Package: AMR 2.1.1.9192

AMR: Antimicrobial Resistance Data Analysis

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.

Authors:Matthijs S. Berends [aut, cre], Dennis Souverein [aut, ctb], Erwin E. A. Hassing [aut, ctb], Aislinn Cook [ctb], Andrew P. Norgan [ctb], Anita Williams [ctb], Annick Lenglet [ctb], Anthony Underwood [ctb], Anton Mymrikov [ctb], Bart C. Meijer [ctb], Christian F. Luz [ctb], Dmytro Mykhailenko [ctb], Eric H. L. C. M. Hazenberg [ctb], Gwen Knight [ctb], Jason Stull [ctb], Javier Sanchez [ctb], Jonas Salm [ctb], Judith M. Fonville [ctb], Larisse Bolton [ctb], Matthew Saab [ctb], Peter Dutey-Magni [ctb], Rogier P. Schade [ctb], Sofia Ny [ctb], Alex W. Friedrich [ths], Bhanu N. M. Sinha [ths], Casper J. Albers [ths], Corinna Glasner [ths]

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NEWS

# Install 'AMR' in R:
install.packages('AMR', repos = c('https://msberends.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/msberends/amr/issues

Pkgdown site:https://msberends.github.io

Datasets:

On CRAN:

Conda:

amrantimicrobial-dataepidemiologymicrobiologysoftware

11.92 score 92 stars 6 packages 182 scripts 2.3k downloads 30 mentions 235 exports 0 dependencies

Last updated 3 hours agofrom:067a8aca66. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 10 2025
R-4.5-winOKMar 10 2025
R-4.5-macOKMar 10 2025
R-4.5-linuxOKMar 10 2025
R-4.4-winOKMar 10 2025
R-4.4-macOKMar 10 2025
R-4.4-linuxOKMar 10 2025
R-4.3-winOKMar 10 2025
R-4.3-macOKMar 10 2025

Exports:%like_case%%like%%unlike_case%%unlike%ab_atcab_atc_group1ab_atc_group2ab_cidab_classab_dddab_ddd_unitsab_from_textab_groupab_infoab_loincab_nameab_propertyab_reset_sessionab_selectorab_synonymsab_tradenamesab_urladd_custom_antimicrobialsadd_custom_microorganismsadministrable_ivadministrable_per_osageage_groupsall_antimicrobialsaminoglycosidesaminopenicillinsamr_classamr_distance_from_rowamr_selectoranti_join_microorganismsantibiogramantibioticsantifungalsantimicrobials_equalantimycobacterialsas.abas.avas.diskas.micas.moas.siratc_online_dddatc_online_ddd_unitsatc_online_groupsatc_online_propertyav_atcav_cidav_dddav_ddd_unitsav_from_textav_groupav_infoav_loincav_nameav_propertyav_synonymsav_tradenamesav_urlavailabilitybetalactamsbetalactams_with_inhibitorbrmobug_drug_combinationscarbapenemscephalosporinscephalosporins_1stcephalosporins_2ndcephalosporins_3rdcephalosporins_4thcephalosporins_5thclear_custom_antimicrobialsclear_custom_microorganismscount_allcount_dfcount_Icount_IRcount_Rcount_resistantcount_Scount_SIcount_susceptiblecustom_eucast_rulescustom_mdro_guidelineeucast_dosageeucast_exceptional_phenotypeseucast_rulesfacet_sirfilter_first_isolatefirst_isolatefluoroquinolonesfull_join_microorganismsg.testgeom_sirget_AMR_localeget_episodeget_mo_sourceggplot_pcaggplot_sirggplot_sir_predictglycopeptidesguess_ab_colinner_join_microorganismsis_new_episodeis_sir_eligibleis.abis.avis.diskis.micis.mois.sirisoxazolylpenicillinsitalicise_taxonomyitalicize_taxonomykey_antimicrobialskurtosislabels_sir_countleft_join_microorganismslikelincosamideslipoglycopeptidesmacrolidesmdr_cmi2012mdr_tbmdromean_amr_distancemic_p50mic_p90mo_authorsmo_classmo_cleaning_regexmo_currentmo_domainmo_failuresmo_familymo_fullnamemo_gbifmo_genusmo_gramstainmo_group_membersmo_infomo_is_anaerobicmo_is_gram_negativemo_is_gram_positivemo_is_intrinsic_resistantmo_is_yeastmo_kingdommo_lpsnmo_matching_scoremo_mycobankmo_namemo_ordermo_oxygen_tolerancemo_pathogenicitymo_phylummo_propertymo_rankmo_refmo_renamedmo_reset_sessionmo_shortnamemo_snomedmo_speciesmo_statusmo_subspeciesmo_synonymsmo_taxonomymo_typemo_uncertaintiesmo_urlmo_yearmonobactamsmrgnn_sirNA_disk_NA_mic_NA_sir_nitrofuransnot_intrinsic_resistantoxazolidinonespcapenicillinsphenicolspolymyxinsproportion_dfproportion_Iproportion_IRproportion_Rproportion_Sproportion_SIquinolonesrandom_diskrandom_micrandom_sirrescale_micreset_AMR_localeresistanceresistance_predictretrieve_wisca_parametersrifamycinsright_join_microorganismsscale_color_micscale_color_sirscale_colour_micscale_colour_sirscale_fill_micscale_fill_sirscale_sir_colorsscale_sir_coloursscale_x_micscale_x_sirscale_y_micscale_y_percentsemi_join_microorganismsset_ab_namesset_AMR_localeset_mo_sourcesir_confidence_intervalsir_dfsir_interpretation_historysir_predictskewnessstreptograminssusceptibilitytetracyclinestheme_sirtop_n_microorganismstranslate_AMRtrimethoprimsureidopenicillinswisca

