AMR/NAMESPACE

354 lines
7.7 KiB
Plaintext
Raw Normal View History

2018-02-21 11:52:31 +01:00
# Generated by roxygen2: do not edit by hand
2021-05-19 22:55:42 +02:00
S3method("!=",ab_selector)
S3method("&",ab_selector)
2021-05-19 22:55:42 +02:00
S3method("==",ab_selector)
S3method("[",ab)
S3method("[",av)
2020-03-14 14:05:43 +01:00
S3method("[",disk)
2020-04-13 21:09:56 +02:00
S3method("[",mic)
S3method("[",mo)
2019-08-14 14:57:06 +02:00
S3method("[<-",ab)
S3method("[<-",av)
2020-03-14 14:05:43 +01:00
S3method("[<-",disk)
2020-04-13 21:09:56 +02:00
S3method("[<-",mic)
2019-08-14 14:57:06 +02:00
S3method("[<-",mo)
2023-01-21 23:47:20 +01:00
S3method("[<-",sir)
2019-08-14 14:57:06 +02:00
S3method("[[",ab)
S3method("[[",av)
2020-03-14 14:05:43 +01:00
S3method("[[",disk)
2020-04-13 21:09:56 +02:00
S3method("[[",mic)
2019-08-14 14:57:06 +02:00
S3method("[[",mo)
S3method("[[<-",ab)
S3method("[[<-",av)
2020-03-14 14:05:43 +01:00
S3method("[[<-",disk)
2020-04-13 21:09:56 +02:00
S3method("[[<-",mic)
2019-08-14 14:57:06 +02:00
S3method("[[<-",mo)
2023-01-21 23:47:20 +01:00
S3method("[[<-",sir)
S3method("|",ab_selector)
2023-10-20 14:51:48 +02:00
S3method(Complex,mic)
S3method(Math,mic)
S3method(Ops,mic)
S3method(Summary,mic)
2021-05-19 22:55:42 +02:00
S3method(all,ab_selector)
S3method(all,ab_selector_any_all)
S3method(any,ab_selector)
S3method(any,ab_selector_any_all)
2019-05-10 16:44:59 +02:00
S3method(as.data.frame,ab)
S3method(as.data.frame,av)
2024-04-07 20:22:59 +02:00
S3method(as.data.frame,mic)
2019-02-10 09:13:06 +01:00
S3method(as.data.frame,mo)
S3method(as.double,mic)
S3method(as.double,sir)
2021-04-07 08:37:42 +02:00
S3method(as.list,custom_eucast_rules)
S3method(as.list,custom_mdro_guideline)
2024-04-07 20:22:59 +02:00
S3method(as.list,mic)
2021-03-07 21:16:45 +01:00
S3method(as.matrix,mic)
2019-02-10 09:13:06 +01:00
S3method(as.numeric,mic)
2023-01-21 23:47:20 +01:00
S3method(as.sir,data.frame)
S3method(as.sir,default)
S3method(as.sir,disk)
S3method(as.sir,mic)
2024-04-07 20:22:59 +02:00
S3method(as.vector,mic)
S3method(barplot,antibiogram)
S3method(barplot,disk)
2019-02-10 09:13:06 +01:00
S3method(barplot,mic)
2023-01-21 23:47:20 +01:00
S3method(barplot,sir)
2019-08-14 14:57:06 +02:00
S3method(c,ab)
2021-05-19 22:55:42 +02:00
S3method(c,ab_selector)
S3method(c,av)
2021-04-07 08:37:42 +02:00
S3method(c,custom_eucast_rules)
S3method(c,custom_mdro_guideline)
2020-03-14 14:05:43 +01:00
S3method(c,disk)
2020-04-13 21:09:56 +02:00
S3method(c,mic)
2019-08-14 14:57:06 +02:00
S3method(c,mo)
2023-01-21 23:47:20 +01:00
S3method(c,sir)
2021-12-13 10:18:28 +01:00
S3method(close,progress_bar)
2019-02-10 09:13:06 +01:00
S3method(droplevels,mic)
2023-01-21 23:47:20 +01:00
S3method(droplevels,sir)
2019-08-27 22:41:09 +02:00
S3method(format,bug_drug_combinations)
2021-03-05 15:36:39 +01:00
S3method(hist,mic)
2019-02-10 09:13:06 +01:00
S3method(kurtosis,data.frame)
S3method(kurtosis,default)
S3method(kurtosis,matrix)
2021-03-05 15:36:39 +01:00
S3method(mean,mic)
2022-08-30 21:48:02 +02:00
S3method(mean_amr_distance,data.frame)
S3method(mean_amr_distance,default)
S3method(mean_amr_distance,disk)
S3method(mean_amr_distance,mic)
2023-01-21 23:47:20 +01:00
S3method(mean_amr_distance,sir)
2021-03-05 15:36:39 +01:00
S3method(median,mic)
