Antimicrobial Resistance Analysis


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Documentation for package ‘AMR’ version 1.3.0

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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)