Dependencies:

AMR for Python

Rendered fromAMR_for_Python.Rmdusingknitr::rmarkdownon Mar 10 2025.

Last update: 2025-03-07
Started: 2024-09-30

Welcome to the AMR package

Rendered fromwelcome_to_AMR.Rmdusingknitr::rmarkdownon Mar 10 2025.

Last update: 2025-03-07
Started: 2020-07-31

Readme and manuals

Help Manual

Help pageTopics
Retrieve Antimicrobial Drug Names and Doses from Clinical Textab_from_text
Get Properties of an Antibioticab_atc ab_atc_group1 ab_atc_group2 ab_cid ab_ddd ab_ddd_units ab_group ab_info ab_loinc ab_name ab_property ab_synonyms ab_tradenames ab_url ATC set_ab_names
Add Custom Antimicrobialsadd_custom_antimicrobials clear_custom_antimicrobials
Add Custom Microorganismsadd_custom_microorganisms clear_custom_microorganisms
Age in Years of Individualsage
Split Ages into Age Groupsage_groups
Generate Traditional, Combination, Syndromic, or WISCA Antibiogramsantibiogram autoplot.antibiogram knit_print.antibiogram plot.antibiogram retrieve_wisca_parameters wisca
Antimicrobial Selectorsadministrable_iv administrable_per_os aminoglycosides aminopenicillins amr_class amr_selector antifungals antimicrobial_selectors antimycobacterials betalactams betalactams_with_inhibitor carbapenems cephalosporins cephalosporins_1st cephalosporins_2nd cephalosporins_3rd cephalosporins_4th cephalosporins_5th fluoroquinolones glycopeptides isoxazolylpenicillins lincosamides lipoglycopeptides macrolides monobactams nitrofurans not_intrinsic_resistant oxazolidinones penicillins phenicols polymyxins quinolones rifamycins streptogramins tetracyclines trimethoprims ureidopenicillins
Data Sets with 608 Antimicrobial Drugsantimicrobials antivirals
Transform Input to an Antibiotic IDab ab_reset_session as.ab is.ab
Transform Input to an Antiviral Drug IDas.av av is.av
Transform Input to Disk Diffusion Diametersas.disk disk is.disk NA_disk_
Transform Input to Minimum Inhibitory Concentrations (MIC)as.mic droplevels.mic is.mic mic mic_p50 mic_p90 NA_mic_ rescale_mic
Transform Arbitrary Input to Valid Microbial Taxonomyas.mo is.mo mo mo_cleaning_regex mo_failures mo_renamed mo_reset_session mo_uncertainties
Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Dataas.sir as.sir.data.frame as.sir.default as.sir.disk as.sir.mic is.sir is_sir_eligible NA_sir_ sir sir_interpretation_history
Get ATC Properties from WHOCC Websiteatc_online_ddd atc_online_ddd_units atc_online_groups atc_online_property
Retrieve Antiviral Drug Names and Doses from Clinical Textav_from_text
Get Properties of an Antiviral Drugav_atc av_cid av_ddd av_ddd_units av_group av_info av_loinc av_name av_property av_synonyms av_tradenames av_url
Check Availability of Columnsavailability
Determine Bug-Drug Combinationsbug_drug_combinations format.bug_drug_combinations
Data Set with Clinical Breakpoints for SIR Interpretationclinical_breakpoints
Count Available Isolatescount count_all count_df count_I count_IR count_R count_resistant count_S count_SI count_susceptible n_sir
Define Custom EUCAST Rulescustom_eucast_rules
Data Set with Treatment Dosages as Defined by EUCASTdosage
Apply EUCAST RulesEUCAST eucast_dosage eucast_rules
Data Set with 2 000 Example Isolatesexample_isolates
