2018-02-21 11:52:31 +01:00
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# Generated by roxygen2: do not edit by hand
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2019-08-12 14:48:09 +02:00
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S3method("[",ab)
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2020-03-14 14:05:43 +01:00
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S3method("[",disk)
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2020-04-13 21:09:56 +02:00
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S3method("[",mic)
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2019-08-12 14:48:09 +02:00
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S3method("[",mo)
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2019-08-14 14:57:06 +02:00
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S3method("[<-",ab)
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2020-03-14 14:05:43 +01:00
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S3method("[<-",disk)
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2020-04-13 21:09:56 +02:00
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S3method("[<-",mic)
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2019-08-14 14:57:06 +02:00
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S3method("[<-",mo)
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2020-04-13 21:09:56 +02:00
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S3method("[<-",rsi)
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2019-08-14 14:57:06 +02:00
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S3method("[[",ab)
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2020-03-14 14:05:43 +01:00
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S3method("[[",disk)
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2020-04-13 21:09:56 +02:00
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S3method("[[",mic)
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2019-08-14 14:57:06 +02:00
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S3method("[[",mo)
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S3method("[[<-",ab)
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2020-03-14 14:05:43 +01:00
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S3method("[[<-",disk)
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2020-04-13 21:09:56 +02:00
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S3method("[[<-",mic)
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2019-08-14 14:57:06 +02:00
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S3method("[[<-",mo)
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2020-04-13 21:09:56 +02:00
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S3method("[[<-",rsi)
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2019-05-10 16:44:59 +02:00
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S3method(as.data.frame,ab)
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2020-03-14 14:05:43 +01:00
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S3method(as.data.frame,disk)
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2019-02-10 09:13:06 +01:00
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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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2019-05-10 16:44:59 +02:00
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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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2019-02-10 09:13:06 +01:00
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S3method(barplot,mic)
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S3method(barplot,rsi)
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2019-08-14 14:57:06 +02:00
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S3method(c,ab)
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2020-03-14 14:05:43 +01:00
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S3method(c,disk)
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2020-04-13 21:09:56 +02:00
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S3method(c,mic)
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2019-08-14 14:57:06 +02:00
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S3method(c,mo)
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2020-04-13 21:09:56 +02:00
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S3method(c,rsi)
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2019-02-10 09:13:06 +01:00
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S3method(droplevels,mic)
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S3method(droplevels,rsi)
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2019-08-27 22:41:09 +02:00
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S3method(format,bug_drug_combinations)
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2019-07-29 13:33:48 +02:00
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S3method(freq,mo)
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S3method(freq,rsi)
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2019-02-10 09:13:06 +01:00
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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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2019-08-07 15:37:39 +02:00
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S3method(pillar_shaft,ab)
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2019-08-12 14:48:09 +02:00
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S3method(pillar_shaft,disk)
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2019-08-07 15:37:39 +02:00
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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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2019-02-10 09:13:06 +01:00
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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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2019-05-10 16:44:59 +02:00
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S3method(print,ab)
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2019-08-27 22:41:09 +02:00
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S3method(print,bug_drug_combinations)
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2019-03-26 14:24:03 +01:00
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S3method(print,catalogue_of_life_version)
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2019-05-10 16:44:59 +02:00
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S3method(print,disk)
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2019-02-10 09:13:06 +01:00
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S3method(print,mic)
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S3method(print,mo)
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2019-02-28 13:56:28 +01:00
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S3method(print,mo_renamed)
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S3method(print,mo_uncertainties)
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2019-02-10 09:13:06 +01:00
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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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2020-03-14 14:05:43 +01:00
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S3method(vec_cast,character.mo)
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S3method(vec_cast,mo)
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S3method(vec_cast,mo.character)
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S3method(vec_cast,mo.mo)
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S3method(vec_ptype2,mo)
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S3method(vec_ptype_abbr,ab)
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S3method(vec_ptype_abbr,disk)
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S3method(vec_ptype_abbr,mic)
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S3method(vec_ptype_abbr,mo)
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S3method(vec_ptype_abbr,rsi)
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S3method(vec_ptype_full,ab)
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S3method(vec_ptype_full,disk)
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S3method(vec_ptype_full,mic)
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S3method(vec_ptype_full,mo)
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S3method(vec_ptype_full,rsi)
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2019-02-10 09:13:06 +01:00
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export("%like%")
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2019-09-15 22:57:30 +02:00
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export("%like_case%")
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2019-02-10 09:13:06 +01:00
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export(ab_atc)
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2019-05-10 16:44:59 +02:00
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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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2019-05-16 22:07:31 +02:00
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export(ab_info)
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2020-01-26 20:20:00 +01:00
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export(ab_loinc)
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2019-02-10 09:13:06 +01:00
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export(ab_name)
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export(ab_property)
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2019-05-10 16:44:59 +02:00
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export(ab_synonyms)
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2019-02-10 09:13:06 +01:00
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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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2019-05-10 16:44:59 +02:00
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export(as.ab)
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export(as.disk)
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2019-02-10 09:13:06 +01:00
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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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2019-08-25 22:53:22 +02:00
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export(bug_drug_combinations)
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2019-02-20 00:04:48 +01:00
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export(catalogue_of_life_version)
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2019-02-10 09:13:06 +01:00
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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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2019-11-10 12:16:56 +01:00
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export(count_resistant)
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export(count_susceptible)
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2019-02-10 09:13:06 +01:00
