API for AMR
Antimicrobial Resistance Data Analysis
| Global functions | |
|---|---|
| %like% | Man page |
| %like_case% | Man page |
| %unlike% | Man page |
| %unlike_case% | Man page |
| .amr_deprecation_warn | Source code |
| .onAttach | Source code |
| .onLoad | Source code |
| 3MRGN | Man page |
| 4MRGN | Man page |
| AMR | Man page |
| AMR-deprecated | Man page |
| AMR-options | Man page |
| AMR-package | Man page |
| ATC | Man page |
| BRMO | Man page |
| EUCAST | Man page |
| MDR | Man page |
| NA_disk_ | Man page |
| NA_mic_ | Man page |
| NA_sir_ | Man page |
| PDR | Man page |
| WHOCC | Man page |
| WHONET | Man page |
| XDR | Man page |
| `!=.amr_selector` | Source code |
| `$.deprecated_amr_dataset` | Source code |
| `%in%` | Source code |
| `%pm>%` | Source code |
| `&.amr_selector` | Source code |
| `+.ab` | Source code |
| `+.amr_selector` | Source code |
| `==.amr_selector` | Source code |
| `[.deprecated_amr_dataset` | Source code |
| `[[.deprecated_amr_dataset` | Source code |
| `|.amr_selector` | Source code |
| ab | Man page |
| ab_atc | Man page Source code |
| ab_atc_group1 | Man page Source code |
| ab_atc_group2 | Man page Source code |
| ab_cid | Man page Source code |
| ab_class | Man page Source code |
| ab_ddd | Man page Source code |
| ab_ddd_units | Man page Source code |
| ab_from_text | Man page Source code |
| ab_group | Man page Source code |
| ab_info | Man page Source code |
| ab_loinc | Man page Source code |
| ab_name | Man page Source code |
| ab_property | Man page Source code |
| ab_reset_session | Man page Source code |
| ab_selector | Man page Source code |
| ab_synonyms | Man page Source code |
| ab_tradenames | Man page Source code |
| ab_url | Man page Source code |
| ab_validate | Source code |
| abbreviate_mo | Source code |
| add_MO_lookup_to_AMR_env | Source code |
| add_custom_antimicrobials | Man page Source code |
| add_custom_microorganisms | Man page Source code |
| add_intrinsic_resistance_to_AMR_env | Source code |
| addin_insert_in | Source code |
| addin_insert_like | Source code |
| administrable_iv | Man page Source code |
| administrable_per_os | Man page Source code |
| age | Man page Source code |
| age_groups | Man page Source code |
| all.amr_selector | Source code |
| all.amr_selector_any_all | Source code |
| all_antimicrobials | Man page Source code |
| all_any_amr_selector | Source code |
| all_valid_disks | Source code |
| all_valid_mics | Source code |
| aminoglycosides | Man page Source code |
| aminopenicillins | Man page Source code |
| amr_class | Man page Source code |
| amr_distance_from_row | Man page Source code |
| amr_select_exec | Source code |
| amr_selector | Man page Source code |
| anti_join_microorganisms | Man page Source code |
| antibiogram | Man page Source code |
| antibiogram.default | Source code |
| antibiogram.grouped_df | Source code |
| antibiotics | Man page |
| antifungals | Man page Source code |
| antimicrobial_selectors | Man page |
| antimicrobials | Man page |
| antimicrobials_equal | Man page Source code |
| antimycobacterials | Man page Source code |
| antivirals | Man page |
| any.amr_selector | Source code |
| any.amr_selector_any_all | Source code |
| as.ab | Man page Source code |
| as.av | Man page Source code |
| as.data.frame.ab | Source code |
| as.data.frame.av | Source code |
| as.data.frame.deprecated_amr_dataset | Source code |
| as.data.frame.mic | Source code |
| as.disk | Man page Source code |
| as.double.mic | Source code |
| as.double.sir | Source code |
| as.list.custom_eucast_rules | Source code |
| as.list.custom_mdro_guideline | Source code |
| as.list.mic | Source code |
| as.matrix.mic | Source code |
| as.mic | Man page Source code |
| as.mo | Man page Source code |
| as.numeric.mic | Source code |
| as.sir | Man page Source code |
| as.sir.data.frame | Man page Source code |
| as.sir.default | Man page Source code |
| as.sir.disk | Man page Source code |
| as.sir.mic | Man page Source code |
