WHOCC Website |
| atc_online_groups | Get ATC Properties from WHOCC Website |
| atc_online_property | Get ATC Properties from WHOCC Website |
| autoplot.antibiogram | Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) |
| autoplot.disk | Plotting for Classes 'sir', 'mic' and 'disk' |
| autoplot.mic | Plotting for Classes 'sir', 'mic' and 'disk' |
| autoplot.resistance_predict | Predict Antimicrobial Resistance |
| autoplot.sir | Plotting for Classes 'sir', 'mic' and 'disk' |
| av | Transform Input to an Antiviral Drug ID |
| availability | Check Availability of Columns |
| av_atc | Get Properties of an Antiviral Drug |
| av_cid | Get Properties of an Antiviral Drug |
| av_ddd | Get Properties of an Antiviral Drug |
| av_ddd_units | Get Properties of an Antiviral Drug |
| av_from_text | Retrieve Antiviral Drug Names and Doses from Clinical Text |
| av_group | Get Properties of an Antiviral Drug |
| av_info | Get Properties of an Antiviral Drug |
| av_loinc | Get Properties of an Antiviral Drug |
| av_name | Get Properties of an Antiviral Drug |
| av_property | Get Properties of an Antiviral Drug |
| av_synonyms | Get Properties of an Antiviral Drug |
| av_tradenames | Get Properties of an Antiviral Drug |
| av_url | Get Properties of an Antiviral Drug |
-- B --
| betalactams | Antibiotic Selectors |
| BRMO | Determine Multidrug-Resistant Organisms (MDRO) |
| brmo | Determine Multidrug-Resistant Organisms (MDRO) |
| bug_drug_combinations | Determine Bug-Drug Combinations |
-- C --
| carbapenems | Antibiotic Selectors |
| cephalosporins | Antibiotic Selectors |
| cephalosporins_1st | Antibiotic Selectors |
| cephalosporins_2nd | Antibiotic Selectors |
| cephalosporins_3rd | Antibiotic Selectors |
| cephalosporins_4th | Antibiotic Selectors |
| cephalosporins_5th | Antibiotic Selectors |
| clear_custom_antimicrobials | Add Custom Antimicrobials |
| clear_custom_microorganisms | Add Custom Microorganisms |
| clinical_breakpoints | Data Set with Clinical Breakpoints for SIR Interpretation |
| count | Count Available Isolates |
| count_all | Count Available Isolates |
| count_df | Count Available Isolates |
| count_I | Count Available Isolates |
| count_IR | Count Available Isolates |
| count_R | Count Available Isolates |
| count_resistant | Count Available Isolates |
| count_S | Count Available Isolates |
| count_SI | Count Available Isolates |
| count_susceptible | Count Available Isolates |
| custom_eucast_rules | Define Custom EUCAST Rules |
| custom_mdro_guideline | Determine Multidrug-Resistant Organisms (MDRO) |
-- D --
| disk | Transform Input to Disk Diffusion Diameters |
| dosage | Data Set with Treatment Dosages as Defined by EUCAST |
| droplevels.mic | Transform Input to Minimum Inhibitory Concentrations (MIC) |
-- E --
| EUCAST | Apply EUCAST Rules |
| eucast_dosage | Apply EUCAST Rules |
| eucast_exceptional_phenotypes | Determine Multidrug-Resistant Organisms (MDRO) |
| eucast_rules | Apply EUCAST Rules |
| example_isolates | Data Set with 2 000 Example Isolates |
| example_isolates_unclean | Data Set with Unclean Data |
-- F --
| facet_sir | AMR Plots with 'ggplot2' |
| filter_first_isolate | Determine First Isolates |
| first_isolate | Determine First Isolates |
| fluoroquinolones | Antibiotic Selectors |
| format.bug_drug_combinations | Determine Bug-Drug Combinations |
| fortify.disk | Plotting for Classes 'sir', 'mic' and 'disk' |
| fortify.mic | Plotting for Classes 'sir', 'mic' and 'disk' |
| fortify.sir | Plotting for Classes 'sir', 'mic' and 'disk' |
| full_join_microorganisms | Join microorganisms to a Data Set |
-- G --
| g.test | _G_-test for Count Data |
| geom_sir | AMR Plots with 'ggplot2' |
| get_AMR_locale | Translate Strings from the AMR Package |
| get_episode | Determine Clinical or Epidemic Episodes |
| get_mo_source | User-Defined Reference Data Set for Microorganisms |
| ggplot_pca | PCA Biplot with 'ggplot2' |
| ggplot_sir | AMR Plots with 'ggplot2' |
| ggplot_sir_predict | Predict Antimicrobial Resistance |
| glycopeptides | Antibiotic Selectors |
| guess_ab_col | Guess Antibiotic Column |
-- I --
| inner_join | Join microorganisms to a Data Set |
