{ "_id": "6a1d40e91d7bb097a0a40a9c", "Package": "AMR", "Version": "3.0.1.9057", "Date": "2026-05-02", "Title": "Antimicrobial Resistance Data Analysis", "Description": "Functions to simplify and standardise antimicrobial\nresistance (AMR) data analysis and to work with microbial and\nantimicrobial properties by using evidence-based methods, as\ndescribed in .", "Authors@R": "c(\nperson(given = c(\"Matthijs\", \"S.\"), family = \"Berends\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7620-1800\"), email = \"m.s.berends@umcg.nl\"),\nperson(given = c(\"Dennis\"), family = \"Souverein\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0003-0455-0336\")),\nperson(given = c(\"Erwin\", \"E.\", \"A.\"), family = \"Hassing\", role = c(\"aut\", \"ctb\")),\nperson(given = c(\"Aislinn\"), family = \"Cook\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9189-7815\")),\nperson(given = c(\"Andrew\", \"P.\"), family = \"Norgan\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2955-2066\")),\nperson(given = c(\"Anita\"), family = \"Williams\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5295-8451\")),\nperson(given = c(\"Annick\"), family = \"Lenglet\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2013-8405\")),\nperson(given = c(\"Anthony\"), family = \"Underwood\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8547-4277\")),\nperson(given = c(\"Anton\"), family = \"Mymrikov\", role = \"ctb\"),\nperson(given = c(\"Bart\", \"C.\"), family = \"Meijer\", role = \"ctb\"),\nperson(given = c(\"Christian\", \"F.\"), family = \"Luz\", role = \"ctb\", comment = c(ORCID = \"0000-0001-5809-5995\")),\nperson(given = c(\"Dmytro\"), family = \"Mykhailenko\", role = \"ctb\"),\nperson(given = c(\"Eric\", \"H.\", \"L.\", \"C.\", \"M.\"), family = \"Hazenberg\", role = \"ctb\"),\nperson(given = c(\"Gwen\"), family = \"Knight\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7263-9896\")),\nperson(given = c(\"Jane\"), family = \"Hawkey\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9661-5293\")),\nperson(given = c(\"Jason\"), family = \"Stull\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9028-8153\")),\nperson(given = c(\"Javier\"), family = \"Sanchez\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2605-8094\")),\nperson(given = c(\"Jonas\"), family = \"Salm\", role = \"ctb\"),\nperson(given = c(\"Judith\", \"M.\"), family = \"Fonville\", role = \"ctb\"),\nperson(given = c(\"Kathryn\"), family = \"Holt\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3949-2471\")),\nperson(given = c(\"Larisse\"), family = \"Bolton\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7879-2173\")),\nperson(given = c(\"Matthew\"), family = \"Saab\", role = \"ctb\", comment = c(ORCID = \"0009-0008-6626-7919\")),\nperson(given = c(\"Natacha\"), family = \"Couto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9152-5464\")),\nperson(given = c(\"Peter\"), family = \"Dutey-Magni\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8942-9836\")),\nperson(given = c(\"Rogier\", \"P.\"), family = \"Schade\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9487-4467\")),\nperson(given = c(\"Sofia\"), family = \"Ny\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2017-1363\")),\nperson(given = c(\"Alex\", \"W.\"), family = \"Friedrich\", role = \"ths\", comment = c(ORCID = \"0000-0003-4881-038X\")),\nperson(given = c(\"Bhanu\", \"N.\", \"M.\"), family = \"Sinha\", role = \"ths\", comment = c(ORCID = \"0000-0003-1634-0010\")),\nperson(given = c(\"Casper\", \"J.