Package: AMR 2.1.1.9110

Matthijs S. Berends

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

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AMR.pdf |AMR.html✨
AMR/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

amrantimicrobial-dataepidemiologymicrobiologysoftware

11.45 score 86 stars 5 packages 160 scripts 2.0k downloads 30 mentions 216 exports 0 dependencies

Last updated 3 days agofrom:059618e710. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

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_selectorab_synonymsab_tradenamesab_urladd_custom_antimicrobialsadd_custom_microorganismsadministrable_ivadministrable_per_osageage_groupsall_antimicrobialsaminoglycosidesaminopenicillinsamr_distance_from_rowanti_join_microorganismsantibiogramantifungalsantimicrobials_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_urlavailabilitybetalactamsbrmobug_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.siritalicise_taxonomyitalicize_taxonomykey_antimicrobialskurtosislabels_sir_countleft_join_microorganismslikelincosamideslipoglycopeptidesmacrolidesmdr_cmi2012mdr_tbmdromean_amr_distancemo_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_yearmrgnn_sirNA_disk_NA_mic_NA_sir_nitrofuransnot_intrinsic_resistantoxazolidinonespcapenicillinspolymyxinsproportion_dfproportion_Iproportion_IRproportion_Rproportion_Sproportion_SIquinolonesrandom_diskrandom_micrandom_sirrescale_micreset_AMR_localeresistanceresistance_predictrifamycinsright_join_microorganismsscale_colour_micscale_fill_micscale_sir_coloursscale_x_micscale_y_micscale_y_percentsemi_join_microorganismsset_ab_namesset_AMR_localeset_mo_sourcesir_confidence_intervalsir_dfsir_interpretation_historysir_predictskewnessstreptograminssusceptibilitytetracyclinestheme_sirtranslate_AMRtrimethoprimsureidopenicillins

Dependencies:

AMR for Python

Rendered fromAMR_for_Python.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-17
Started: 2024-09-30

Welcome to the AMR package

Rendered fromwelcome_to_AMR.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-09-29
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
Antibiotic Selectorsab_class ab_selector administrable_iv administrable_per_os aminoglycosides aminopenicillins antibiotic_class_selectors antifungals antimycobacterials betalactams carbapenems cephalosporins cephalosporins_1st cephalosporins_2nd cephalosporins_3rd cephalosporins_4th cephalosporins_5th fluoroquinolones glycopeptides lincosamides lipoglycopeptides macrolides nitrofurans not_intrinsic_resistant oxazolidinones penicillins polymyxins quinolones rifamycins streptogramins tetracyclines trimethoprims ureidopenicillins
Data Sets with 605 Antimicrobial Drugsantibiotics antivirals
Transform Input to an Antibiotic IDab 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 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'facet_sir geom_sir ggplot_sir labels_sir_count scale_sir_colours scale_y_percent theme_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 for Classes 'sir', 'mic' and 'disk'autoplot.disk autoplot.mic autoplot.sir fortify.disk fortify.mic fortify.sir plot plot.disk plot.mic plot.sir scale_colour_mic scale_fill_mic scale_x_mic scale_y_mic
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
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