A B C D E F G I J K L M N P R S T W X misc
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 |
BRMO | Determine multidrug-resistant organisms (MDRO) |
brmo | Determine multidrug-resistant organisms (MDRO) |
bug_drug_combinations | Determine bug-drug combinations |
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 |
disk | Class 'disk' |
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 |
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.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 |
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' |
join | Join microorganisms to a data set |
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 |
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 |
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_rsi | Count available isolates |
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 |
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 |
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 |
tetracyclines | Antibiotic class selectors |
theme_rsi | AMR plots with 'ggplot2' |
translate | Translate strings from AMR package |
WHOCC | WHOCC: WHO Collaborating Centre for Drug Statistics Methodology |
WHONET | Data set with 500 isolates - WHONET example |
XDR | Determine multidrug-resistant organisms (MDRO) |
%like% | Pattern Matching |
%like_case% | Pattern Matching |
3MRGN | Determine multidrug-resistant organisms (MDRO) |
4MRGN | Determine multidrug-resistant organisms (MDRO) |