R: Antimicrobial Resistance Data Analysis

# Antimicrobial Resistance Data Analysis

## Documentation for package ‘AMR’ version 3.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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_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_reset_session | Transform Input to an Antibiotic ID
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 | Antimicrobial Selectors
administrable_per_os | Antimicrobial Selectors
age | Age in Years of Individuals
age_groups | Split Ages into Age Groups
all_antimicrobials | (Key) Antimicrobials for First Weighted Isolates
aminoglycosides | Antimicrobial Selectors
aminopenicillins | Antimicrobial Selectors
amr_class | Antimicrobial Selectors
amr_distance_from_row | Calculate the Mean AMR Distance
amr_selector | Antimicrobial Selectors
antibiogram | Generate Traditional, Combination, Syndromic, or WISCA Antibiograms
antibiotics | Data Sets with 616 Antimicrobial Drugs
antifungals | Antimicrobial Selectors
antimicrobials | Data Sets with 616 Antimicrobial Drugs
antimicrobials_equal | (Key) Antimicrobials for First Weighted Isolates
antimicrobial_selectors | Antimicrobial Selectors
antimycobacterials | Antimicrobial Selectors
antivirals | Data Sets with 616 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 | Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
as.sir.data.frame | Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
as.sir.default | Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
as.sir.disk | Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
as.sir.mic | Interpret MIC and Disk Diffusion as 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 Traditional, Combination, Syndromic, or WISCA Antibiograms
autoplot.disk | Plotting Helpers for AMR Data Analysis
autoplot.mic | Plotting Helpers for AMR Data Analysis
autoplot.resistance_predict | Predict Antimicrobial Resistance
autoplot.sir | Plotting Helpers for AMR Data Analysis
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 | Antimicrobial Selectors
betalactams_with_inhibitor | Antimicrobial Selectors
BRMO | Determine Multidrug-Resistant Organisms (MDRO)
brmo | Determine Multidrug-Resistant Organisms (MDRO)
bug_drug_combinations | Determine Bug-Drug Combinations

## -- C --

c.custom_mdro_guideline | Define Custom MDRO Guideline
carbapenems | Antimicrobial Selectors
cephalosporins | Antimicrobial Selectors
cephalosporins_1st | Antimicrobial Selectors
cephalosporins_2nd | Antimicrobial Selectors
cephalosporins_3rd | Antimicrobial Selectors
cephalosporins_4th | Antimicrobial Selectors
cephalosporins_5th | Antimicrobial 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 | Define Custom MDRO Guideline

## -- 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 | Plotting Helpers for AMR Data Analysis
filter_first_isolate | Determine First Isolates
first_isolate | Determine First Isolates
fluoroquinolones | Antimicrobial Selectors
format.bug_drug_combinations | Determine Bug-Drug Combinations
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 | Antimicrobial 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 Denoting 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 | Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
isoxazolylpenicillins | Antimicrobial Selectors
is_new_episode | Determine Clinical or Epidemic Episodes
is_sir_eligible | Interpret MIC and Disk Diffusion as 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 Traditional, Combination, Syndromic, or WISCA Antibiograms
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 | Plotting Helpers for AMR Data Analysis
left_join_microorganisms | Join microorganisms to a Data Set
like | Vectorised Pattern Matching with Keyboard Shortcut
lincosamides | Antimicrobial Selectors
lipoglycopeptides | Antimicrobial Selectors

## -- M --

macrolides | Antimicrobial 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 78 679 Taxonomic Records of Microorganisms
microorganisms.codes | Data Set with 6 036 Common Microorganism Codes
microorganisms.groups | Data Set with 534 Microorganisms In Species Groups
mic_p50 | Transform Input to Minimum Inhibitory Concentrations (MIC)
mic_p90 | Transform Input to Minimum Inhibitory Concentrations (MIC)
mo | Transform Arbitrary Input to Valid Microbial Taxonomy
monobactams | Antimicrobial Selectors
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_group_members | 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_mycobank | Get Properties of a Microorganism
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_ | Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
nitrofurans | Antimicrobial Selectors
not_intrinsic_resistant | Antimicrobial Selectors
n_sir | Count Available Isolates

## -- O --

oxazolidinones | Antimicrobial Selectors

## -- P --

pca | Principal Component Analysis (for AMR)
PDR | Determine Multidrug-Resistant Organisms (MDRO)
penicillins | Antimicrobial Selectors
phenicols | Antimicrobial Selectors
plot | Plotting Helpers for AMR Data Analysis
plot.antibiogram | Generate Traditional, Combination, Syndromic, or WISCA Antibiograms
plot.disk | Plotting Helpers for AMR Data Analysis
plot.mic | Plotting Helpers for AMR Data Analysis
plot.resistance_predict | Predict Antimicrobial Resistance
plot.sir | Plotting Helpers for AMR Data Analysis
polymyxins | Antimicrobial 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 | Antimicrobial 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
rescale_mic | Transform Input to Minimum Inhibitory Concentrations (MIC)
reset_AMR_locale | Translate Strings from the AMR Package
resistance | Calculate Antimicrobial Resistance
resistance_predict | Predict Antimicrobial Resistance
retrieve_wisca_parameters | Generate Traditional, Combination, Syndromic, or WISCA Antibiograms
rifamycins | Antimicrobial Selectors
right_join_microorganisms | Join microorganisms to a Data Set

## -- S --

scale_color_mic | Plotting Helpers for AMR Data Analysis
scale_color_sir | Plotting Helpers for AMR Data Analysis
scale_colour_mic | Plotting Helpers for AMR Data Analysis
scale_colour_sir | Plotting Helpers for AMR Data Analysis
scale_fill_mic | Plotting Helpers for AMR Data Analysis
scale_fill_sir | Plotting Helpers for AMR Data Analysis
scale_sir_colors | Plotting Helpers for AMR Data Analysis
scale_sir_colours | Plotting Helpers for AMR Data Analysis
scale_x_mic | Plotting Helpers for AMR Data Analysis
scale_x_sir | Plotting Helpers for AMR Data Analysis
scale_y_mic | Plotting Helpers for AMR Data Analysis
scale_y_percent | Plotting Helpers for AMR Data Analysis
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 | Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
sir_confidence_interval | Calculate Antimicrobial Resistance
sir_df | Calculate Antimicrobial Resistance
sir_interpretation_history | Interpret MIC and Disk Diffusion as 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 | Antimicrobial Selectors
sulfonamides | Antimicrobial Selectors
susceptibility | Calculate Antimicrobial Resistance

## -- T --

tetracyclines | Antimicrobial Selectors
theme_sir | Plotting Helpers for AMR Data Analysis
top_n_microorganisms | Filter Top _n_ Microorganisms
translate | Translate Strings from the AMR Package
translate_AMR | Translate Strings from the AMR Package
trimethoprims | Antimicrobial Selectors

## -- U --

ureidopenicillins | Antimicrobial Selectors

## -- W --

WHOCC | WHOCC: WHO Collaborating Centre for Drug Statistics Methodology
WHONET | Data Set with 500 Isolates - WHONET Example
wisca | Generate Traditional, Combination, Syndromic, or WISCA Antibiograms

## -- 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)