\"), family = \"Albers\", role = \"ths\", comment = c(ORCID = \"0000-0002-9213-6743\")),\nperson(given = c(\"Corinna\"), family = \"Glasner\", role = \"ths\", comment = c(ORCID = \"0000-0003-1241-1328\")))", "VignetteBuilder": "knitr,rmarkdown", "URL": "https://amr-for-r.org, https://github.com/msberends/AMR", "BugReports": "https://github.com/msberends/AMR/issues", "License": "GPL-2 | file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE, old_usage = TRUE)", "Repository": "https://msberends.r-universe.dev", "Date/Publication": "2026-05-02 12:56:26 UTC", "RemoteUrl": "https://github.com/msberends/AMR", "RemoteRef": "HEAD", "RemoteSha": "0af3f84655693bdb03159fa95e6fba904b0d4395", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-01 08:15:24 UTC", "User": "root" }, "Author": "Matthijs S. Berends [aut, cre] (ORCID:\n),\nDennis Souverein [aut, ctb] (ORCID:\n),\nErwin E. A. Hassing [aut, ctb],\nAislinn Cook [ctb] (ORCID: ),\nAndrew P. Norgan [ctb] (ORCID: ),\nAnita Williams [ctb] (ORCID: ),\nAnnick Lenglet [ctb] (ORCID: ),\nAnthony Underwood [ctb] (ORCID:\n),\nAnton Mymrikov [ctb],\nBart C. Meijer [ctb],\nChristian F. Luz [ctb] (ORCID: ),\nDmytro Mykhailenko [ctb],\nEric H. L. C. M. Hazenberg [ctb],\nGwen Knight [ctb] (ORCID: ),\nJane Hawkey [ctb] (ORCID: ),\nJason Stull [ctb] (ORCID: ),\nJavier Sanchez [ctb] (ORCID: ),\nJonas Salm [ctb],\nJudith M. Fonville [ctb],\nKathryn Holt [ctb] (ORCID: ),\nLarisse Bolton [ctb] (ORCID: ),\nMatthew Saab [ctb] (ORCID: ),\nNatacha Couto [ctb] (ORCID: ),\nPeter Dutey-Magni [ctb] (ORCID:\n),\nRogier P. Schade [ctb] (ORCID: ),\nSofia Ny [ctb] (ORCID: ),\nAlex W. Friedrich [ths] (ORCID:\n),\nBhanu N. M. Sinha [ths] (ORCID:\n),\nCasper J. Albers [ths] (ORCID: ),\nCorinna Glasner [ths] (ORCID: )", "Maintainer": "Matthijs S. Berends ", "MD5sum": "842dad17ddcdf7d8108548282ec09004", "_user": "msberends", "_type": "src", "_file": "AMR_3.0.1.9057.tar.gz", "_fileid": "788666e9e70aff2471a9ffeec6a05f45ddc7f2de5e16a753f90ee2c0071425c0", "_filesize": 3633708, "_sha256": "788666e9e70aff2471a9ffeec6a05f45ddc7f2de5e16a753f90ee2c0071425c0", "_created": "2026-06-01T08:15:24.000Z", "_published": "2026-06-01T08:20:57.232Z", "_distro": "noble", "_jobs": [ { "job": 78812364009, "time": 216, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7326595438" }, { "job": 78812364142, "time": 234, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7326601392" }, { "job": 78812364004, "time": 244, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7326592563" }, { "job": 78812364021, "time": 268, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7326597657" }, { "job": 78811608407, "time": 309, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7326526652" }, { "job": 78812363976, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7326568594" }, { "job": 78812364065, "time": 180, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7326584045" }, { "job": 78812363985, "time": 198, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7326590294" }, { "job": 78812364010, "time": 220, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7326596789" } ], "_buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/msberends/AMR", "_commit": { "id": "0af3f84655693bdb03159fa95e6fba904b0d4395", "author": "Matthijs Berends ", "committer": "Matthijs Berends ", "message": "(v3.0.1.9057) website fix\n", "time": 1777726586 }, "_maintainer": { "name": "Matthijs S. Berends", "email": "m.s.berends@umcg.nl", "login": "msberends", "mastodon": "@msberends@mastodon.social", "linkedin": "https://LinkedIn.com/in/msberends", "orcid": "0000-0001-7620-1800", "description": "Medical epidemiologist/microbiologist, head of @umcg-mmbi-epidemiology and @certe-medical-epidemiology", "uuid": 31037261 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "cleaner", "role": "Suggests" }, { "package": "cli", "role": "Suggests" }, { "package": "crayon", "role": "Suggests" }, { "package": "curl", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "future", "role": "Suggests" }, { "package": "future.apply", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "openxlsx", "role": "Suggests" }, { "package": "pillar", "role": "Suggests" }, { "package": "progress", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "recipes", "role": "Suggests" }, { "package": "rlang", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rstudioapi", "role": "Suggests" }, { "package": "rvest", "role": "Suggests" }, { "package": "skimr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "tidymodels", "role": "Suggests" }, { "package": "tidyselect", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" }, { "package": "vctrs", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" } ], "_owner": "msberends", "_selfowned": true, "_usedby": 