# Antimicrobial Resistance Analysis

## Documentation for package ‘AMR’ version 1.3.0

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

## Help Pages

A B C D E F G I J K L M N P R S T W X misc

## -- A --

ab | Transform to antibiotic ID
ab_atc | Property of an antibiotic
ab_atc_group1 | Property of an antibiotic
ab_atc_group2 | Property of an antibiotic
ab_cid | Property of an antibiotic
ab_class | Antibiotic class selectors
ab_ddd | Property of an antibiotic
ab_from_text | Retrieve antimicrobial drug names and doses from clinical text
ab_group | Property of an antibiotic
ab_info | Property of an antibiotic
ab_loinc | Property of an antibiotic
ab_name | Property of an antibiotic
ab_property | Property of an antibiotic
ab_synonyms | Property of an antibiotic
ab_tradenames | Property of an antibiotic
ab_url | Property of an antibiotic
age | Age in years of individuals
age_groups | Split ages into age groups
aminoglycosides | Antibiotic class selectors
AMR | The 'AMR' Package
antibiotics | Data sets with 558 antimicrobials
antibiotic_class_selectors | Antibiotic class selectors
antivirals | Data sets with 558 antimicrobials
anti_join_microorganisms | Join microorganisms to a data set
as.ab | Transform to antibiotic ID
as.disk | Class 'disk'
as.mic | Class 'mic'
as.mo | Transform to microorganism ID
as.rsi | Class 'rsi'
as.rsi.data.frame | Class 'rsi'
as.rsi.disk | Class 'rsi'
as.rsi.mic | Class 'rsi'
ATC | Property of an antibiotic
atc_online_ddd | Get ATC properties from WHOCC website
atc_online_groups | Get ATC properties from WHOCC website
atc_online_property | Get ATC properties from WHOCC website
availability | Check availability of columns

## -- B --

BRMO | Determine multidrug-resistant organisms (MDRO)
brmo | Determine multidrug-resistant organisms (MDRO)
bug_drug_combinations | Determine bug-drug combinations

## -- C --

carbapenems | Antibiotic class selectors
catalogue_of_life | The Catalogue of Life
catalogue_of_life_version | Version info of included Catalogue of Life
cephalosporins | Antibiotic class selectors
cephalosporins_1st | Antibiotic class selectors
cephalosporins_2nd | Antibiotic class selectors
cephalosporins_3rd | Antibiotic class selectors
cephalosporins_4th | Antibiotic class selectors
cephalosporins_5th | Antibiotic class 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

## -- D --

disk | Class 'disk'

## -- E --

EUCAST | 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_1st_cephalosporins | Filter isolates on result in antimicrobial class
filter_2nd_cephalosporins | Filter isolates on result in antimicrobial class
filter_3rd_cephalosporins | Filter isolates on result in antimicrobial class
filter_4th_cephalosporins | Filter isolates on result in antimicrobial class
filter_5th_cephalosporins | Filter isolates on result in antimicrobial class
filter_ab_class | Filter isolates on result in antimicrobial class
filter_aminoglycosides | Filter isolates on result in antimicrobial class
filter_carbapenems | Filter isolates on result in antimicrobial class
filter_cephalosporins | Filter isolates on result in antimicrobial class
filter_first_isolate | Determine first (weighted) isolates
filter_first_weighted_isolate | Determine first (weighted) isolates
filter_fluoroquinolones | Filter isolates on result in antimicrobial class
filter_glycopeptides | Filter isolates on result in antimicrobial class
filter_macrolides | Filter isolates on result in antimicrobial class
filter_penicillins | Filter isolates on result in antimicrobial class
filter_tetracyclines | Filter isolates on result in antimicrobial class
first_isolate | Determine first (weighted) isolates
fluoroquinolones | Antibiotic class 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_rsi | AMR plots with 'ggplot2'
get_locale | Translate strings from AMR package
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 class 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
is.ab | Transform to antibiotic ID
is.disk | Class 'disk'
is.mic | Class 'mic'
is.mo | Transform to microorganism ID
is.rsi | Class 'rsi'
is.rsi.eligible | Class 'rsi'

## -- J --

join | Join microorganisms to a data set

## -- K --

key_antibiotics | Key antibiotics for first _weighted_ isolates
key_antibiotics_equal | Key antibiotics 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 | Pattern Matching

## -- M --

macrolides | Antibiotic class 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 | Class 'mic'
microorganisms | Data set with 67,151 microorganisms
microorganisms.codes | Translation table with 5,582 common microorganism codes
microorganisms.old | Data set with previously accepted taxonomic names
mo | Transform to microorganism ID
mo_authors | Property of a microorganism
mo_class | Property of a microorganism
mo_domain | Property of a microorganism
mo_failures | Transform to microorganism ID
mo_family | Property of a microorganism
mo_fullname | Property of a microorganism
mo_genus | Property of a microorganism
mo_gramstain | Property of a microorganism
mo_info | Property of a microorganism
mo_kingdom | Property of a microorganism
mo_name | Property of a microorganism
mo_order | Property of a microorganism
mo_phylum | Property of a microorganism
mo_property | Property of a microorganism
mo_rank | Property of a microorganism
mo_ref | Property of a microorganism
mo_renamed | Transform to microorganism ID
mo_shortname | Property of a microorganism
mo_snomed | Property of a microorganism
mo_source | User-defined reference data set for microorganisms
mo_species | Property of a microorganism
mo_subspecies | Property of a microorganism
mo_synonyms | Property of a microorganism
mo_taxonomy | Property of a microorganism
mo_type | Property of a microorganism
mo_uncertainties | Transform to microorganism ID
mo_url | Property of a microorganism
mo_year | Property of a microorganism
mrgn | Determine multidrug-resistant organisms (MDRO)

## -- N --

n_rsi | Count available isolates

## -- P --

pca | Principal Component Analysis (for AMR)
PDR | Determine multidrug-resistant organisms (MDRO)
penicillins | Antibiotic class selectors
plot.resistance_predict | Predict antimicrobial resistance
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
p_symbol | Symbol of a p-value

## -- R --

resistance | Calculate microbial resistance
resistance_predict | Predict antimicrobial resistance
right_join_microorganisms | Join microorganisms to a data set
rsi | Class 'rsi'
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_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
susceptibility | Calculate microbial resistance

## -- T --

tetracyclines | Antibiotic class selectors
theme_rsi | AMR plots with 'ggplot2'
translate | Translate strings from AMR package

## -- 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% | Pattern Matching
%like_case% | Pattern Matching
3MRGN | Determine multidrug-resistant organisms (MDRO)
4MRGN | Determine multidrug-resistant organisms (MDRO)