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Preparing data: microorganisms

These functions are meant to get taxonomically valid properties of microorganisms from any input. Use mo_source() to teach this package how to translate your own codes to valid microorganism codes.

Preparing data: antibiotics

Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using ab_from_text().

as.ab() is.ab()
Transform Input to an Antibiotic ID
ab_name() ab_cid() ab_synonyms() ab_tradenames() ab_group() ab_atc() ab_atc_group1() ab_atc_group2() ab_loinc() ab_ddd() ab_ddd_units() ab_info() ab_url() ab_property() set_ab_names()
Get Properties of an Antibiotic
ab_from_text()
Retrieve Antimicrobial Drug Names and Doses from Clinical Text
atc_online_property() atc_online_groups() atc_online_ddd() atc_online_ddd_units()
Get ATC Properties from WHOCC Website

Preparing data: antimicrobial resistance

With as.mic() and as.disk() you can transform your raw input to valid MIC or disk diffusion values. Use as.rsi() for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying EUCAST rules with eucast_rules().

as.rsi() NA_rsi_ is.rsi() is.rsi.eligible() rsi_interpretation_history()
Interpret MIC and Disk Values, or Clean Raw R/SI Data
as.mic() NA_mic_ is.mic() droplevels(<mic>)
Transform Input to Minimum Inhibitory Concentrations (MIC)
as.disk() NA_disk_ is.disk()
Transform Input to Disk Diffusion Diameters
eucast_rules() eucast_dosage()
Apply EUCAST Rules
custom_eucast_rules()
Define Custom EUCAST Rules

Analysing data: antimicrobial resistance

Use these function for the analysis part. You can use susceptibility() or resistance() on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using first_isolate() or is_new_episode(). You can also filter your data on certain resistance in certain antibiotic classes (carbapenems(), aminoglycosides()), or determine multi-drug resistant microorganisms (MDRO, mdro()).

resistance() susceptibility() proportion_R() proportion_IR() proportion_I() proportion_SI() proportion_S() proportion_df() rsi_df()
Calculate Microbial Resistance
count_resistant() count_susceptible() count_R() count_IR() count_I() count_SI() count_S() count_all() n_rsi() count_df()
Count Available Isolates
get_episode() is_new_episode()
Determine (New) Episodes for Patients
first_isolate() filter_first_isolate()
Determine First Isolates
key_antimicrobials() all_antimicrobials() antimicrobials_equal()
(Key) Antimicrobials for First Weighted Isolates
mdro() custom_mdro_guideline() brmo() mrgn() mdr_tb() mdr_cmi2012() eucast_exceptional_phenotypes()
Determine Multidrug-Resistant Organisms (MDRO)
plot(<mic>) autoplot(<mic>) fortify(<mic>) plot(<disk>) autoplot(<disk>) fortify(<disk>) plot(<rsi>) autoplot(<rsi>) fortify(<rsi>)
Plotting for Classes rsi, mic and disk
ggplot_rsi() geom_rsi() facet_rsi() scale_y_percent() scale_rsi_colours() theme_rsi() labels_rsi_count()
AMR Plots with ggplot2
bug_drug_combinations() format(<bug_drug_combinations>)
Determine Bug-Drug Combinations
ab_class() ab_selector() aminoglycosides() aminopenicillins() antifungals() antimycobacterials() betalactams() carbapenems() cephalosporins() cephalosporins_1st() cephalosporins_2nd() cephalosporins_3rd() cephalosporins_4th() cephalosporins_5th() fluoroquinolones() glycopeptides() lincosamides() lipoglycopeptides() macrolides() oxazolidinones() penicillins() polymyxins() streptogramins() quinolones() tetracyclines() trimethoprims() ureidopenicillins() administrable_per_os() administrable_iv() not_intrinsic_resistant()
Antibiotic Selectors
mean_amr_distance() distance_from_row()
Mean AMR Distance
resistance_predict() rsi_predict() plot(<resistance_predict>) ggplot_rsi_predict() autoplot(<resistance_predict>)
Predict Antimicrobial Resistance
guess_ab_col()
Guess Antibiotic Column

Background information on included data

Some pages about our package and its external sources. Be sure to read our How To’s for more information about how to work with functions in this package.

AMR
The AMR Package
example_isolates
Data Set with 2,000 Example Isolates
microorganisms
Data Set with 70,764 Microorganisms
microorganisms.codes
Data Set with 5,604 Common Microorganism Codes
microorganisms.old
Data Set with Previously Accepted Taxonomic Names
antibiotics antivirals
Data Sets with 566 Antimicrobial Drugs
intrinsic_resistant
Data Set with Bacterial Intrinsic Resistance
dosage
Data Set with Treatment Dosages as Defined by EUCAST
catalogue_of_life
The Catalogue of Life
catalogue_of_life_version()
Version info of included Catalogue of Life
WHOCC
WHOCC: WHO Collaborating Centre for Drug Statistics Methodology
example_isolates_unclean
Data Set with Unclean Data
rsi_translation
Data Set for R/SI Interpretation
WHONET
Data Set with 500 Isolates - WHONET Example

Other: miscellaneous functions

These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: if (x %like% y) {...}.

age_groups()
Split Ages into Age Groups
age()
Age in Years of Individuals
availability()
Check Availability of Columns
get_AMR_locale() set_AMR_locale() reset_AMR_locale() translate_AMR()
Translate Strings from the AMR Package
ggplot_pca()
PCA Biplot with ggplot2
italicise_taxonomy() italicize_taxonomy()
Italicise Taxonomic Families, Genera, Species, Subspecies
inner_join_microorganisms() left_join_microorganisms() right_join_microorganisms() full_join_microorganisms() semi_join_microorganisms() anti_join_microorganisms()
Join microorganisms to a Data Set
like() `%like%` `%unlike%` `%like_case%` `%unlike_case%`
Vectorised Pattern Matching with Keyboard Shortcut
mo_matching_score()
Calculate the Matching Score for Microorganisms
pca()
Principal Component Analysis (for AMR)
random_mic() random_disk() random_rsi()
Random MIC Values/Disk Zones/RSI Generation

Other: statistical tests

Some statistical tests or methods are not part of base R and were added to this package for convenience.

g.test()
G-test for Count Data
kurtosis()
Kurtosis of the Sample
skewness()
Skewness of the Sample

Other: deprecated functions

These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.

AMR-deprecated
Deprecated Functions