6, "_updates": [ { "week": "2025-22", "n": 5 }, { "week": "2025-23", "n": 3 }, { "week": "2025-24", "n": 3 }, { "week": "2025-25", "n": 1 }, { "week": "2025-29", "n": 9 }, { "week": "2025-30", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-32", "n": 1 }, { "week": "2025-36", "n": 8 }, { "week": "2025-37", "n": 6 }, { "week": "2025-38", "n": 5 }, { "week": "2025-40", "n": 1 }, { "week": "2025-42", "n": 1 }, { "week": "2025-48", "n": 1 }, { "week": "2025-51", "n": 3 }, { "week": "2026-02", "n": 8 }, { "week": "2026-03", "n": 1 }, { "week": "2026-06", "n": 1 }, { "week": "2026-07", "n": 2 }, { "week": "2026-10", "n": 10 }, { "week": "2026-11", "n": 2 }, { "week": "2026-12", "n": 4 }, { "week": "2026-13", "n": 2 }, { "week": "2026-14", "n": 5 }, { "week": "2026-17", "n": 7 }, { "week": "2026-18", "n": 5 } ], "_tags": [ { "name": "v3.0.0", "date": "2025-06-02" }, { "name": "v3.0.1", "date": "2025-09-20" } ], "_topics": [ "amr", "antimicrobial-data", "epidemiology", "microbiology", "software" ], "_stars": 110, "_contributors": [ { "user": "msberends", "count": 1742, "uuid": 31037261 }, { "user": "thomsonn", "count": 2, "uuid": 23429340 }, { "user": "gxpcluster", "count": 1, "uuid": 1017969 }, { "user": "ceefluz", "count": 1, "uuid": 33626459 }, { "user": "blackedder", "count": 1, "uuid": 845741 }, { "user": "r0ssing", "count": 1, "uuid": 5277585 } ], "_userbio": { "uuid": 31037261, "type": "user", "name": "Matthijs Berends", "description": "Medical epidemiologist/microbiologist, head of @umcg-mmbi-epidemiology and @certe-medical-epidemiology" }, "_downloads": { "count": 1730, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/AMR" }, "_mentions": 30, "_devurl": "https://github.com/msberends/amr", "_pkgdown": "https://amr-for-r.org", "_searchresults": 262, "_rbuild": "4.6.0", "_assets": [ "extra/AMR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/msberends/amr", "_realowner": "msberends", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2018-02-22" }, { "version": "0.1.1", "date": "2018-03-14" }, { "version": "0.2.0", "date": "2018-05-03" }, { "version": "0.3.0", "date": "2018-08-14" }, { "version": "0.4.0", "date": "2018-10-01" }, { "version": "0.5.0", "date": "2018-11-30" }, { "version": "0.6.0", "date": "2019-03-27" }, { "version": "0.6.1", "date": "2019-03-29" }, { "version": "0.7.0", "date": "2019-06-03" }, { "version": "0.7.1", "date": "2019-06-23" }, { "version": "0.8.0", "date": "2019-10-15" }, { "version": "0.9.0", "date": "2019-11-29" }, { "version": "1.0.0", "date": "2020-02-17" }, { "version": "1.0.1", "date": "2020-02-23" }, { "version": "1.1.0", "date": "2020-04-15" }, { "version": "1.2.0", "date": "2020-05-28" }, { "version": "1.3.0", "date": "2020-07-31" }, { "version": "1.4.0", "date": "2020-10-08" }, { "version": "1.5.0", "date": "2021-01-06" }, { "version": "1.6.0", "date": "2021-03-15" }, { "version": "1.7.1", "date": "2021-06-03" }, { "version": "1.8.0", "date": "2022-01-07" }, { "version": "1.8.1", "date": "2022-03-24" }, { "version": "1.8.2", "date": "2022-09-29" }, { "version": "2.0.0", "date": "2023-03-12" }, { "version": "2.1.0", "date": "2023-07-16" }, { "version": "2.1.1", "date": "2023-10-22" }, { "version": "3.0.0", "date": "2025-06-02" }, { "version": "3.0.1", "date": "2025-09-20" } ], "_exports": [ "%like_case%", "%like%", "%unlike_case%", "%unlike%", "ab_atc", "ab_atc_group1", "ab_atc_group2", "ab_cid", "ab_class", "ab_ddd", "ab_ddd_units", "ab_from_text", "ab_group", "ab_info", "ab_loinc", "ab_name", "ab_property", "ab_reset_session", "ab_selector", "ab_synonyms", "ab_tradenames", "ab_url", "add_custom_antimicrobials", "add_custom_microorganisms", "administrable_iv", "administrable_per_os", "age", "age_groups", "all_antimicrobials", "all_disk", "all_disk_predictors", "all_mic", "all_mic_predictors", "all_sir", "all_sir_predictors", "aminoglycosides", "aminopenicillins", "amr_class", "amr_course", "amr_distance_from_row", "amr_selector", "anti_join_microorganisms", "antibiogram", "antifungals", "antimicrobials_equal", "antimycobacterials", "as.ab", "as.av", "as.disk", "as.mic", "as.mo", "as.sir", "atc_online_ddd", "atc_online_ddd_units", "atc_online_groups", "atc_online_property", "av_atc", "av_cid", "av_ddd", "av_ddd_units", "av_from_text", "av_group", "av_info", "av_loinc", "av_name", "av_property", "av_synonyms", "av_tradenames", "av_url", "availability", "betalactams", "betalactams_with_inhibitor", "brmo", "bug_drug_combinations", "carbapenems", "cephalosporins", "cephalosporins_1st", "cephalosporins_2nd", "cephalosporins_3rd", "cephalosporins_4th", "cephalosporins_5th", "clear_custom_antimicrobials", "clear_custom_microorganisms", "clsi_rules", "count_all", "count_df", "count_I", "count_IR", "count_R", "count_resistant", "count_S", "count_SI", "count_susceptible", "custom_eucast_rules", "custom_interpretive_rules", "custom_mdro_guideline", "eucast_dosage", "eucast_exceptional_phenotypes", "eucast_rules", "facet_sir", "filter_first_isolate", "first_isolate", "fluoroquinolones", "full_join_microorganisms", "g.test", "geom_sir", "get_AMR_locale", "get_episode", "get_mo_source", "ggplot_pca", "ggplot_sir", "ggplot_sir_predict", "glycopeptides", "guess_ab_col", "inner_join_microorganisms", "interpretive_rules", "ionophores", "is_new_episode", "is_sir_eligible", "is.ab", "is.av", "is.disk", "is.mic", "is.mo", "is.sir", "isoxazolylpenicillins", "italicise_taxonomy", "italicize_taxonomy", "key_antimicrobials", "kurtosis", "labels_sir_count", "left_join_microorganisms", "like", "lincosamides", "lipoglycopeptides", "macrolides", "mdr_cmi2012", "mdr_tb", "mdro", "mean_amr_distance", "mic_p50", "mic_p90", "mo_authors", "mo_class", "mo_cleaning_regex", "mo_current", "mo_domain", "mo_failures", "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_matching_score", "mo_mycobank", "mo_name", "mo_order", "mo_oxygen_tolerance", "mo_pathogenicity", "mo_phylum", "mo_property", "mo_rank", "mo_ref", "mo_renamed", "mo_reset_session", "mo_shortname", "mo_snomed", "mo_species", "mo_status", "mo_subspecies", "mo_synonyms", "mo_taxonomy", "mo_type", "mo_uncertainties", "mo_url", "mo_year", "monobactams", "mrgn", "n_sir", "NA_ab_", "NA_disk_", "NA_mic_", "NA_mo_", "NA_sir_", "nitrofurans", "not_intrinsic_resistant", "oxazolidinones", "pca", "penicillins", "peptides", "phenicols", "phosphonics", "polymyxins", "proportion_df", "proportion_I", "proportion_IR", "proportion_R", "proportion_S", "proportion_SI", "quinolones", "random_disk", "random_mic", "random_sir", "rescale_mic", "reset_AMR_locale", "resistance", "resistance_predict", "retrieve_wisca_parameters", "rifamycins", "right_join_microorganisms", "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", "semi_join_microorganisms", "set_ab_names", "set_AMR_locale", "set_mo_source", "sir_confidence_interval", "sir_df", "sir_interpretation_history", "sir_predict", "skewness", "spiropyrimidinetriones", "step_mic_log2", "step_sir_numeric", "streptogramins", "sulfonamides", "susceptibility", "tetracyclines", "theme_sir", "top_n_microorganisms", "translate_AMR", "trimethoprims", "ureidopenicillins", "wisca" ], "_datasets": [ { "name": "antibiotics", "title": "Data Sets with 625 Antimicrobial Drugs", "object": "antibiotics", "class": [ "deprecated_amr_dataset", "tbl_df", "tbl", "data.frame" ], "fields": [ "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", "loinc" ], "rows": 505, "table": true, "tojson": true }, { "name": "antimicrobials", "title": "Data Sets with 625 Antimicrobial Drugs", "object": "antimicrobials", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", "loinc" ], "rows": 505, "table": true, "tojson": true }, { "name": "antivirals", "title": "Data