Data Set with Unclean Dataexample_isolates_unclean
Determine First Isolatesfilter_first_isolate first_isolate
_G_-test for Count Datag.test
Determine Clinical or Epidemic Episodesget_episode is_new_episode
PCA Biplot with 'ggplot2'ggplot_pca
AMR Plots with 'ggplot2'geom_sir ggplot_sir
Guess Antibiotic Columnguess_ab_col
Data Set with Bacterial Intrinsic Resistanceintrinsic_resistant
Italicise Taxonomic Families, Genera, Species, Subspeciesitalicise_taxonomy italicize_taxonomy
Join microorganisms to a Data Setanti_join_microorganisms full_join_microorganisms inner_join inner_join_microorganisms join left_join_microorganisms right_join_microorganisms semi_join_microorganisms
(Key) Antimicrobials for First Weighted Isolatesall_antimicrobials antimicrobials_equal key_antimicrobials
Kurtosis of the Samplekurtosis kurtosis.data.frame kurtosis.default kurtosis.matrix
Vectorised Pattern Matching with Keyboard Shortcut%like% %like_case% %unlike% %unlike_case% like
Determine Multidrug-Resistant Organisms (MDRO)3MRGN 4MRGN BRMO brmo custom_mdro_guideline eucast_exceptional_phenotypes MDR mdro mdr_cmi2012 mdr_tb mrgn PDR XDR
Calculate the Mean AMR Distanceamr_distance_from_row mean_amr_distance mean_amr_distance.data.frame mean_amr_distance.sir
Data Set with 78 678 Taxonomic Records of Microorganismsmicroorganisms
Data Set with 4 971 Common Microorganism Codesmicroorganisms.codes
Data Set with 521 Microorganisms In Species Groupsmicroorganisms.groups
Calculate the Matching Score for Microorganismsmo_matching_score
Get Properties of a Microorganismmo_authors mo_class mo_current mo_domain mo_family mo_fullname mo_gbif mo_genus mo_gramstain mo_group_members mo_info mo_is_anaerobic mo_is_gram_negative mo_is_gram_positive mo_is_intrinsic_resistant mo_is_yeast mo_kingdom mo_lpsn mo_mycobank mo_name mo_order mo_oxygen_tolerance mo_pathogenicity mo_phylum mo_property mo_rank mo_ref mo_shortname mo_snomed mo_species mo_status mo_subspecies mo_synonyms mo_taxonomy mo_type mo_url mo_year
User-Defined Reference Data Set for Microorganismsget_mo_source mo_source set_mo_source
Principal Component Analysis (for AMR)pca
Plotting Helpers for AMR Data Analysisautoplot.disk autoplot.mic autoplot.sir facet_sir labels_sir_count plot plot.disk plot.mic plot.sir scale_color_mic scale_color_sir scale_colour_mic scale_colour_sir scale_fill_mic scale_fill_sir scale_sir_colors scale_sir_colours scale_x_mic scale_x_sir scale_y_mic scale_y_percent theme_sir
Calculate Antimicrobial Resistanceportion proportion proportion_df proportion_I proportion_IR proportion_R proportion_S proportion_SI resistance sir_confidence_interval sir_df susceptibility
Random MIC Values/Disk Zones/SIR Generationrandom random_disk random_mic random_sir
Predict Antimicrobial Resistanceautoplot.resistance_predict ggplot_sir_predict plot.resistance_predict resistance_predict sir_predict
Skewness of the Sampleskewness skewness.data.frame skewness.default skewness.matrix
Filter Top _n_ Microorganismstop_n_microorganisms
Translate Strings from the AMR Packageget_AMR_locale reset_AMR_locale set_AMR_locale translate translate_AMR
WHOCC: WHO Collaborating Centre for Drug Statistics MethodologyWHOCC
Data Set with 500 Isolates - WHONET ExampleWHONET