S3method(plot,antibiogram)
2020-12-12 23:17:29 +01:00
S3method(plot,disk)
2019-02-10 09:13:06 +01:00
S3method(plot,mic)
S3method(plot,resistance_predict)
2023-01-21 23:47:20 +01:00
S3method(plot,sir)
2019-05-10 16:44:59 +02:00
S3method(print,ab)
S3method(print,ab_selector)
S3method(print,av)
2019-08-27 22:41:09 +02:00
S3method(print,bug_drug_combinations)
2021-04-07 08:37:42 +02:00
S3method(print,custom_eucast_rules)
2021-01-17 00:26:48 +01:00
S3method(print,custom_mdro_guideline)
2019-05-10 16:44:59 +02:00
S3method(print,disk)
2019-02-10 09:13:06 +01:00
S3method(print,mic)
S3method(print,mo)
2019-02-28 13:56:28 +01:00
S3method(print,mo_renamed)
S3method(print,mo_uncertainties)
S3method(print,pca)
2023-01-21 23:47:20 +01:00
S3method(print,sir)
2021-03-05 15:36:39 +01:00
S3method(quantile,mic)
2021-07-06 16:35:14 +02:00
S3method(rep,ab)
S3method(rep,av)
2021-07-06 16:35:14 +02:00
S3method(rep,disk)
S3method(rep,mic)
2021-02-22 20:21:33 +01:00
S3method(rep,mo)
2023-01-21 23:47:20 +01:00
S3method(rep,sir)
2019-02-10 09:13:06 +01:00
S3method(skewness,data.frame)
S3method(skewness,default)
S3method(skewness,matrix)
2021-03-05 15:36:39 +01:00
S3method(sort,mic)
2019-02-10 09:13:06 +01:00
S3method(summary,mic)
S3method(summary,mo)
S3method(summary,pca)
2023-01-21 23:47:20 +01:00
S3method(summary,sir)
S3method(unique,ab)
S3method(unique,av)
S3method(unique,disk)
S3method(unique,mic)
S3method(unique,mo)
2023-01-21 23:47:20 +01:00
S3method(unique,sir)
2019-02-10 09:13:06 +01:00
export("%like%")
export("%like_case%")
export("%unlike%")
export("%unlike_case%")
export(NA_disk_)
export(NA_mic_)
2023-01-21 23:47:20 +01:00
export(NA_sir_)
2019-02-10 09:13:06 +01:00
export(ab_atc)
2019-05-10 16:44:59 +02:00
export(ab_atc_group1)
export(ab_atc_group2)
export(ab_cid)
2020-06-17 15:14:37 +02:00
export(ab_class)
2019-05-10 16:44:59 +02:00
export(ab_ddd)
export(ab_ddd_units)
2020-06-25 19:20:50 +02:00
export(ab_from_text)
2019-05-10 16:44:59 +02:00
export(ab_group)
2019-05-16 22:07:31 +02:00
export(ab_info)
2020-01-26 20:20:00 +01:00
export(ab_loinc)
2019-02-10 09:13:06 +01:00
export(ab_name)
export(ab_property)
export(ab_selector)
2019-05-10 16:44:59 +02:00
export(ab_synonyms)
2019-02-10 09:13:06 +01:00
export(ab_tradenames)
export(ab_url)
2022-10-10 20:20:39 +02:00
export(add_custom_antimicrobials)
2022-12-27 15:16:15 +01:00
export(add_custom_microorganisms)
export(administrable_iv)
export(administrable_per_os)
2019-02-10 09:13:06 +01:00
export(age)
export(age_groups)
export(all_antimicrobials)
2020-06-17 01:39:30 +02:00
export(aminoglycosides)
export(aminopenicillins)
2022-10-21 16:02:14 +02:00
export(amr_distance_from_row)
2019-02-10 09:13:06 +01:00
export(anti_join_microorganisms)
export(antibiogram)
export(antifungals)
export(antimicrobials_equal)
export(antimycobacterials)
2019-05-10 16:44:59 +02:00
export(as.ab)
export(as.av)
2019-05-10 16:44:59 +02:00
export(as.disk)
2019-02-10 09:13:06 +01:00
export(as.mic)
export(as.mo)
2023-01-21 23:47:20 +01:00
export(as.sir)
2019-02-10 09:13:06 +01:00
export(atc_online_ddd)
2021-08-19 23:43:02 +02:00
export(atc_online_ddd_units)
2019-02-10 09:13:06 +01:00
export(atc_online_groups)
export(atc_online_property)
export(av_atc)
export(av_cid)
export(av_ddd)
export(av_ddd_units)
export(av_from_text)
export(av_group)