| as.vector.mic | Source code |
| as_original_data_class | Source code |
| as_sir_method | Source code |
| as_sir_structure | Source code |
| ascertain_sir_classes | Source code |
| atc_online_ddd | Man page Source code |
| atc_online_ddd_units | Man page Source code |
| atc_online_groups | Man page Source code |
| atc_online_property | Man page Source code |
| autoplot.antibiogram | Man page Source code |
| autoplot.disk | Man page Source code |
| autoplot.mic | Man page Source code |
| autoplot.resistance_predict | Man page Source code |
| autoplot.sir | Man page Source code |
| av | Man page |
| av_atc | Man page Source code |
| av_cid | Man page Source code |
| av_ddd | Man page Source code |
| av_ddd_units | Man page Source code |
| av_from_text | Man page Source code |
| av_group | Man page Source code |
| av_info | Man page Source code |
| av_loinc | Man page Source code |
| av_name | Man page Source code |
| av_property | Man page Source code |
| av_synonyms | Man page Source code |
| av_tradenames | Man page Source code |
| av_url | Man page Source code |
| av_validate | Source code |
| availability | Man page Source code |
| barplot.antibiogram | Source code |
| barplot.disk | Source code |
| barplot.mic | Source code |
| barplot.sir | Source code |
| betalactams | Man page Source code |
| betalactams_with_inhibitor | Man page Source code |
| brmo | Man page Source code |
| bug_drug_combinations | Man page Source code |
| c.ab | Source code |
| c.amr_selector | Source code |
| c.av | Source code |
| c.custom_eucast_rules | Source code |
| c.custom_mdro_guideline | Man page Source code |
| c.disk | Source code |
| c.mic | Source code |
| c.sir | Source code |
| carbapenems | Man page Source code |
| case_when_AMR | Source code |
| cephalosporins | Man page Source code |
| cephalosporins_1st | Man page Source code |
| cephalosporins_2nd | Man page Source code |
| cephalosporins_3rd | Man page Source code |
| cephalosporins_4th | Man page Source code |
| cephalosporins_5th | Man page Source code |
| check_reference_data | Source code |
| check_validity_mo_source | Source code |
| clean | Source code |
| clear_custom_antimicrobials | Man page Source code |
| clear_custom_microorganisms | Man page Source code |
| clinical_breakpoints | Man page |
| close.progress_bar | Source code |
| coerce_method | Source code |
| convert_host | Source code |
| count | Man page |
| count_I | Man page Source code |
| count_IR | Man page Source code |
| count_R | Man page Source code |
| count_S | Man page Source code |
| count_SI | Man page Source code |
| count_all | Man page Source code |
| count_df | Man page Source code |
| count_resistant | Man page Source code |
| count_susceptible | Man page Source code |
| create_AB_AV_lookup | Source code |
| create_pillar_column | Source code |
| create_scale_mic | Source code |
| create_scale_sir | Source code |
| create_wisca_priors | Source code |
| custom_eucast_rules | Man page Source code |
| custom_mdro_guideline | Man page Source code |
| dataset_UTF8_to_ASCII | Source code |
| deprecation_warning | Source code |
| disk | Man page |
| documentation_date | Source code |
| dosage | Man page |
| dots2vars | Source code |
| droplevels.mic | Man page Source code |
| droplevels.sir | Source code |
| duplicated_antibiogram | Source code |
| edit_sir | Source code |
| eucast_dosage | Man page Source code |
| eucast_exceptional_phenotypes | Man page Source code |
| eucast_rules | Man page Source code |
| example_isolates | Man page |
| example_isolates_unclean | Man page |
| exec_episode | Source code |
| export_ncbi_biosample | Man page Source code |
| facet_sir | Man page |
| filter_first_isolate | Man page Source code |
| find_ab_group | Source code |
| find_ab_names | Source code |
| find_language | Source code |
| find_mo_col | Source code |
| first_isolate | Man page Source code |
| fluoroquinolones | Man page Source code |
| font_black | Source code |
| font_blue | Source code |
| font_bold | Source code |
