# Antimicrobial Resistance Data Analysis

## Documentation for package ‘AMR’ version 1.8.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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_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
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 | The 'AMR' Package
antibiotics | Data Sets with 566 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 566 Antimicrobial Drugs
anti_join_microorganisms | Join microorganisms to a Data Set
as.ab | Transform Input to an Antibiotic ID
as.disk | Transform Input to Disk Diffusion Diameters
as.mic | Transform Input to Minimum Inhibitory Concentrations (MIC)
as.mo | Transform Input to a Microorganism Code
as.rsi | Interpret MIC and Disk Values, or Clean Raw R/SI Data
as.rsi.data.frame | Interpret MIC and Disk Values, or Clean Raw R/SI Data
as.rsi.disk | Interpret MIC and Disk Values, or Clean Raw R/SI Data
as.rsi.mic | Interpret MIC and Disk Values, or Clean Raw R/SI 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.disk | Plotting for Classes 'rsi', 'mic' and 'disk'
autoplot.mic | Plotting for Classes 'rsi', 'mic' and 'disk'
autoplot.resistance_predict | Predict Antimicrobial Resistance
autoplot.rsi | Plotting for Classes 'rsi', 'mic' and 'disk'
availability | Check Availability of Columns

## -- 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
catalogue_of_life | The Catalogue of Life
catalogue_of_life_version | Version info of included Catalogue of Life
cephalosporins | Antibiotic Selectors
cephalosporins_1st | Antibiotic Selectors
cephalosporins_2nd | Antibiotic Selectors
cephalosporins_3rd | Antibiotic Selectors
cephalosporins_4th | Antibiotic Selectors
cephalosporins_5th | Antibiotic Selectors
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

## -- 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_rsi | 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 'rsi', 'mic' and 'disk'
fortify.mic | Plotting for Classes 'rsi', 'mic' and 'disk'
fortify.rsi | Plotting for Classes 'rsi', 'mic' and 'disk'
full_join_microorganisms | Join microorganisms to a Data Set

## -- G --

g.test | _G_-test for Count Data
geom_rsi | AMR Plots with 'ggplot2'
get_AMR_locale | Translate Strings from AMR Package
get_episode | Determine (New) Episodes for Patients
get_mo_source | User-Defined Reference Data Set for Microorganisms
ggplot_pca | PCA Biplot with 'ggplot2'
ggplot_rsi | AMR Plots with 'ggplot2'
ggplot_rsi_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.disk | Transform Input to Disk Diffusion Diameters
is.mic | Transform Input to Minimum Inhibitory Concentrations (MIC)
is.mo | Transform Input to a Microorganism Code
is.rsi | Interpret MIC and Disk Values, or Clean Raw R/SI Data
is.rsi.eligible | Interpret MIC and Disk Values, or Clean Raw R/SI Data
is_new_episode | Determine (New) Episodes for Patients
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
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_rsi_count | AMR Plots with 'ggplot2'
left_join_microorganisms | Join microorganisms to a Data Set
lifecycle | Lifecycles of Functions in the 'AMR' Package
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)
mic | Transform Input to Minimum Inhibitory Concentrations (MIC)
microorganisms | Data Set with 70,760 Microorganisms
microorganisms.codes | Data Set with 5,604 Common Microorganism Codes
microorganisms.old | Data Set with Previously Accepted Taxonomic Names
mo | Transform Input to a Microorganism Code
mo_authors | Get Properties of a Microorganism
mo_class | Get Properties of a Microorganism
mo_domain | Get Properties of a Microorganism
mo_failures | Transform Input to a Microorganism Code
mo_family | Get Properties of a Microorganism
mo_fullname | 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_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_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 Input to a Microorganism Code
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_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 Input to a Microorganism Code
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_rsi_ | Interpret MIC and Disk Values, or Clean Raw R/SI Data
not_intrinsic_resistant | Antibiotic Selectors
n_rsi | 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 'rsi', 'mic' and 'disk'
plot.disk | Plotting for Classes 'rsi', 'mic' and 'disk'
plot.mic | Plotting for Classes 'rsi', 'mic' and 'disk'
plot.resistance_predict | Predict Antimicrobial Resistance
plot.rsi | Plotting for Classes 'rsi', 'mic' and 'disk'
polymyxins | Antibiotic Selectors
portion | Calculate Microbial Resistance
proportion | Calculate Microbial Resistance
proportion_df | Calculate Microbial Resistance
proportion_I | Calculate Microbial Resistance
proportion_IR | Calculate Microbial Resistance
proportion_R | Calculate Microbial Resistance
proportion_S | Calculate Microbial Resistance
proportion_SI | Calculate Microbial Resistance

## -- Q --

quinolones | Antibiotic Selectors

## -- R --

random | Random MIC Values/Disk Zones/RSI Generation
random_disk | Random MIC Values/Disk Zones/RSI Generation
random_mic | Random MIC Values/Disk Zones/RSI Generation
random_rsi | Random MIC Values/Disk Zones/RSI Generation
resistance | Calculate Microbial Resistance
resistance_predict | Predict Antimicrobial Resistance
right_join_microorganisms | Join microorganisms to a Data Set
rsi | Interpret MIC and Disk Values, or Clean Raw R/SI Data
rsi_df | Calculate Microbial Resistance
rsi_predict | Predict Antimicrobial Resistance
rsi_translation | Data Set for R/SI Interpretation

## -- S --

scale_rsi_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_mo_source | User-Defined Reference Data Set for Microorganisms
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 Microbial Resistance

## -- T --

tetracyclines | Antibiotic Selectors
theme_rsi | AMR Plots with 'ggplot2'
translate | Translate Strings from 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)