Package: AMR 2.1.1.9103
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:
AMR_2.1.1.9103.tar.gz
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AMR_2.1.1.9103.tgz(r-4.4-any)AMR_2.1.1.9103.tgz(r-4.3-any)
AMR_2.1.1.9103.tar.gz(r-4.5-noble)AMR_2.1.1.9103.tar.gz(r-4.4-noble)
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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')) |
Bug tracker:https://github.com/msberends/amr/issues
- WHONET - Data Set with 500 Isolates - WHONET Example
- antibiotics - Data Sets with 605 Antimicrobial Drugs
- antivirals - Data Sets with 605 Antimicrobial Drugs
- clinical_breakpoints - Data Set with Clinical Breakpoints for SIR Interpretation
- dosage - Data Set with Treatment Dosages as Defined by EUCAST
- example_isolates - Data Set with 2 000 Example Isolates
- example_isolates_unclean - Data Set with Unclean Data
- intrinsic_resistant - Data Set with Bacterial Intrinsic Resistance
- microorganisms - Data Set with 78 678 Taxonomic Records of Microorganisms
- microorganisms.codes - Data Set with 4 971 Common Microorganism Codes
- microorganisms.groups - Data Set with 521 Microorganisms In Species Groups
amrantimicrobial-dataepidemiologymicrobiologysoftware
Last updated 5 days agofrom:f424c39474. Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 18 2024 |
| R-4.5-win | OK | Oct 18 2024 |
| R-4.5-linux | OK | Oct 18 2024 |
| R-4.4-win | OK | Oct 18 2024 |
| R-4.4-mac | OK | Oct 18 2024 |
| R-4.3-win | OK | Oct 18 2024 |
| R-4.3-mac | OK | Oct 18 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:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve Antimicrobial Drug Names and Doses from Clinical Text | ab_from_text |
| Get Properties of an Antibiotic | ab_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 Antimicrobials | add_custom_antimicrobials clear_custom_antimicrobials |
| Add Custom Microorganisms | add_custom_microorganisms clear_custom_microorganisms |
| Age in Years of Individuals | age |
| Split Ages into Age Groups | age_groups |
| Generate Traditional, Combination, Syndromic, or WISCA Antibiograms | antibiogram autoplot.antibiogram knit_print.antibiogram plot.antibiogram |
| Antibiotic Selectors | ab_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 Drugs | antibiotics antivirals |
| Transform Input to an Antibiotic ID | ab as.ab is.ab |
| Transform Input to an Antiviral Drug ID | as.av av is.av |
| Transform Input to Disk Diffusion Diameters | as.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 Taxonomy | as.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 Data | as.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 Website | atc_online_ddd atc_online_ddd_units atc_online_groups atc_online_property |
| Retrieve Antiviral Drug Names and Doses from Clinical Text | av_from_text |
| Get Properties of an Antiviral Drug | av_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 Columns | availability |
| Determine Bug-Drug Combinations | bug_drug_combinations format.bug_drug_combinations |
| Data Set with Clinical Breakpoints for SIR Interpretation | clinical_breakpoints |
| Count Available Isolates | count count_all count_df count_I count_IR count_R count_resistant count_S count_SI count_susceptible n_sir |
| Define Custom EUCAST Rules | custom_eucast_rules |
| Data Set with Treatment Dosages as Defined by EUCAST | dosage |
| Apply EUCAST Rules | EUCAST eucast_dosage eucast_rules |
| Data Set with 2 000 Example Isolates | example_isolates |
| Data Set with Unclean Data | example_isolates_unclean |
| Determine First Isolates | filter_first_isolate first_isolate |
| _G_-test for Count Data | g.test |
| Determine Clinical or Epidemic Episodes | get_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 Column | guess_ab_col |
| Data Set with Bacterial Intrinsic Resistance | intrinsic_resistant |
| Italicise Taxonomic Families, Genera, Species, Subspecies | italicise_taxonomy italicize_taxonomy |
| Join microorganisms to a Data Set | anti_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 Isolates | all_antimicrobials antimicrobials_equal key_antimicrobials |
| Kurtosis of the Sample | kurtosis 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 Distance | amr_distance_from_row mean_amr_distance mean_amr_distance.data.frame mean_amr_distance.sir |
| Data Set with 78 678 Taxonomic Records of Microorganisms | microorganisms |
| Data Set with 4 971 Common Microorganism Codes | microorganisms.codes |
| Data Set with 521 Microorganisms In Species Groups | microorganisms.groups |
| Calculate the Matching Score for Microorganisms | mo_matching_score |
| Get Properties of a Microorganism | mo_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 Microorganisms | get_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 Resistance | portion 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 Generation | random random_disk random_mic random_sir |
| Predict Antimicrobial Resistance | autoplot.resistance_predict ggplot_sir_predict plot.resistance_predict resistance_predict sir_predict |
| Skewness of the Sample | skewness skewness.data.frame skewness.default skewness.matrix |
| Translate Strings from the AMR Package | get_AMR_locale reset_AMR_locale set_AMR_locale translate translate_AMR |
| WHOCC: WHO Collaborating Centre for Drug Statistics Methodology | WHOCC |
| Data Set with 500 Isolates - WHONET Example | WHONET |