| font_green | Source code |
| font_green_bg | Source code |
| font_grey | Source code |
| font_grey_bg | Source code |
| font_italic | Source code |
| font_magenta | Source code |
| font_na | Source code |
| font_orange_bg | Source code |
| font_purple_bg | Source code |
| font_red | Source code |
| font_red_bg | Source code |
| font_rose_bg | Source code |
| font_silver | Source code |
| font_stripstyle | Source code |
| font_subtle | Source code |
| font_underline | Source code |
| font_url | Source code |
| font_white | Source code |
| font_yellow | Source code |
| font_yellow_bg | Source code |
| format.bug_drug_combinations | Man page Source code |
| format_class | Source code |
| format_custom_query_rule | Source code |
| format_eucast_version_nr | Source code |
| format_included_data_number | Source code |
| formatted_filesize | Source code |
| fortify.disk | Source code |
| fortify.mic | Source code |
| fortify.resistance_predict | Source code |
| fortify.sir | Source code |
| freq.mo | Source code |
| freq.sir | Source code |
| full_join_microorganisms | Man page Source code |
| g.test | Man page Source code |
| generalise_antibiotic_name | Source code |
| generate_antimicrobials_string | Source code |
| generate_warning_abs_missing | Source code |
| geom_sir | Man page Source code |
| get_AMR_locale | Man page Source code |
| get_ab_from_namespace | Source code |
| get_colnames | Source code |
| get_column_abx | Source code |
| get_current_column | Source code |
| get_current_data | Source code |
| get_data | Source code |
| get_episode | Man page Source code |
| get_group_names | Source code |
| get_guideline | Source code |
| get_mo_source | Man page Source code |
| get_n_cores | Source code |
| get_nrow | Source code |
| get_skimmers.disk | Source code |
| get_skimmers.mic | Source code |
| get_skimmers.mo | Source code |
| get_skimmers.sir | Source code |
| get_translate_ab | Source code |
| get_translate_av | Source code |
| ggplot2_get_from_dots | Source code |
| ggplot_pca | Man page Source code |
| ggplot_sir | Man page Source code |
| ggplot_sir_predict | Man page Source code |
| glycopeptides | Man page Source code |
| guess_ab_col | Man page Source code |
| has_colour | Source code |
| hist.mic | Source code |
| import_fn | Source code |
| inner_join | Man page |
| inner_join_microorganisms | Man page Source code |
| intrinsic_resistant | Man page |
| is.ab | Man page Source code |
| is.av | Man page Source code |
| is.disk | Man page Source code |
| is.mic | Man page Source code |
| is.mo | Man page Source code |
| is.sir | Man page Source code |
| is_all | Source code |
| is_any | Source code |
| is_dark | Source code |
| is_new_episode | Man page Source code |
| is_null_or_grouped_tbl | Source code |
| is_sir_eligible | Man page Source code |
| is_valid_regex | Source code |
| isoxazolylpenicillins | Man page Source code |
| italicise_taxonomy | Man page Source code |
| italicize_taxonomy | Man page Source code |
| join | Man page |
| join_microorganisms | Source code |
| key_antimicrobials | Man page Source code |
| knit_print.antibiogram | Man page Source code |
| knit_print.formatted_bug_drug_combinations | Source code |
| kurtosis | Man page Source code |
| kurtosis.data.frame | Man page Source code |
| kurtosis.default | Man page Source code |
| kurtosis.matrix | Man page Source code |
| labels_sir_count | Man page |
| left_join_microorganisms | Man page Source code |
| like | Man page Source code |
| lincosamides | Man page Source code |
| lipoglycopeptides | Man page Source code |
| macrolides | Man page Source code |
| match | Source code |
| mdr_cmi2012 | Man page Source code |
| mdr_tb | Man page Source code |
| mdro | Man page Source code |
| mean_amr_distance | Man page Source code |
| mean_amr_distance.data.frame | Man page Source code |
| mean_amr_distance.default | Source code |
| mean_amr_distance.disk | Source code |
| mean_amr_distance.mic | Source code |
| mean_amr_distance.sir | Man page Source code |
