mirror of https://github.com/msberends/AMR.git
333 lines
7.8 KiB
Plaintext
Executable File
333 lines
7.8 KiB
Plaintext
Executable File
# Generated by roxygen2: do not edit by hand
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S3method("[",ab)
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S3method("[",mo)
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S3method("[<-",ab)
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S3method("[<-",mo)
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S3method("[[",ab)
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S3method("[[",mo)
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S3method("[[<-",ab)
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S3method("[[<-",mo)
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S3method(as.data.frame,ab)
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S3method(as.data.frame,mo)
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S3method(as.double,mic)
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S3method(as.integer,mic)
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S3method(as.numeric,mic)
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S3method(as.rsi,data.frame)
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S3method(as.rsi,default)
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S3method(as.rsi,disk)
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S3method(as.rsi,mic)
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S3method(barplot,mic)
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S3method(barplot,rsi)
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S3method(c,ab)
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S3method(c,mo)
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S3method(droplevels,mic)
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S3method(droplevels,rsi)
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S3method(format,bug_drug_combinations)
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S3method(freq,mo)
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S3method(freq,rsi)
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S3method(kurtosis,data.frame)
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S3method(kurtosis,default)
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S3method(kurtosis,matrix)
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S3method(pillar_shaft,ab)
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S3method(pillar_shaft,disk)
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S3method(pillar_shaft,mic)
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S3method(pillar_shaft,mo)
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S3method(pillar_shaft,rsi)
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S3method(plot,mic)
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S3method(plot,resistance_predict)
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S3method(plot,rsi)
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S3method(print,ab)
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S3method(print,bug_drug_combinations)
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S3method(print,catalogue_of_life_version)
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S3method(print,disk)
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S3method(print,mic)
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S3method(print,mo)
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S3method(print,mo_renamed)
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S3method(print,mo_uncertainties)
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S3method(print,rsi)
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S3method(skewness,data.frame)
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S3method(skewness,default)
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S3method(skewness,matrix)
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S3method(summary,mic)
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S3method(summary,mo)
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S3method(summary,rsi)
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S3method(type_sum,ab)
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S3method(type_sum,disk)
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S3method(type_sum,mic)
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S3method(type_sum,mo)
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S3method(type_sum,rsi)
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export("%like%")
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export("%like_case%")
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export(ab_atc)
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export(ab_atc_group1)
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export(ab_atc_group2)
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export(ab_cid)
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export(ab_ddd)
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export(ab_group)
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export(ab_info)
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export(ab_loinc)
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export(ab_name)
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export(ab_property)
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export(ab_synonyms)
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export(ab_tradenames)
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export(age)
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export(age_groups)
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export(anti_join_microorganisms)
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export(as.ab)
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export(as.disk)
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export(as.mic)
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export(as.mo)
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export(as.rsi)
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export(atc_online_ddd)
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export(atc_online_groups)
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export(atc_online_property)
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export(availability)
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export(brmo)
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export(bug_drug_combinations)
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export(catalogue_of_life_version)
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export(clear_mo_history)
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export(count_I)
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export(count_IR)
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export(count_R)
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export(count_S)
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export(count_SI)
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export(count_all)
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export(count_df)
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export(count_resistant)
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export(count_susceptible)
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export(eucast_exceptional_phenotypes)
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export(eucast_rules)
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export(facet_rsi)
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export(filter_1st_cephalosporins)
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export(filter_2nd_cephalosporins)
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export(filter_3rd_cephalosporins)
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export(filter_4th_cephalosporins)
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export(filter_5th_cephalosporins)
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export(filter_ab_class)
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export(filter_aminoglycosides)
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export(filter_carbapenems)
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export(filter_cephalosporins)
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export(filter_first_isolate)
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export(filter_first_weighted_isolate)
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export(filter_fluoroquinolones)
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export(filter_glycopeptides)
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export(filter_macrolides)
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export(filter_tetracyclines)
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export(first_isolate)
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export(freq)
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export(full_join_microorganisms)
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export(g.test)
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export(geom_rsi)
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export(get_locale)
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export(get_mo_source)
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export(ggplot_rsi)
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export(ggplot_rsi_predict)
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export(guess_ab_col)
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export(inner_join_microorganisms)
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export(is.ab)
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export(is.disk)
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export(is.mic)
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export(is.mo)
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export(is.rsi)
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export(is.rsi.eligible)
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export(key_antibiotics)
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export(key_antibiotics_equal)
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export(kurtosis)
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export(labels_rsi_count)
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export(left_join_microorganisms)
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export(like)
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export(mdr_cmi2012)
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export(mdr_tb)
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export(mdro)
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export(mo_authors)
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export(mo_class)
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export(mo_failures)
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export(mo_family)
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export(mo_fullname)
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export(mo_genus)
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export(mo_gramstain)
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export(mo_info)
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export(mo_kingdom)
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export(mo_name)
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export(mo_order)
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export(mo_phylum)
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export(mo_property)
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export(mo_rank)
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export(mo_ref)
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export(mo_renamed)
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export(mo_shortname)
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export(mo_species)
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export(mo_subspecies)
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export(mo_synonyms)
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export(mo_taxonomy)
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export(mo_type)
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export(mo_uncertainties)
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export(mo_url)
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export(mo_year)
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export(mrgn)
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export(n_rsi)
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export(p.symbol)
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export(p_symbol)
