R: Antimicrobial Resistance Data Analysis

# Antimicrobial Resistance Data Analysis

## Documentation for package ‘AMR’ version 2.1.1

- 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
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)