export(av_info)
export(av_loinc)
export(av_name)
export(av_property)
export(av_synonyms)
export(av_tradenames)
export(av_url)
2019-02-10 09:13:06 +01:00
export(availability)
2021-05-18 00:53:04 +02:00
export(betalactams)
2019-02-10 09:13:06 +01:00
export(brmo)
2019-08-25 22:53:22 +02:00
export(bug_drug_combinations)
2020-06-17 01:39:30 +02:00
export(carbapenems)
export(cephalosporins)
export(cephalosporins_1st)
export(cephalosporins_2nd)
export(cephalosporins_3rd)
export(cephalosporins_4th)
export(cephalosporins_5th)
2022-10-10 20:20:39 +02:00
export(clear_custom_antimicrobials)
2022-12-27 15:16:15 +01:00
export(clear_custom_microorganisms)
2019-02-10 09:13:06 +01:00
export(count_I)
export(count_IR)
export(count_R)
export(count_S)
export(count_SI)
export(count_all)
export(count_df)
export(count_resistant)
export(count_susceptible)
2021-04-07 08:37:42 +02:00
export(custom_eucast_rules)
2021-01-17 00:26:48 +01:00
export(custom_mdro_guideline)
export(eucast_dosage)
2019-02-10 09:13:06 +01:00
export(eucast_exceptional_phenotypes)
export(eucast_rules)
2023-01-21 23:47:20 +01:00
export(facet_sir)
2019-02-10 09:13:06 +01:00
export(filter_first_isolate)
export(first_isolate)
2020-06-17 01:39:30 +02:00
export(fluoroquinolones)
2019-02-10 09:13:06 +01:00
export(full_join_microorganisms)
export(g.test)
2023-01-21 23:47:20 +01:00
export(geom_sir)
export(get_AMR_locale)
2020-12-27 00:07:00 +01:00
export(get_episode)
2019-02-10 09:13:06 +01:00
export(get_mo_source)
2020-03-07 21:48:21 +01:00
export(ggplot_pca)
2023-01-21 23:47:20 +01:00
export(ggplot_sir)
export(ggplot_sir_predict)
2020-06-17 01:39:30 +02:00
export(glycopeptides)
2019-02-10 09:13:06 +01:00
export(guess_ab_col)
export(inner_join_microorganisms)
2019-05-10 16:44:59 +02:00
export(is.ab)
export(is.av)
2019-05-10 16:44:59 +02:00
export(is.disk)
2019-02-10 09:13:06 +01:00
export(is.mic)
export(is.mo)
2023-01-21 23:47:20 +01:00
export(is.sir)
2020-11-17 16:57:41 +01:00
export(is_new_episode)
2023-01-21 23:47:20 +01:00
export(is_sir_eligible)
2021-05-03 10:47:32 +02:00
export(italicise_taxonomy)
export(italicize_taxonomy)
export(key_antimicrobials)
2019-02-10 09:13:06 +01:00
export(kurtosis)
2023-01-21 23:47:20 +01:00
export(labels_sir_count)
2019-02-10 09:13:06 +01:00
export(left_join_microorganisms)
export(like)
export(lincosamides)
export(lipoglycopeptides)
2020-06-17 01:39:30 +02:00
export(macrolides)
export(mdr_cmi2012)
2019-05-23 16:58:59 +02:00
export(mdr_tb)
2019-02-10 09:13:06 +01:00
export(mdro)
2022-08-30 21:48:02 +02:00
export(mean_amr_distance)
2019-02-10 09:13:06 +01:00
export(mo_authors)
export(mo_class)
2022-10-05 09:12:22 +02:00
export(mo_cleaning_regex)
2022-10-10 10:12:08 +02:00
export(mo_current)
export(mo_domain)
2019-02-10 09:13:06 +01:00
export(mo_failures)
export(mo_family)
export(mo_fullname)
2022-10-05 09:12:22 +02:00
export(mo_gbif)
2019-02-10 09:13:06 +01:00
export(mo_genus)
export(mo_gramstain)
2024-04-19 10:18:21 +02:00
export(mo_group_members)
2019-06-11 14:18:25 +02:00
export(mo_info)
2023-05-11 21:56:27 +02:00
export(mo_is_anaerobic)
export(mo_is_gram_negative)
export(mo_is_gram_positive)
export(mo_is_intrinsic_resistant)
export(mo_is_yeast)
2019-02-10 09:13:06 +01:00
export(mo_kingdom)
2021-12-09 10:48:25 +01:00
export(mo_lpsn)
export(mo_matching_score)