Sets with 625 Antimicrobial Drugs", "object": "antivirals", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "av", "name", "atc", "cid", "atc_group", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", "loinc" ], "rows": 120, "table": true, "tojson": true }, { "name": "clinical_breakpoints", "title": "Data Set with Clinical Breakpoints for SIR Interpretation", "object": "clinical_breakpoints", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "guideline", "type", "host", "method", "site", "mo", "rank_index", "ab", "ref_tbl", "disk_dose", "breakpoint_S", "breakpoint_R", "uti", "is_SDD" ], "rows": 45730, "table": true, "tojson": true }, { "name": "dosage", "title": "Data Set with Treatment Dosages as Defined by EUCAST", "object": "dosage", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "ab", "name", "type", "dose", "dose_times", "administration", "notes", "original_txt", "eucast_version" ], "rows": 759, "table": true, "tojson": true }, { "name": "esbl_isolates", "title": "Data Set with 500 ESBL Isolates", "object": "esbl_isolates", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "esbl", "genus", "AMC", "AMP", "TZP", "CXM", "FOX", "CTX", "CAZ", "GEN", "TOB", "TMP", "SXT", "NIT", "FOS", "CIP", "IPM", "MEM", "COL" ], "rows": 500, "table": true, "tojson": true }, { "name": "example_isolates", "title": "Data Set with 2 000 Example Isolates", "object": "example_isolates", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "date", "patient", "age", "gender", "ward", "mo", "PEN", "OXA", "FLC", "AMX", "AMC", "AMP", "TZP", "CZO", "FEP", "CXM", "FOX", "CTX", "CAZ", "CRO", "GEN", "TOB", "AMK", "KAN", "TMP", "SXT", "NIT", "FOS", "LNZ", "CIP", "MFX", "VAN", "TEC", "TCY", "TGC", "DOX", "ERY", "CLI", "AZM", "IPM", "MEM", "MTR", "CHL", "COL", "MUP", "RIF" ], "rows": 2000, "table": true, "tojson": true }, { "name": "example_isolates_unclean", "title": "Data Set with Unclean Data", "object": "example_isolates_unclean", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "patient_id", "hospital", "date", "bacteria", "AMX", "AMC", "CIP", "GEN" ], "rows": 3000, "table": true, "tojson": true }, { "name": "intrinsic_resistant", "title": "Data Set Denoting Bacterial Intrinsic Resistance", "object": "intrinsic_resistant", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "mo", "ab" ], "rows": 285928, "table": true, "tojson": true }, { "name": "microorganisms", "title": "Data Set with 78 679 Taxonomic Records of Microorganisms", "object": "microorganisms", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", "snomed" ], "rows": 78679, "table": true, "tojson": true }, { "name": "microorganisms.codes", "title": "Data Set with 6 050 Common Microorganism Codes", "object": "microorganisms.codes", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "code", "mo" ], "rows": 6050, "table": true, "tojson": true }, { "name": "microorganisms.groups", "title": "Data Set with 534 Microorganisms In Species Groups", "object": "microorganisms.groups", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "mo_group", "mo", "mo_group_name", "mo_name" ], "rows": 534, "table": true, "tojson": true }, { "name": "WHONET", "title": "Data Set with 500 Isolates - WHONET Example", "object": "WHONET", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Identification number", "Specimen number", "Organism", "Country", "Laboratory", "Last name", "First name", "Sex", "Age", "Age category", "Date of admission", "Specimen date", "Specimen type", "Specimen type (Numeric)", "Reason", "Isolate number", "Organism type", "Serotype", "Beta-lactamase", "ESBL", "Carbapenemase", "MRSA screening test", "Inducible clindamycin resistance", "Comment", "Date of data entry", "AMP_ND10", "AMC_ED20", "TZP_ED30", "FEP_ED30", "CTX_ED5", "FOX_ED30", "CAZ_ED10", "CRO_ED30", "CIP_ED5", "AMK_ED30", "GEN_ED10", "TOB_ED10", "SXT_ED1.2", "IPM_ND10", "PEN_ND1", "AMP_ND2", "AMC_ND2", "CHL_ND30", "VAN_ED5", "OXA_ED1", "ERY_ED15", "CLI_ED2", "TCY_ED30", "RIF_ED5", "PEN_EE", "AMP_EE", "CRO_EE", "CIP_EE" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "ab_from_text", "title": "Retrieve