Package: AMR 3.0.1.9057
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_3.0.1.9057.tar.gz
AMR_3.0.1.9057.zip(r-4.7)AMR_3.0.1.9057.zip(r-4.6)AMR_3.0.1.9057.zip(r-4.5)
AMR_3.0.1.9057.tgz(r-4.6-any)AMR_3.0.1.9057.tgz(r-4.5-any)
AMR_3.0.1.9057.tar.gz(r-4.7-any)AMR_3.0.1.9057.tar.gz(r-4.6-any)
AMR_3.0.1.9057.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
AMR/json (API)
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/docs site:https://amr-for-r.org
- antibiotics - Data Sets with 625 Antimicrobial Drugs
- antimicrobials - Data Sets with 625 Antimicrobial Drugs
- antivirals - Data Sets with 625 Antimicrobial Drugs
- clinical_breakpoints - Data Set with Clinical Breakpoints for SIR Interpretation
- dosage - Data Set with Treatment Dosages as Defined by EUCAST
- esbl_isolates - Data Set with 500 ESBL Isolates
- example_isolates - Data Set with 2 000 Example Isolates
- example_isolates_unclean - Data Set with Unclean Data
- intrinsic_resistant - Data Set Denoting Bacterial Intrinsic Resistance
- microorganisms - Data Set with 78 679 Taxonomic Records of Microorganisms
- microorganisms.codes - Data Set with 6 050 Common Microorganism Codes
- microorganisms.groups - Data Set with 534 Microorganisms In Species Groups
- WHONET - Data Set with 500 Isolates - WHONET Example
amrantimicrobial-dataepidemiologymicrobiologysoftware
Last updated from:0af3f84655. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 216 | ||
| source / vignettes | OK | 309 | ||
| linux-release-x86_64 | NOTE | 234 | ||
| macos-release-arm64 | NOTE | 268 | ||
| macos-oldrel-arm64 | NOTE | 244 | ||
| windows-devel | NOTE | 180 | ||
| windows-release | NOTE | 220 | ||
| windows-oldrel | NOTE | 198 | ||
| wasm-release | OK | 128 |
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_antimicrobialsall_diskall_disk_predictorsall_micall_mic_predictorsall_sirall_sir_predictorsaminoglycosidesaminopenicillinsamr_classamr_courseamr_distance_from_rowamr_selectoranti_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_urlavailabilitybetalactamsbetalactams_with_inhibitorbrmobug_drug_combinationscarbapenemscephalosporinscephalosporins_1stcephalosporins_2ndcephalosporins_3rdcephalosporins_4thcephalosporins_5thclear_custom_antimicrobialsclear_custom_microorganismsclsi_rulescount_allcount_dfcount_Icount_IRcount_Rcount_resistantcount_Scount_SIcount_susceptiblecustom_eucast_rulescustom_interpretive_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_microorganismsinterpretive_rulesionophoresis_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_ab_NA_disk_NA_mic_NA_mo_NA_sir_nitrofuransnot_intrinsic_resistantoxazolidinonespcapenicillinspeptidesphenicolsphosphonicspolymyxinsproportion_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_predictskewnessspiropyrimidinetrionesstep_mic_log2step_sir_numericstreptograminssulfonamidessusceptibilitytetracyclinestheme_sirtop_n_microorganismstranslate_AMRtrimethoprimsureidopenicillinswisca
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 |
| Download and Unpack an AMR Course Repository | amr_course |
| Generate Traditional, Combination, Syndromic, or WISCA Antibiograms | antibiogram autoplot.antibiogram knit_print.antibiogram plot.antibiogram retrieve_wisca_parameters wisca |
| Antimicrobial Selectors | administrable_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 ionophores isoxazolylpenicillins lincosamides lipoglycopeptides macrolides monobactams nitrofurans not_intrinsic_resistant oxazolidinones penicillins peptides phenicols phosphonics polymyxins quinolones rifamycins spiropyrimidinetriones streptogramins sulfonamides tetracyclines trimethoprims ureidopenicillins |
| Data Sets with 625 Antimicrobial Drugs | antibiotics antimicrobials antivirals |
| Transform Input to an Antibiotic ID | ab ab_reset_session as.ab is.ab NA_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 mic_p50 mic_p90 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 NA_mo_ |
| Interpret MIC and Disk Diffusion as 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 Interpretive Rules | custom_interpretive_rules |
| Define Custom MDRO Guideline | c.custom_mdro_guideline custom_mdro_guideline |
| Data Set with Treatment Dosages as Defined by EUCAST | dosage |
| Data Set with 500 ESBL Isolates | esbl_isolates |
| 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' | geom_sir ggplot_sir |
| Guess Antibiotic Column | guess_ab_col |
| Apply Interpretive Rules | clsi_rules EUCAST eucast_dosage eucast_rules interpretive_rules |
| Data Set Denoting 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 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 78 679 Taxonomic Records of Microorganisms | microorganisms |
| Data Set with 6 050 Common Microorganism Codes | microorganisms.codes |
| Data Set with 534 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 Helpers for AMR Data Analysis | autoplot.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 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 |
| Filter Top _n_ Microorganisms | top_n_microorganisms |
| 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 |
