2018-02-21 11:52:31 +01:00
|
|
|
# Generated by roxygen2: do not edit by hand
|
|
|
|
|
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method("!",mic)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method("!=",mic)
|
|
|
|
|
S3method("%%",mic)
|
|
|
|
|
S3method("%/%",mic)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method("&",mic)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method("*",mic)
|
|
|
|
|
S3method("+",mic)
|
|
|
|
|
S3method("-",mic)
|
|
|
|
|
S3method("/",mic)
|
|
|
|
|
S3method("<",mic)
|
|
|
|
|
S3method("<=",mic)
|
|
|
|
|
S3method("==",mic)
|
|
|
|
|
S3method(">",mic)
|
|
|
|
|
S3method(">=",mic)
|
2019-08-12 14:48:09 +02:00
|
|
|
S3method("[",ab)
|
2020-03-14 14:05:43 +01:00
|
|
|
S3method("[",disk)
|
2021-01-12 22:08:04 +01:00
|
|
|
S3method("[",isolate_identifier)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method("[",mic)
|
2019-08-12 14:48:09 +02:00
|
|
|
S3method("[",mo)
|
2019-08-14 14:57:06 +02:00
|
|
|
S3method("[<-",ab)
|
2020-03-14 14:05:43 +01:00
|
|
|
S3method("[<-",disk)
|
2021-01-12 22:08:04 +01:00
|
|
|
S3method("[<-",isolate_identifier)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method("[<-",mic)
|
2019-08-14 14:57:06 +02:00
|
|
|
S3method("[<-",mo)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method("[<-",rsi)
|
2019-08-14 14:57:06 +02:00
|
|
|
S3method("[[",ab)
|
2020-03-14 14:05:43 +01:00
|
|
|
S3method("[[",disk)
|
2021-01-12 22:08:04 +01:00
|
|
|
S3method("[[",isolate_identifier)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method("[[",mic)
|
2019-08-14 14:57:06 +02:00
|
|
|
S3method("[[",mo)
|
|
|
|
|
S3method("[[<-",ab)
|
2020-03-14 14:05:43 +01:00
|
|
|
S3method("[[<-",disk)
|
2021-01-12 22:08:04 +01:00
|
|
|
S3method("[[<-",isolate_identifier)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method("[[<-",mic)
|
2019-08-14 14:57:06 +02:00
|
|
|
S3method("[[<-",mo)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method("[[<-",rsi)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method("^",mic)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method("|",mic)
|
|
|
|
|
S3method(abs,mic)
|
|
|
|
|
S3method(acos,mic)
|
|
|
|
|
S3method(acosh,mic)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method(all,mic)
|
2021-01-22 10:20:41 +01:00
|
|
|
S3method(all.equal,isolate_identifier)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method(any,mic)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(as.data.frame,ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(as.data.frame,mo)
|
|
|
|
|
S3method(as.double,mic)
|
|
|
|
|
S3method(as.integer,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)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(as.rsi,data.frame)
|
|
|
|
|
S3method(as.rsi,default)
|
|
|
|
|
S3method(as.rsi,disk)
|
|
|
|
|
S3method(as.rsi,mic)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(asin,mic)
|
|
|
|
|
S3method(asinh,mic)
|
|
|
|
|
S3method(atan,mic)
|
|
|
|
|
S3method(atanh,mic)
|
2021-02-25 10:33:08 +01:00
|
|
|
S3method(barplot,disk)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(barplot,mic)
|
|
|
|
|
S3method(barplot,rsi)
|
2019-08-14 14:57:06 +02:00
|
|
|
S3method(c,ab)
|
2020-03-14 14:05:43 +01:00
|
|
|
S3method(c,disk)
|
2021-01-12 22:08:04 +01:00
|
|
|
S3method(c,isolate_identifier)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method(c,mic)
|
2019-08-14 14:57:06 +02:00
|
|
|
S3method(c,mo)
|
2020-04-13 21:09:56 +02:00
|
|
|
S3method(c,rsi)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method(ceiling,mic)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(cos,mic)
|
|
|
|
|
S3method(cosh,mic)
|
|
|
|
|
S3method(cospi,mic)
|
|
|
|
|
S3method(cummax,mic)
|
|
|
|
|
S3method(cummin,mic)
|
|
|
|
|
S3method(cumprod,mic)
|
|
|
|
|
S3method(cumsum,mic)
|
|
|
|
|
S3method(digamma,mic)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(droplevels,mic)
|
|
|
|
|
S3method(droplevels,rsi)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(exp,mic)
|
|
|
|
|
S3method(expm1,mic)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method(floor,mic)
|
2019-08-27 22:41:09 +02:00
|
|
|
S3method(format,bug_drug_combinations)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(gamma,mic)
|
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)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(lgamma,mic)