| meet_criteria | Source code |
| message_ | Source code |
| message_agent_names | Source code |
| message_not_thrown_before | Source code |
| mic | Man page |
| mic_p50 | Man page Source code |
| mic_p90 | Man page Source code |
| microorganisms | Man page |
| microorganisms.codes | Man page |
| microorganisms.groups | Man page |
| mo | Man page |
| mo_authors | Man page Source code |
| mo_class | Man page Source code |
| mo_cleaning_regex | Man page Source code |
| mo_current | Man page Source code |
| mo_domain | Man page Source code |
| mo_failures | Man page Source code |
| mo_family | Man page Source code |
| mo_fullname | Man page Source code |
| mo_gbif | Man page Source code |
| mo_genus | Man page Source code |
| mo_gramstain | Man page Source code |
| mo_group_members | Man page Source code |
| mo_info | Man page Source code |
| mo_is_anaerobic | Man page Source code |
| mo_is_gram_negative | Man page Source code |
| mo_is_gram_positive | Man page Source code |
| mo_is_intrinsic_resistant | Man page Source code |
| mo_is_yeast | Man page Source code |
| mo_kingdom | Man page Source code |
| mo_lpsn | Man page Source code |
| mo_matching_score | Man page Source code |
| mo_mycobank | Man page Source code |
| mo_name | Man page Source code |
| mo_order | Man page Source code |
| mo_oxygen_tolerance | Man page Source code |
| mo_pathogenicity | Man page Source code |
| mo_phylum | Man page Source code |
| mo_property | Man page Source code |
| mo_rank | Man page Source code |
| mo_ref | Man page Source code |
| mo_renamed | Man page Source code |
| mo_reset_session | Man page Source code |
| mo_shortname | Man page Source code |
| mo_snomed | Man page Source code |
| mo_source | Man page |
| mo_species | Man page Source code |
| mo_status | Man page Source code |
| mo_subspecies | Man page Source code |
| mo_synonyms | Man page Source code |
| mo_taxonomy | Man page Source code |
| mo_type | Man page Source code |
| mo_uncertainties | Man page Source code |
| mo_url | Man page Source code |
| mo_validate | Source code |
| mo_year | Man page Source code |
| monobactams | Man page Source code |
| mrgn | Man page Source code |
| n_sir | Man page |
| nitrofurans | Man page Source code |
| not_intrinsic_resistant | Man page Source code |
| oxazolidinones | Man page Source code |
| pca | Man page Source code |
| pca_calculations | Source code |
| penicillins | Man page Source code |
| percentage | Source code |
| phenicols | Man page Source code |
| pillar_shaft.ab | Source code |
| pillar_shaft.av | Source code |
| pillar_shaft.disk | Source code |
| pillar_shaft.mic | Source code |
| pillar_shaft.mo | Source code |
| pillar_shaft.sir | Source code |
| pkg_is_available | Source code |
| plot | Man page |
| plot.antibiogram | Man page Source code |
| plot.disk | Man page Source code |
| plot.mic | Man page Source code |
| plot.resistance_predict | Man page Source code |
| plot.sir | Man page Source code |
| plot_colours_subtitle_guideline | Source code |
| plot_name_of_I | Source code |
| plotrange_as_table | Source code |
| pm_add_count | Source code |
| pm_add_tally | Source code |
| pm_all_of | Source code |
| pm_anti_join | Source code |
| pm_any_of | Source code |
| pm_apply_grouped_function | Source code |
| pm_arrange | Source code |
| pm_arrange.default | Source code |
| pm_arrange.grouped_data | Source code |
| pm_between | Source code |
| pm_check_class | Source code |
| pm_check_group_pm_context | Source code |
| pm_check_length | Source code |
| pm_check_name | Source code |
| pm_check_type | Source code |
| pm_contains | Source code |
| pm_count | Source code |
| pm_cur_data | Source code |
| pm_cur_group | Source code |
| pm_cur_group_id | Source code |
| pm_cur_group_rows | Source code |
| pm_desc | Source code |
| pm_distinct | Source code |
| pm_distinct.default | Source code |
| pm_distinct.grouped_data | Source code |
| pm_ends_with | Source code |
| pm_eval_call | Source code |
| pm_eval_expr | Source code |