Antimicrobial Drug Names and Doses from Clinical Text", "topics": [ "ab_from_text" ] }, { "page": "ab_property", "title": "Get Properties of an Antibiotic", "topics": [ "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" ] }, { "page": "add_custom_antimicrobials", "title": "Add Custom Antimicrobials", "topics": [ "add_custom_antimicrobials", "clear_custom_antimicrobials" ] }, { "page": "add_custom_microorganisms", "title": "Add Custom Microorganisms", "topics": [ "add_custom_microorganisms", "clear_custom_microorganisms" ] }, { "page": "age", "title": "Age in Years of Individuals", "topics": [ "age" ] }, { "page": "age_groups", "title": "Split Ages into Age Groups", "topics": [ "age_groups" ] }, { "page": "amr_course", "title": "Download and Unpack an AMR Course Repository", "topics": [ "amr_course" ] }, { "page": "antibiogram", "title": "Generate Traditional, Combination, Syndromic, or WISCA Antibiograms", "topics": [ "antibiogram", "autoplot.antibiogram", "knit_print.antibiogram", "plot.antibiogram", "retrieve_wisca_parameters", "wisca" ] }, { "page": "antimicrobial_selectors", "title": "Antimicrobial Selectors", "topics": [ "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" ] }, { "page": "antimicrobials", "title": "Data Sets with 625 Antimicrobial Drugs", "topics": [ "antibiotics", "antimicrobials", "antivirals" ] }, { "page": "as.ab", "title": "Transform Input to an Antibiotic ID", "topics": [ "ab", "ab_reset_session", "as.ab", "is.ab", "NA_ab_" ] }, { "page": "as.av", "title": "Transform Input to an Antiviral Drug ID", "topics": [ "as.av", "av", "is.av" ] }, { "page": "as.disk", "title": "Transform Input to Disk Diffusion Diameters", "topics": [ "as.disk", "disk", "is.disk", "NA_disk_" ] }, { "page": "as.mic", "title": "Transform Input to Minimum Inhibitory Concentrations (MIC)", "topics": [ "as.mic", "droplevels.mic", "is.mic", "mic", "mic_p50", "mic_p90", "NA_mic_", "rescale_mic" ] }, { "page": "as.mo", "title": "Transform Arbitrary Input to Valid Microbial Taxonomy", "topics": [ "as.mo", "is.mo", "mo", "mo_cleaning_regex", "mo_failures", "mo_renamed", "mo_reset_session", "mo_uncertainties", "NA_mo_" ] }, { "page": "as.sir", "title": "Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data", "topics": [ "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" ] }, { "page": "atc_online", "title": "Get ATC Properties from WHOCC Website", "topics": [ "atc_online_ddd", "atc_online_ddd_units", "atc_online_groups", "atc_online_property" ] }, { "page": "av_from_text", "title": "Retrieve Antiviral Drug Names and Doses from Clinical Text", "topics": [ "av_from_text" ] }, { "page": "av_property", "title": "Get Properties of an Antiviral Drug", "topics": [ "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" ] }, { "page": "availability", "title": "Check Availability of Columns", "topics": [ "availability" ] }, { "page": "bug_drug_combinations", "title": "Determine Bug-Drug Combinations", "topics": [ "bug_drug_combinations", "format.bug_drug_combinations" ] }, { "page": "clinical_breakpoints", "title": "Data Set with Clinical Breakpoints for SIR Interpretation", "topics": [ "clinical_breakpoints" ] }, { "page": "count", "title": "Count Available Isolates", "topics": [ "count", "count_all", "count_df", "count_I", "count_IR", "count_R", "count_resistant", "count_S", "count_SI", "count_susceptible", "n_sir" ] }, { "page": "custom_interpretive_rules", "title": "Define Custom Interpretive Rules", "topics": [ "custom_interpretive_rules" ] }, { "page": "custom_mdro_guideline", "title": "Define Custom MDRO Guideline", "topics": [ "c.custom_mdro_guideline", "custom_mdro_guideline" ] }, { "page": "dosage", "title": "Data Set with Treatment Dosages as Defined by EUCAST", "topics": [ "dosage" ] }, { "page": "esbl_isolates", "title": "Data Set with 500 ESBL Isolates", "topics": [ "esbl_isolates" ] }, { "page": "example_isolates", "title": "Data Set with 2 000 Example Isolates", "topics": [ "example_isolates" ] }, { "page": "example_isolates_unclean", "title": "Data Set with Unclean Data", "topics": [ "example_isolates_unclean" ] }, { "page": "first_isolate", "title": "Determine First Isolates", "topics": [ "filter_first_isolate", "first_isolate" ] }, { "page": "g.test", "title": "_G_-test for Count Data", "topics": [ "g.test" ] }, { "page": "get_episode", "title": "Determine Clinical or Epidemic Episodes", "topics": [ "get_episode", "is_new_episode" ] }, { "page": "ggplot_pca", "title": "PCA Biplot with 'ggplot2'", "topics": [ "ggplot_pca" ] }, { "page": "ggplot_sir", "title": "AMR Plots with 'ggplot2'", "topics": [ "geom_sir", "ggplot_sir" ] }, { "page": "guess_ab_col", "title": "Guess Antibiotic Column", "topics": [ "guess_ab_col" ] }, { "page": "interpretive_rules", "title": "Apply Interpretive Rules", "topics": [ "clsi_rules", "EUCAST", "eucast_dosage", "eucast_rules", "interpretive_rules" ] }, { "page": "intrinsic_resistant", "title": "Data Set Denoting Bacterial Intrinsic Resistance", "topics": [ "intrinsic_resistant" ] }, { "page": "italicise_taxonomy", "title": "Italicise Taxonomic Families, Genera, Species, Subspecies", "topics": [ "italicise_taxonomy", "italicize_taxonomy" ] }, { "page": "join", "title": "Join microorganisms to a Data Set", "topics": [ "anti_join_microorganisms", "full_join_microorganisms", "inner_join", "inner_join_microorganisms", "join", "left_join_microorganisms", "right_join_microorganisms", "semi_join_microorganisms" ] }, { "page": "key_antimicrobials", "title": "(Key) Antimicrobials for First Weighted Isolates", "topics": [ "all_antimicrobials", "antimicrobials_equal", "key_antimicrobials" ] }, { "page": "kurtosis", "title": "Kurtosis of the Sample", "topics": [ "kurtosis", "kurtosis.data.frame", "kurtosis.default", "kurtosis.matrix" ] }, { "page": "like", "title": "Vectorised Pattern Matching with Keyboard Shortcut", "topics": [ "%like%", "%like_case%", "%unlike%", "%unlike_case%", "like" ] }, { "page": "mdro", "title": "Determine Multidrug-Resistant Organisms (MDRO)", "topics": [ "3MRGN", "4MRGN", "BRMO", "brmo", "eucast_exceptional_phenotypes", "MDR", "mdro", "mdr_cmi2012", "mdr_tb", "mrgn", "PDR", "XDR" ] }, { "page": "mean_amr_distance", "title": "Calculate the Mean AMR Distance", "topics": [ "amr_distance_from_row", "mean_amr_distance", "mean_amr_distance.data.frame", "mean_amr_distance.sir" ] }, { "page": "microorganisms", "title": "Data Set with 78 679 Taxonomic Records of Microorganisms", "topics": [ "microorganisms" ] }, { "page": "microorganisms.codes", "title": "Data Set with 6 050 Common Microorganism Codes", "topics": [ "microorganisms.codes" ] }, { "page": "microorganisms.groups", "title": "Data Set with 534 Microorganisms In Species Groups", "topics": [ "microorganisms.groups" ] }, { "page": "mo_matching_score", "title": "Calculate the Matching Score for Microorganisms", "topics": [ "mo_matching_score" ] }, { "page": "mo_property", "title": "Get Properties of a Microorganism", "topics": [ "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" ] }, { "page": "mo_source", "title": "User-Defined Reference Data Set for Microorganisms", "topics": [ "get_mo_source", "mo_source", "set_mo_source" ] }, { "page": "pca", "title": "Principal Component Analysis (for AMR)", "topics": [ "pca" ] }, { "page": "plot", "title": "Plotting Helpers for AMR Data Analysis", "topics": [ "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" ] }, { "page": "proportion", "title": "Calculate Antimicrobial Resistance", "topics": [ "portion", "proportion", "proportion_df", "proportion_I", "proportion_IR", "proportion_R", "proportion_S", "proportion_SI", "resistance", "sir_confidence_interval", "sir_df", "susceptibility" ] }, { "page": "random", "title": "Random MIC Values/Disk Zones/SIR Generation", "topics": [ "random", "random_disk", "random_mic", "random_sir" ] }, { "page": "resistance_predict", "title": "Predict