|
|
|
|
|
S3method(log,mic)
|
|
|
|
|
S3method(log10,mic)
|
|
|
|
|
S3method(log1p,mic)
|
|
|
|
|
S3method(log2,mic)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method(max,mic)
|
|
|
|
|
S3method(mean,mic)
|
|
|
|
|
S3method(median,mic)
|
|
|
|
|
S3method(min,mic)
|
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)
|
|
|
|
|
S3method(plot,rsi)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(print,ab)
|
2019-08-27 22:41:09 +02:00
|
|
|
S3method(print,bug_drug_combinations)
|
2019-03-26 14:24:03 +01:00
|
|
|
S3method(print,catalogue_of_life_version)
|
2021-01-17 00:26:48 +01:00
|
|
|
S3method(print,custom_mdro_guideline)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(print,disk)
|
2021-01-12 22:08:04 +01:00
|
|
|
S3method(print,isolate_identifier)
|
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)
|
2021-01-28 16:09:30 +01:00
|
|
|
S3method(print,pca)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(print,rsi)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(prod,mic)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method(quantile,mic)
|
|
|
|
|
S3method(range,mic)
|
2021-02-22 20:21:33 +01:00
|
|
|
S3method(rep,mo)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(round,mic)
|
|
|
|
|
S3method(sign,mic)
|
|
|
|
|
S3method(signif,mic)
|
|
|
|
|
S3method(sin,mic)
|
|
|
|
|
S3method(sinh,mic)
|
|
|
|
|
S3method(sinpi,mic)
|
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)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(sqrt,mic)
|
2021-03-05 15:36:39 +01:00
|
|
|
S3method(sum,mic)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(summary,mic)
|
|
|
|
|
S3method(summary,mo)
|
2021-01-28 16:09:30 +01:00
|
|
|
S3method(summary,pca)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(summary,rsi)
|
2021-03-07 13:52:39 +01:00
|
|
|
S3method(tan,mic)
|
|
|
|
|
S3method(tanh,mic)
|
|
|
|
|
S3method(tanpi,mic)
|
|
|
|
|
S3method(trigamma,mic)
|
|
|
|
|
S3method(trunc,mic)
|
2020-09-25 14:44:50 +02:00
|
|
|
S3method(unique,ab)
|
|
|
|
|
S3method(unique,disk)
|
2021-01-12 22:08:04 +01:00
|
|
|
S3method(unique,isolate_identifier)
|
2020-09-25 14:44:50 +02:00
|
|
|
S3method(unique,mic)
|
|
|
|
|
S3method(unique,mo)
|
|
|
|
|
S3method(unique,rsi)
|
2019-02-10 09:13:06 +01:00
|
|
|
export("%like%")
|
2019-09-15 22:57:30 +02:00
|
|
|
export("%like_case%")
|
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)
|
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)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(ab_synonyms)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(ab_tradenames)
|
2020-05-22 20:15:19 +02:00
|
|
|
export(ab_url)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(age)
|
|
|
|
|
export(age_groups)
|
2020-06-17 01:39:30 +02:00
|
|
|
export(aminoglycosides)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(anti_join_microorganisms)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(as.ab)
|
|
|
|
|
export(as.disk)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(as.mic)
|
|
|
|
|
export(as.mo)
|
|
|
|
|
export(as.rsi)
|
|
|
|
|
export(atc_online_ddd)
|
|
|
|
|
export(atc_online_groups)
|
|
|
|
|
export(atc_online_property)
|
|
|
|
|
export(availability)
|
|
|
|
|
export(brmo)
|
2019-08-25 22:53:22 +02:00
|
|
|
export(bug_drug_combinations)
|
2020-06-17 01:39:30 +02:00
|
|
|
export(carbapenems)
|
2019-02-20 00:04:48 +01:00
|
|
|
export(catalogue_of_life_version)
|
2020-06-17 01:39:30 +02:00
|
|
|
export(cephalosporins)
|
|
|
|
|
export(cephalosporins_1st)
|
|
|
|
|
export(cephalosporins_2nd)
|
|
|
|
|
export(cephalosporins_3rd)
|
|
|
|
|
export(cephalosporins_4th)
|
|
|
|
|
export(cephalosporins_5th)
|
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)
|
2019-11-10 12:16:56 +01:00
|
|
|
export(count_resistant)
|
|
|
|
|
export(count_susceptible)
|
2021-01-17 00:26:48 +01:00
|
|
|
export(custom_mdro_guideline)
|
2021-01-12 22:08:04 +01:00
|
|
|
export(eucast_dosage)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(eucast_exceptional_phenotypes)
|
|
|
|
|
export(eucast_rules)
|
|
|
|
|
export(facet_rsi)
|
2019-03-05 22:47:42 +01:00
|
|
|
export(filter_1st_cephalosporins)
|
|
|
|
|
export(filter_2nd_cephalosporins)
|
|
|
|
|
export(filter_3rd_cephalosporins)
|
|
|
|
|
export(filter_4th_cephalosporins)
|