| pm_everything | Source code |
| pm_filter | Source code |
| pm_filter.default | Source code |
| pm_filter.grouped_data | Source code |
| pm_filter_join_worker | Source code |
| pm_full_join | Source code |
| pm_get_group_details | Source code |
| pm_get_groups | Source code |
| pm_group_by | Source code |
| pm_group_data | Source code |
| pm_group_data_worker | Source code |
| pm_group_indices | Source code |
| pm_group_keys | Source code |
| pm_group_rows | Source code |
| pm_group_size | Source code |
| pm_group_vars | Source code |
| pm_groups | Source code |
| pm_has_groups | Source code |
| pm_if_else | Source code |
| pm_inner_join | Source code |
| pm_join_message | Source code |
| pm_join_worker | Source code |
| pm_lag | Source code |
| pm_last_col | Source code |
| pm_lead | Source code |
| pm_left_join | Source code |
| pm_matches | Source code |
| pm_mutate | Source code |
| pm_mutate.default | Source code |
| pm_mutate.grouped_data | Source code |
| pm_n | Source code |
| pm_n_distinct | Source code |
| pm_n_groups | Source code |
| pm_na_if | Source code |
| pm_near | Source code |
| pm_num_range | Source code |
| pm_peek_vars | Source code |
| pm_print.grouped_data | Source code |
| pm_pull | Source code |
| pm_relocate | Source code |
| pm_rename | Source code |
| pm_rename_with | Source code |
| pm_replace_with | Source code |
| pm_right_join | Source code |
| pm_rownames_to_column | Source code |
| pm_select_char | Source code |
| pm_select_positions | Source code |
| pm_select_symbol | Source code |
| pm_semi_join | Source code |
| pm_set_groups | Source code |
| pm_set_names | Source code |
| pm_split_into_groups | Source code |
| pm_starts_with | Source code |
| pm_tally | Source code |
| pm_tally_n | Source code |
| pm_ungroup | Source code |
| pm_vec_head | Source code |
| polymyxins | Man page Source code |
| portion | Man page |
| print.ab | Source code |
| print.amr_selector | Source code |
| print.av | Source code |
| print.bug_drug_combinations | Source code |
| print.custom_eucast_rules | Source code |
| print.custom_mdro_guideline | Source code |
| print.deprecated_amr_dataset | Source code |
| print.disk | Source code |
| print.mic | Source code |
| print.pca | Source code |
| print.sir | Source code |
| print.sir_log | Source code |
| print_pca_group | Source code |
| progress_ticker | Source code |
| proportion | Man page |
| proportion_I | Man page Source code |
| proportion_IR | Man page Source code |
| proportion_R | Man page Source code |
| proportion_S | Man page Source code |
| proportion_SI | Man page Source code |
| proportion_df | Man page Source code |
| quinolones | Man page Source code |
| random | Man page |
| random_disk | Man page Source code |
| random_exec | Source code |
| random_mic | Man page Source code |
| random_sir | Man page Source code |
| rbind_AMR | Source code |
| readRDS_AMR | Source code |
| rep.ab | Source code |
| rep.av | Source code |
| rep.disk | Source code |
| rep.mic | Source code |
| rep.sir | Source code |
| rescale_mic | Man page Source code |
| reset_AMR_locale | Man page Source code |
| reset_all_thrown_messages | Source code |
| resistance | Man page Source code |
| resistance_predict | Man page Source code |
| retrieve_wisca_parameters | Man page Source code |
| return_after_integrity_check | Source code |
| rifamycins | Man page Source code |
| right_join_microorganisms | Man page Source code |
| round2 | Source code |
| run_custom_mdro_guideline | Source code |
| s3_register | Source code |
| scale_color_mic | Man page |
| scale_color_sir | Man page |
| scale_colour_mic | Man page Source code |
| scale_colour_sir | Man page Source code |
| scale_fill_mic | Man page Source code |
| scale_fill_sir | Man page Source code |
| scale_sir_colors | Man page |
| scale_sir_colours | Man page |
| scale_x_mic | Man page Source code |
| scale_x_sir | Man page Source code |
| scale_y_mic | Man page Source code |
| scale_y_percent | Man page |
| search_type_in_df | Source code |
