A B C D E F G I J K L M N O P R S T W X misc
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 |
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 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 ID |
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 |
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 |
custom_mdro_guideline | Determine Multidrug-Resistant Organisms (MDRO) |
disk | Transform Input to Disk Diffusion Diameters |
dosage | Data Set with Treatment Dosages as Defined by EUCAST |
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 |
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_oxazolidinones | 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_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.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 |
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 ID |
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 |
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 with Keyboard Shortcut |
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 5,580 Common Microorganism Codes |
microorganisms.old | Data Set with Previously Accepted Taxonomic Names |
mo | Transform Input to a Microorganism ID |
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 ID |
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 ID |
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 ID |
mo_url | Get Properties of a Microorganism |
mo_year | Get Properties of a Microorganism |
mrgn | Determine Multidrug-Resistant Organisms (MDRO) |
n_rsi | Count Available Isolates |
oxazolidinones | Antibiotic Class Selectors |
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 |
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 |
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 with Keyboard Shortcut |
%like_case% | Pattern Matching with Keyboard Shortcut |
3MRGN | Determine Multidrug-Resistant Organisms (MDRO) |
4MRGN | Determine Multidrug-Resistant Organisms (MDRO) |