2019-08-12 14:48:09 +02:00
|
|
|
export(filter_5th_cephalosporins)
|
2019-03-05 22:47:42 +01:00
|
|
|
export(filter_ab_class)
|
|
|
|
|
export(filter_aminoglycosides)
|
|
|
|
|
export(filter_carbapenems)
|
|
|
|
|
export(filter_cephalosporins)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(filter_first_isolate)
|
|
|
|
|
export(filter_first_weighted_isolate)
|
2019-03-05 22:47:42 +01:00
|
|
|
export(filter_fluoroquinolones)
|
|
|
|
|
export(filter_glycopeptides)
|
|
|
|
|
export(filter_macrolides)
|
2021-02-08 14:18:42 +01:00
|
|
|
export(filter_oxazolidinones)
|
2020-06-03 11:48:00 +02:00
|
|
|
export(filter_penicillins)
|
2019-03-05 22:47:42 +01:00
|
|
|
export(filter_tetracyclines)
|
2019-02-10 09:13:06 +01:00
|
|
|
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)
|
|
|
|
|
export(geom_rsi)
|
2020-12-27 00:07:00 +01:00
|
|
|
export(get_episode)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(get_locale)
|
|
|
|
|
export(get_mo_source)
|
2020-03-07 21:48:21 +01:00
|
|
|
export(ggplot_pca)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(ggplot_rsi)
|
|
|
|
|
export(ggplot_rsi_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.disk)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(is.mic)
|
|
|
|
|
export(is.mo)
|
|
|
|
|
export(is.rsi)
|
|
|
|
|
export(is.rsi.eligible)
|
2020-11-17 16:57:41 +01:00
|
|
|
export(is_new_episode)
|
2021-01-12 22:08:04 +01:00
|
|
|
export(isolate_identifier)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(key_antibiotics)
|
|
|
|
|
export(key_antibiotics_equal)
|
|
|
|
|
export(kurtosis)
|
|
|
|
|
export(labels_rsi_count)
|
|
|
|
|
export(left_join_microorganisms)
|
|
|
|
|
export(like)
|
2020-06-17 01:39:30 +02:00
|
|
|
export(macrolides)
|
2019-10-26 21:56:41 +02:00
|
|
|
export(mdr_cmi2012)
|
2019-05-23 16:58:59 +02:00
|
|
|
export(mdr_tb)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mdro)
|
|
|
|
|
export(mo_authors)
|
|
|
|
|
export(mo_class)
|
2020-06-22 11:18:40 +02:00
|
|
|
export(mo_domain)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mo_failures)
|
|
|
|
|
export(mo_family)
|
|
|
|
|
export(mo_fullname)
|
|
|
|
|
export(mo_genus)
|
|
|
|
|
export(mo_gramstain)
|
2019-06-11 14:18:25 +02:00
|
|
|
export(mo_info)
|
2020-11-16 11:03:24 +01:00
|
|
|
export(mo_is_gram_negative)
|
|
|
|
|
export(mo_is_gram_positive)
|
|
|
|
|
export(mo_is_intrinsic_resistant)
|
2021-01-12 22:08:04 +01:00
|
|
|
export(mo_is_yeast)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mo_kingdom)
|
2020-09-18 16:05:53 +02:00
|
|
|
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)
|
|
|
|
|
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)
|
|
|
|
|
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)
|
|
|
|
|
export(mo_subspecies)
|
2019-06-16 21:42:40 +02:00
|
|
|
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)
|
|
|
|
|
export(n_rsi)
|
2021-02-08 14:18:42 +01:00
|
|
|
export(oxazolidinones)
|
2019-09-03 09:47:39 +02:00
|
|
|
export(p_symbol)
|
2020-03-07 21:48:21 +01:00
|
|
|
export(pca)
|
2020-06-17 01:39:30 +02:00
|
|
|
export(penicillins)
|
2019-11-10 12:16:56 +01:00
|
|
|
export(proportion_I)
|
|
|
|
|
export(proportion_IR)
|
|
|
|
|
export(proportion_R)
|
|
|
|
|
export(proportion_S)
|
|
|
|
|
export(proportion_SI)
|
|
|
|
|
export(proportion_df)
|
2020-12-12 23:17:29 +01:00
|
|
|
export(random_disk)
|
|
|
|
|
export(random_mic)
|
|
|
|
|
export(random_rsi)
|
2019-11-10 12:16:56 +01:00
|
|
|
export(resistance)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(resistance_predict)
|
|
|
|
|
export(right_join_microorganisms)
|
2019-06-13 14:28:46 +02:00
|
|
|
export(rsi_df)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(rsi_predict)
|
|
|
|
|
export(scale_rsi_colours)
|
|
|
|
|
export(scale_y_percent)
|
|
|
|
|
export(semi_join_microorganisms)
|
|
|
|
|
export(set_mo_source)
|
|
|
|
|
export(skewness)
|
2019-11-10 12:16:56 +01:00
|
|
|
export(susceptibility)
|
2020-06-17 01:39:30 +02:00
|
|
|
export(tetracyclines)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(theme_rsi)
|
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)
|
2021-02-25 12:31:12 +01:00
|
|
|
importFrom(graphics,legend)
|
2021-02-25 10:33:08 +01:00
|
|
|
importFrom(graphics,mtext)
|
2020-09-25 14:44:50 +02:00
|
|
|
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)
|