Antimicrobial Resistance", "topics": [ "autoplot.resistance_predict", "ggplot_sir_predict", "plot.resistance_predict", "resistance_predict", "sir_predict" ] }, { "page": "skewness", "title": "Skewness of the Sample", "topics": [ "skewness", "skewness.data.frame", "skewness.default", "skewness.matrix" ] }, { "page": "top_n_microorganisms", "title": "Filter Top _n_ Microorganisms", "topics": [ "top_n_microorganisms" ] }, { "page": "translate", "title": "Translate Strings from the AMR Package", "topics": [ "get_AMR_locale", "reset_AMR_locale", "set_AMR_locale", "translate", "translate_AMR" ] }, { "page": "WHOCC", "title": "WHOCC: WHO Collaborating Centre for Drug Statistics Methodology", "topics": [ "WHOCC" ] }, { "page": "WHONET", "title": "Data Set with 500 Isolates - WHONET Example", "topics": [ "WHONET" ] } ], "_pkglogo": "https://github.com/msberends/AMR/raw/HEAD/logo.svg", "_readme": "https://github.com/msberends/AMR/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "AMR_for_Python.Rmd", "filename": "AMR_for_Python.html", "title": "AMR for Python", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Install AMR", "Examples of Usage", "Cleaning Taxonomy", "Explanation", "Calculating AMR", "Generating Antibiograms", "Taxonomic Data Sets Now in Python!", "Conclusion" ], "created": "2024-09-30 20:04:44", "modified": "2025-03-18 15:35:22", "commits": 10 }, { "source": "welcome_to_AMR.Rmd", "filename": "welcome_to_AMR.html", "title": "Welcome to the AMR package", "engine": "knitr::rmarkdown", "headings": [], "created": "2020-07-31 09:39:56", "modified": "2025-06-13 12:03:21", "commits": 31 } ], "_score": 12.066955937016909, "_indexed": true, "_nocasepkg": "amr", "_universes": [ "msberends" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.0.1.9057", "date": "2026-06-01T08:18:40.000Z", "distro": "noble", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "1d9d6abd4a5a863c06f8fd80d46211e75ac26fdaf14a055c34fca317e9f8abe7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" }, { "r": "4.6.0", "os": "linux", "version": "3.0.1.9057", "date": "2026-06-01T08:18:21.000Z", "distro": "noble", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "81d8928916c39c81613f3216c949f1b47a30ba2658e591caa5f26492b7cd491c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" }, { "r": "4.5.3", "os": "mac", "version": "3.0.1.9057", "date": "2026-06-01T08:18:08.000Z", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "61235e0587eb161ad23312dee732a5cc6ea0878fcbee153d9cb52139d981806e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" }, { "r": "4.6.0", "os": "mac", "version": "3.0.1.9057", "date": "2026-06-01T08:18:13.000Z", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "1d8cbf39dc0e2a61bb46bf0009050f6aba8ea808866d38275e368089db326464", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" }, { "r": "4.6.0", "os": "wasm", "version": "3.0.1.9057", "date": "2026-06-01T08:18:13.000Z", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "2761fc128eba81d1090434436c1b77c9cf3a4d1209224083fa426b8d34291783", "status": "success", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" }, { "r": "4.7.0", "os": "win", "version": "3.0.1.9057", "date": "2026-06-01T08:17:26.000Z", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "0ab26a7f73131cb9fb48f353bcab1a20d3e703bf537380f5b0873fd776c6056f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" }, { "r": "4.5.3", "os": "win", "version": "3.0.1.9057", "date": "2026-06-01T08:17:45.000Z", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "17f3cc4de28690f7ad592bcfb83860bb61a757416326e1aad43f73f011456261", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" }, { "r": "4.6.0", "os": "win", "version": "3.0.1.9057", "date": "2026-06-01T08:17:38.000Z", "commit": "0af3f84655693bdb03159fa95e6fba904b0d4395", "fileid": "26045093a86fb610105fcc54ad4207bbce003b87ae8619c2971d7730d0145151", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/msberends/actions/runs/26743055064" } ] }