| inner_join_microorganisms | Join microorganisms to a Data Set |
| intrinsic_resistant | Data Set with Bacterial Intrinsic Resistance |
| is.ab | Transform Input to an Antibiotic ID |
| is.av | Transform Input to an Antiviral Drug ID |
| is.disk | Transform Input to Disk Diffusion Diameters |
| is.mic | Transform Input to Minimum Inhibitory Concentrations (MIC) |
| is.mo | Transform Arbitrary Input to Valid Microbial Taxonomy |
| is.sir | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| is_new_episode | Determine Clinical or Epidemic Episodes |
| is_sir_eligible | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| italicise_taxonomy | Italicise Taxonomic Families, Genera, Species, Subspecies |
| italicize_taxonomy | Italicise Taxonomic Families, Genera, Species, Subspecies |
-- J --
| join | Join microorganisms to a Data Set |
-- K --
| key_antimicrobials | (Key) Antimicrobials for First Weighted Isolates |
| knit_print.antibiogram | Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) |
| kurtosis | Kurtosis of the Sample |
| kurtosis.data.frame | Kurtosis of the Sample |
| kurtosis.default | Kurtosis of the Sample |
| kurtosis.matrix | Kurtosis of the Sample |
-- L --
| labels_sir_count | AMR Plots with 'ggplot2' |
| left_join_microorganisms | Join microorganisms to a Data Set |
| like | Vectorised Pattern Matching with Keyboard Shortcut |
| lincosamides | Antibiotic Selectors |
| lipoglycopeptides | Antibiotic Selectors |
-- M --
| macrolides | Antibiotic Selectors |
| MDR | Determine Multidrug-Resistant Organisms (MDRO) |
| mdro | Determine Multidrug-Resistant Organisms (MDRO) |
| mdr_cmi2012 | Determine Multidrug-Resistant Organisms (MDRO) |
| mdr_tb | Determine Multidrug-Resistant Organisms (MDRO) |
| mean_amr_distance | Calculate the Mean AMR Distance |
| mean_amr_distance.data.frame | Calculate the Mean AMR Distance |
| mean_amr_distance.sir | Calculate the Mean AMR Distance |
| mic | Transform Input to Minimum Inhibitory Concentrations (MIC) |
| microorganisms | Data Set with 52 171 Microorganisms |
| microorganisms.codes | Data Set with 4 957 Common Microorganism Codes |
| microorganisms.groups | Data Set with 521 Microorganisms In Species Groups |
| mo | Transform Arbitrary Input to Valid Microbial Taxonomy |
| mo_authors | Get Properties of a Microorganism |
| mo_class | Get Properties of a Microorganism |
| mo_cleaning_regex | Transform Arbitrary Input to Valid Microbial Taxonomy |
| mo_current | Get Properties of a Microorganism |
| mo_domain | Get Properties of a Microorganism |
| mo_failures | Transform Arbitrary Input to Valid Microbial Taxonomy |
| mo_family | Get Properties of a Microorganism |
| mo_fullname | Get Properties of a Microorganism |
| mo_gbif | Get Properties of a Microorganism |
| mo_genus | Get Properties of a Microorganism |
| mo_gramstain | Get Properties of a Microorganism |
| mo_info | Get Properties of a Microorganism |
| mo_is_anaerobic | Get Properties of a Microorganism |
| mo_is_gram_negative | Get Properties of a Microorganism |
| mo_is_gram_positive | Get Properties of a Microorganism |
| mo_is_intrinsic_resistant | Get Properties of a Microorganism |
| mo_is_yeast | Get Properties of a Microorganism |
| mo_kingdom | Get Properties of a Microorganism |
| mo_lpsn | Get Properties of a Microorganism |
| mo_matching_score | Calculate the Matching Score for Microorganisms |
| mo_name | Get Properties of a Microorganism |
| mo_order | Get Properties of a Microorganism |
| mo_oxygen_tolerance | Get Properties of a Microorganism |
| mo_pathogenicity | Get Properties of a Microorganism |
| mo_phylum | Get Properties of a Microorganism |
| mo_property | Get Properties of a Microorganism |
| mo_rank | Get Properties of a Microorganism |
| mo_ref | Get Properties of a Microorganism |
| mo_renamed | Transform Arbitrary Input to Valid Microbial Taxonomy |
| mo_reset_session | Transform Arbitrary Input to Valid Microbial Taxonomy |
| mo_shortname | Get Properties of a Microorganism |
| mo_snomed | Get Properties of a Microorganism |
| mo_source | User-Defined Reference Data Set for Microorganisms |
| mo_species | Get Properties of a Microorganism |