2019-05-13 12:21:57 +02:00
export(mo_name)
2019-02-10 09:13:06 +01:00
export(mo_order)
2023-05-11 21:56:27 +02:00
export(mo_oxygen_tolerance)
2023-01-06 13:35:37 +01:00
export(mo_pathogenicity)
2019-02-10 09:13:06 +01:00
export(mo_phylum)
export(mo_property)
2019-02-22 22:12:10 +01:00
export(mo_rank)
2019-02-10 09:13:06 +01:00
export(mo_ref)
export(mo_renamed)
2022-10-05 09:12:22 +02:00
export(mo_reset_session)
2019-02-10 09:13:06 +01:00
export(mo_shortname)
2020-01-27 19:14:23 +01:00
export(mo_snomed)
2019-02-10 09:13:06 +01:00
export(mo_species)
2022-10-05 09:12:22 +02:00
export(mo_status)
2019-02-10 09:13:06 +01:00
export(mo_subspecies)
export(mo_synonyms)
2019-02-10 09:13:06 +01:00
export(mo_taxonomy)
export(mo_type)
export(mo_uncertainties)
2019-02-20 00:04:48 +01:00
export(mo_url)
2019-02-10 09:13:06 +01:00
export(mo_year)
export(mrgn)
2023-01-21 23:47:20 +01:00
export(n_sir)
2024-06-08 17:35:25 +02:00
export(nitrofurans)
2021-12-09 10:48:25 +01:00
export(not_intrinsic_resistant)
export(oxazolidinones)
2020-03-07 21:48:21 +01:00
export(pca)
2020-06-17 01:39:30 +02:00
export(penicillins)
export(polymyxins)
export(proportion_I)
export(proportion_IR)
export(proportion_R)
export(proportion_S)
export(proportion_SI)
export(proportion_df)
export(quinolones)
2020-12-12 23:17:29 +01:00
export(random_disk)
export(random_mic)
2023-01-21 23:47:20 +01:00
export(random_sir)
export(rescale_mic)
2022-08-19 12:33:14 +02:00
export(reset_AMR_locale)
export(resistance)
2019-02-10 09:13:06 +01:00
export(resistance_predict)
2024-06-08 17:35:25 +02:00
export(rifamycins)
2019-02-10 09:13:06 +01:00
export(right_join_microorganisms)
export(scale_colour_mic)
export(scale_fill_mic)
2023-01-21 23:47:20 +01:00
export(scale_sir_colours)
2023-12-03 01:06:00 +01:00
export(scale_x_mic)
export(scale_y_mic)
2019-02-10 09:13:06 +01:00
export(scale_y_percent)
export(semi_join_microorganisms)
2022-08-19 12:33:14 +02:00
export(set_AMR_locale)
export(set_ab_names)
2019-02-10 09:13:06 +01:00
export(set_mo_source)
2023-01-21 23:47:20 +01:00
export(sir_confidence_interval)
export(sir_df)
export(sir_interpretation_history)
export(sir_predict)
2019-02-10 09:13:06 +01:00
export(skewness)
export(streptogramins)
export(susceptibility)
2020-06-17 01:39:30 +02:00
export(tetracyclines)
2023-01-21 23:47:20 +01:00
export(theme_sir)
2022-08-19 12:33:14 +02:00
export(translate_AMR)
export(trimethoprims)
export(ureidopenicillins)
2019-01-15 12:45:24 +01:00
importFrom(graphics,arrows)
2018-03-13 15:40:10 +01:00
importFrom(graphics,axis)
importFrom(graphics,barplot)
2021-03-07 21:16:45 +01:00
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,mtext)
importFrom(graphics,plot)
2019-02-11 10:27:10 +01:00
importFrom(graphics,points)
2018-02-21 11:52:31 +01:00
importFrom(graphics,text)
2018-07-10 12:27:07 +02:00
importFrom(stats,complete.cases)
2018-07-26 16:30:42 +02:00
importFrom(stats,glm)
importFrom(stats,lm)
2021-03-07 21:16:45 +01:00
importFrom(stats,median)
2018-07-01 21:40:37 +02:00
importFrom(stats,pchisq)
2020-03-08 09:12:11 +01:00
importFrom(stats,prcomp)
2018-07-26 16:30:42 +02:00
importFrom(stats,predict)
2020-03-08 11:18:59 +01:00
importFrom(stats,qchisq)
2021-03-07 21:16:45 +01:00
importFrom(stats,quantile)
2020-03-08 11:18:59 +01:00
importFrom(stats,var)