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export(portion_I)
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export(portion_IR)
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export(portion_R)
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export(portion_S)
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export(portion_SI)
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export(portion_df)
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export(proportion_I)
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export(proportion_IR)
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export(proportion_R)
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export(proportion_S)
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export(proportion_SI)
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export(proportion_df)
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export(read.4D)
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export(resistance)
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export(resistance_predict)
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export(right_join_microorganisms)
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export(rsi_df)
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export(rsi_predict)
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export(scale_rsi_colours)
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export(scale_type.ab)
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export(scale_type.mo)
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export(scale_y_percent)
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export(semi_join_microorganisms)
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export(set_mo_source)
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export(skewness)
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export(susceptibility)
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export(theme_rsi)
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exportMethods("[.ab")
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exportMethods("[.mo")
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exportMethods("[<-.ab")
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exportMethods("[<-.mo")
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exportMethods("[[.ab")
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exportMethods("[[.mo")
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exportMethods("[[<-.ab")
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exportMethods("[[<-.mo")
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exportMethods(as.data.frame.ab)
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exportMethods(as.data.frame.mo)
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exportMethods(as.double.mic)
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exportMethods(as.integer.mic)
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exportMethods(as.numeric.mic)
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exportMethods(barplot.mic)
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exportMethods(barplot.rsi)
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exportMethods(c.ab)
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exportMethods(c.mo)
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exportMethods(droplevels.mic)
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exportMethods(droplevels.rsi)
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exportMethods(format.bug_drug_combinations)
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exportMethods(freq.mo)
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exportMethods(freq.rsi)
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exportMethods(kurtosis)
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exportMethods(kurtosis.data.frame)
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exportMethods(kurtosis.default)
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exportMethods(kurtosis.matrix)
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exportMethods(plot.mic)
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exportMethods(plot.rsi)
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exportMethods(print.ab)
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exportMethods(print.bug_drug_combinations)
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exportMethods(print.catalogue_of_life_version)
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exportMethods(print.disk)
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exportMethods(print.mic)
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exportMethods(print.mo)
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exportMethods(print.mo_renamed)
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exportMethods(print.mo_uncertainties)
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exportMethods(print.rsi)
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exportMethods(scale_type.ab)
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exportMethods(scale_type.mo)
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exportMethods(skewness)
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exportMethods(skewness.data.frame)
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exportMethods(skewness.default)
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exportMethods(skewness.matrix)
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exportMethods(summary.mic)
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exportMethods(summary.mo)
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exportMethods(summary.rsi)
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importFrom(cleaner,freq)
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importFrom(cleaner,freq.default)
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importFrom(cleaner,percentage)
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importFrom(cleaner,top_freq)
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importFrom(crayon,bgGreen)
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importFrom(crayon,bgRed)
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importFrom(crayon,bgYellow)
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importFrom(crayon,black)
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importFrom(crayon,blue)
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importFrom(crayon,bold)
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importFrom(crayon,green)
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importFrom(crayon,italic)
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importFrom(crayon,magenta)
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importFrom(crayon,make_style)
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importFrom(crayon,red)
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importFrom(crayon,silver)
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importFrom(crayon,strip_style)
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importFrom(crayon,underline)
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importFrom(crayon,white)
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importFrom(crayon,yellow)
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importFrom(data.table,as.data.table)
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importFrom(data.table,data.table)
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importFrom(data.table,setkey)
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importFrom(dplyr,"%>%")
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importFrom(dplyr,all_vars)
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importFrom(dplyr,any_vars)
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importFrom(dplyr,arrange)
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importFrom(dplyr,arrange_at)
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importFrom(dplyr,between)
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importFrom(dplyr,bind_rows)
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importFrom(dplyr,case_when)
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importFrom(dplyr,desc)
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importFrom(dplyr,distinct)
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importFrom(dplyr,everything)
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importFrom(dplyr,filter)
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importFrom(dplyr,filter_all)
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importFrom(dplyr,filter_at)
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importFrom(dplyr,funs)
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importFrom(dplyr,group_by)
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importFrom(dplyr,group_by_at)
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importFrom(dplyr,group_vars)
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importFrom(dplyr,if_else)
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importFrom(dplyr,lag)
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importFrom(dplyr,left_join)
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importFrom(dplyr,mutate)
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importFrom(dplyr,mutate_all)
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importFrom(dplyr,mutate_at)
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importFrom(dplyr,n)
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importFrom(dplyr,n_distinct)
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importFrom(dplyr,n_groups)
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importFrom(dplyr,progress_estimated)
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importFrom(dplyr,pull)
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importFrom(dplyr,rename)
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importFrom(dplyr,row_number)
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importFrom(dplyr,select)
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importFrom(dplyr,select_if)
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importFrom(dplyr,slice)
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importFrom(dplyr,summarise)
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importFrom(dplyr,summarise_if)
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importFrom(dplyr,tibble)
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importFrom(dplyr,transmute)
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importFrom(dplyr,ungroup)
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importFrom(dplyr,vars)
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importFrom(graphics,arrows)
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importFrom(graphics,axis)
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importFrom(graphics,barplot)
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importFrom(graphics,par)
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importFrom(graphics,plot)
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importFrom(graphics,points)
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importFrom(graphics,text)
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importFrom(knitr,kable)
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importFrom(microbenchmark,microbenchmark)
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importFrom(pillar,pillar_shaft)
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importFrom(pillar,type_sum)
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importFrom(rlang,as_label)
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importFrom(rlang,enquos)
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importFrom(stats,complete.cases)
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importFrom(stats,glm)
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importFrom(stats,lm)
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importFrom(stats,pchisq)
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importFrom(stats,predict)
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importFrom(tidyr,pivot_longer)
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importFrom(tidyr,pivot_wider)
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importFrom(utils,adist)
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importFrom(utils,browseURL)
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importFrom(utils,menu)
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importFrom(utils,read.csv)
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importFrom(utils,write.csv)
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