| mo_status | Get Properties of a Microorganism |
| mo_subspecies | Get Properties of a Microorganism |
| mo_synonyms | Get Properties of a Microorganism |
| mo_taxonomy | Get Properties of a Microorganism |
| mo_type | Get Properties of a Microorganism |
| mo_uncertainties | Transform Arbitrary Input to Valid Microbial Taxonomy |
| mo_url | Get Properties of a Microorganism |
| mo_year | Get Properties of a Microorganism |
| mrgn | Determine Multidrug-Resistant Organisms (MDRO) |
-- N --
| NA_disk_ | Transform Input to Disk Diffusion Diameters |
| NA_mic_ | Transform Input to Minimum Inhibitory Concentrations (MIC) |
| NA_sir_ | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| not_intrinsic_resistant | Antibiotic Selectors |
| n_sir | Count Available Isolates |
-- O --
| oxazolidinones | Antibiotic Selectors |
-- P --
| pca | Principal Component Analysis (for AMR) |
| PDR | Determine Multidrug-Resistant Organisms (MDRO) |
| penicillins | Antibiotic Selectors |
| plot | Plotting for Classes 'sir', 'mic' and 'disk' |
| plot.antibiogram | Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) |
| plot.disk | Plotting for Classes 'sir', 'mic' and 'disk' |
| plot.mic | Plotting for Classes 'sir', 'mic' and 'disk' |
| plot.resistance_predict | Predict Antimicrobial Resistance |
| plot.sir | Plotting for Classes 'sir', 'mic' and 'disk' |
| polymyxins | Antibiotic Selectors |
| portion | Calculate Antimicrobial Resistance |
| proportion | Calculate Antimicrobial Resistance |
| proportion_df | Calculate Antimicrobial Resistance |
| proportion_I | Calculate Antimicrobial Resistance |
| proportion_IR | Calculate Antimicrobial Resistance |
| proportion_R | Calculate Antimicrobial Resistance |
| proportion_S | Calculate Antimicrobial Resistance |
| proportion_SI | Calculate Antimicrobial Resistance |
-- Q --
| quinolones | Antibiotic Selectors |
-- R --
| random | Random MIC Values/Disk Zones/SIR Generation |
| random_disk | Random MIC Values/Disk Zones/SIR Generation |
| random_mic | Random MIC Values/Disk Zones/SIR Generation |
| random_sir | Random MIC Values/Disk Zones/SIR Generation |
| reset_AMR_locale | Translate Strings from the AMR Package |
| resistance | Calculate Antimicrobial Resistance |
| resistance_predict | Predict Antimicrobial Resistance |
| right_join_microorganisms | Join microorganisms to a Data Set |
-- S --
| scale_sir_colours | AMR Plots with 'ggplot2' |
| scale_y_percent | AMR Plots with 'ggplot2' |
| semi_join_microorganisms | Join microorganisms to a Data Set |
| set_ab_names | Get Properties of an Antibiotic |
| set_AMR_locale | Translate Strings from the AMR Package |
| set_mo_source | User-Defined Reference Data Set for Microorganisms |
| sir | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| sir_confidence_interval | Calculate Antimicrobial Resistance |
| sir_df | Calculate Antimicrobial Resistance |
| sir_interpretation_history | Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data |
| sir_predict | Predict Antimicrobial Resistance |
| skewness | Skewness of the Sample |
| skewness.data.frame | Skewness of the Sample |
| skewness.default | Skewness of the Sample |
| skewness.matrix | Skewness of the Sample |
| streptogramins | Antibiotic Selectors |
| susceptibility | Calculate Antimicrobial Resistance |
-- T --
| tetracyclines | Antibiotic Selectors |
| theme_sir | AMR Plots with 'ggplot2' |
| translate | Translate Strings from the AMR Package |
| translate_AMR | Translate Strings from the AMR Package |
| trimethoprims | Antibiotic Selectors |
-- U --
| ureidopenicillins | Antibiotic Selectors |
-- W --
| WHOCC | WHOCC: WHO Collaborating Centre for Drug Statistics Methodology |
| WHONET | Data Set with 500 Isolates - WHONET Example |
-- X --
| XDR | Determine Multidrug-Resistant Organisms (MDRO) |
-- misc --
| %like% | Vectorised Pattern Matching with Keyboard Shortcut |
| %like_case% | Vectorised Pattern Matching with Keyboard Shortcut |
| %unlike% | Vectorised Pattern Matching with Keyboard Shortcut |
| %unlike_case% | Vectorised Pattern Matching with Keyboard Shortcut |
| 3MRGN | Determine Multidrug-Resistant Organisms (MDRO) |
| 4MRGN | Determine Multidrug-Resistant Organisms (MDRO) |