| semi_join_microorganisms | Man page Source code |
| set_AMR_locale | Man page Source code |
| set_ab_names | Man page Source code |
| set_clean_class | Source code |
| set_mo_source | Man page Source code |
| setup | Source code |
| simulate_coverage | Source code |
| sir | Man page |
| sir_calc | Source code |
| sir_calc_df | Source code |
| sir_confidence_interval | Man page Source code |
| sir_df | Man page Source code |
| sir_interpretation_history | Man page Source code |
| sir_predict | Man page |
| skewness | Man page Source code |
| skewness.data.frame | Man page Source code |
| skewness.default | Man page Source code |
| skewness.matrix | Man page Source code |
| sort.mic | Source code |
| stop_ | Source code |
| stop_if | Source code |
| stop_ifnot | Source code |
| stop_ifnot_installed | Source code |
| streptogramins | Man page Source code |
| sulfonamides | Man page Source code |
| summary.mic | Source code |
| summary.pca | Source code |
| summary.sir | Source code |
| susceptibility | Man page Source code |
| tbl_format_footer.antibiogram | Source code |
| tbl_sum.antibiogram | Source code |
| tetracyclines | Man page Source code |
| theme_sir | Man page |
| top_n_microorganisms | Man page Source code |
| totitle | Source code |
| translate | Man page |
| translate_AMR | Man page Source code |
| translate_into_language | Source code |
| trimethoprims | Man page Source code |
| trimws2 | Source code |
| try_colour | Source code |
| type_sum.ab | Source code |
| type_sum.av | Source code |
| type_sum.mic | Source code |
| type_sum.mo | Source code |
| type_sum.sir | Source code |
| unique.ab | Source code |
| unique.av | Source code |
| unique.disk | Source code |
| unique.mic | Source code |
| unique.sir | Source code |
| unique_call_id | Source code |
| ureidopenicillins | Man page Source code |
| validate_language | Source code |
| vec_arith.mic | Source code |
| vec_cast.ab.character | Source code |
| vec_cast.av.character | Source code |
| vec_cast.character.ab | Source code |
| vec_cast.character.amr_selector | Source code |
| vec_cast.character.av | Source code |
| vec_cast.character.disk | Source code |
| vec_cast.character.mic | Source code |
| vec_cast.character.mo | Source code |
| vec_cast.character.sir | Source code |
| vec_cast.disk.character | Source code |
| vec_cast.disk.disk | Source code |
| vec_cast.disk.double | Source code |
| vec_cast.disk.integer | Source code |
| vec_cast.double.disk | Source code |
| vec_cast.double.mic | Source code |
| vec_cast.factor.mic | Source code |
| vec_cast.integer.disk | Source code |
| vec_cast.integer.mic | Source code |
| vec_cast.logical.amr_selector_any_all | Source code |
| vec_cast.mic.character | Source code |
| vec_cast.mic.double | Source code |
| vec_cast.mic.factor | Source code |
| vec_cast.mic.integer | Source code |
| vec_cast.mic.mic | Source code |
| vec_cast.mo.character | Source code |
| vec_cast.sir.character | Source code |
| vec_cast.sir.sir | Source code |
| vec_math.mic | Source code |
| vec_ptype2.ab.ab | Source code |
| vec_ptype2.ab.default | Source code |
| vec_ptype2.amr_selector.character | Source code |
| vec_ptype2.amr_selector_any_all.logical | Source code |
| vec_ptype2.av.av | Source code |
| vec_ptype2.av.default | Source code |
| vec_ptype2.character.amr_selector | Source code |
| vec_ptype2.character.sir | Source code |
| vec_ptype2.disk.default | Source code |
| vec_ptype2.disk.disk | Source code |
| vec_ptype2.logical.amr_selector_any_all | Source code |
| vec_ptype2.mic.default | Source code |
| vec_ptype2.mic.mic | Source code |
| vec_ptype2.mo.default | Source code |
| vec_ptype2.mo.mo | Source code |
| vec_ptype2.sir.default | Source code |
| vec_ptype2.sir.sir | Source code |
| vec_ptype_abbr.disk | Source code |
| vec_ptype_full.disk | Source code |
| vector_and | Source code |
| vector_or | Source code |
| warning_ | Source code |
| where | Source code |
| wisca | Man page Source code |
| word_wrap | Source code |
