Antimicrobial Resistance Data Analysis


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Documentation for package ‘AMR’ version 1.7.1

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A B C D E F G I J K L M N O P R S T 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 Class Selectors
ab_ddd 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_synonyms Get Properties of an Antibiotic
ab_tradenames Get Properties of an Antibiotic
ab_url Get Properties of an Antibiotic
age Age in Years of Individuals
age_groups Split Ages into Age Groups
all_antimicrobials (Key) Antimicrobials for First Weighted Isolates
aminoglycosides Antibiotic Class Selectors
AMR The 'AMR' Package
antibiotics Data Sets with 558 Antimicrobials
antibiotic_class_selectors Antibiotic Class Selectors
antimicrobials_equal (Key) Antimicrobials for First Weighted Isolates
antivirals Data Sets with 558 Antimicrobials
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_groups Get ATC Properties from WHOCC Website
atc_online_property Get ATC Properties from WHOCC Website
availability Check Availability of Columns

-- B --

betalactams Antibiotic Class Selectors
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
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 (Weighted) Isolates
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_episode Determine (New) Episodes for Patients
get_locale Translate Strings from AMR Package
get_mo_source User-Defined Reference Data Set for Microorganisms
ggplot.disk Plotting for Classes 'rsi', 'mic' and 'disk'
ggplot.mic Plotting for Classes 'rsi', 'mic' and 'disk'
ggplot.resistance_predict Predict antimicrobial resistance
ggplot.rsi Plotting for Classes 'rsi', 'mic' and 'disk'
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
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

-- 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 Transform Input to Minimum Inhibitory Concentrations (MIC)
microorganisms Data Set with 70,026 Microorganisms
microorganisms.codes Data Set with 5,605 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_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 --

n_rsi Count Available Isolates

-- O --

oxazolidinones Antibiotic Class Selectors

-- P --

pca Principal Component Analysis (for AMR)
PDR Determine Multidrug-Resistant Organisms (MDRO)
penicillins Antibiotic Class 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'
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

-- 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_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% 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)