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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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2019-03-05 22:47:42 +01:00
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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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2019-08-12 14:48:09 +02:00
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export(filter_5th_cephalosporins)
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2019-03-05 22:47:42 +01:00
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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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2019-02-10 09:13:06 +01:00
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export(filter_first_isolate)
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export(filter_first_weighted_isolate)
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2019-03-05 22:47:42 +01:00
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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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2019-02-10 09:13:06 +01:00
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export(first_isolate)
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2019-08-25 22:53:22 +02:00
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export(freq)
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2019-02-10 09:13:06 +01:00
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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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2020-03-07 21:48:21 +01:00
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export(ggplot_pca)
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2019-02-10 09:13:06 +01:00
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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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2019-05-10 16:44:59 +02:00
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export(is.ab)
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export(is.disk)
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2019-02-10 09:13:06 +01:00
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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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2019-10-26 21:56:41 +02:00
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export(mdr_cmi2012)
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2019-05-23 16:58:59 +02:00
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export(mdr_tb)
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2019-02-10 09:13:06 +01:00
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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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2019-06-11 14:18:25 +02:00
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export(mo_info)
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2019-02-10 09:13:06 +01:00
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export(mo_kingdom)
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2019-05-13 12:21:57 +02:00
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export(mo_name)
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2019-02-10 09:13:06 +01:00
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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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2019-02-22 22:12:10 +01:00
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export(mo_rank)
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2019-02-10 09:13:06 +01:00
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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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2020-01-27 19:14:23 +01:00
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export(mo_snomed)
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2019-02-10 09:13:06 +01:00
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export(mo_species)
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export(mo_subspecies)
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2019-06-16 21:42:40 +02:00
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export(mo_synonyms)
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2019-02-10 09:13:06 +01:00
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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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2019-02-20 00:04:48 +01:00
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export(mo_url)
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2019-02-10 09:13:06 +01:00
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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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2019-09-03 09:47:39 +02:00
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export(p_symbol)
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2020-03-07 21:48:21 +01:00
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export(pca)
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2019-02-10 09:13:06 +01:00
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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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2019-11-28 22:32:17 +01:00
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export(portion_df)
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2019-11-10 12:16:56 +01:00
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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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2019-02-10 09:13:06 +01:00
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export(read.4D)
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2019-11-10 12:16:56 +01:00
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export(resistance)
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2019-02-10 09:13:06 +01:00
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export(resistance_predict)
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export(right_join_microorganisms)
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2019-06-13 14:28:46 +02:00
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export(rsi_df)
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2019-02-10 09:13:06 +01:00
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export(rsi_predict)
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export(scale_rsi_colours)
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2019-06-08 23:50:06 +02:00
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export(scale_type.ab)
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export(scale_type.mo)
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2019-02-10 09:13:06 +01:00
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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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2019-11-10 12:16:56 +01:00
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export(susceptibility)
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2019-02-10 09:13:06 +01:00
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export(theme_rsi)
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2019-08-12 14:48:09 +02:00
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exportMethods("[.ab")
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2020-03-14 14:05:43 +01:00
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exportMethods("[.disk")
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2020-04-13 21:09:56 +02:00
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exportMethods("[.mic")
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2019-08-12 14:48:09 +02:00
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exportMethods("[.mo")
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2019-08-14 14:57:06 +02:00
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exportMethods("[<-.ab")
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2020-03-14 14:05:43 +01:00
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exportMethods("[<-.disk")
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2020-04-13 21:09:56 +02:00
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exportMethods("[<-.mic")
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2019-08-14 14:57:06 +02:00
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exportMethods("[<-.mo")
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2020-04-13 21:09:56 +02:00
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exportMethods("[<-.rsi")
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2019-08-14 14:57:06 +02:00
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exportMethods("[[.ab")
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2020-03-14 14:05:43 +01:00
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exportMethods("[[.disk")
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2020-04-13 21:09:56 +02:00
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exportMethods("[[.mic")
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2019-08-14 14:57:06 +02:00
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exportMethods("[[.mo")
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exportMethods("[[<-.ab")
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2020-03-14 14:05:43 +01:00
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exportMethods("[[<-.disk")
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2020-04-13 21:09:56 +02:00
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exportMethods("[[<-.mic")
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2019-08-14 14:57:06 +02:00
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exportMethods("[[<-.mo")
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2020-04-13 21:09:56 +02:00
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exportMethods("[[<-.rsi")
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2019-05-10 16:44:59 +02:00
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exportMethods(as.data.frame.ab)
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2020-03-14 14:05:43 +01:00
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exportMethods(as.data.frame.disk)
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2019-02-10 09:13:06 +01:00
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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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2019-08-14 14:57:06 +02:00
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exportMethods(c.ab)
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2020-03-14 14:05:43 +01:00
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exportMethods(c.disk)
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2020-04-13 21:09:56 +02:00
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exportMethods(c.mic)
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2019-08-14 14:57:06 +02:00
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exportMethods(c.mo)
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2020-04-13 21:09:56 +02:00
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exportMethods(c.rsi)
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2019-02-10 09:13:06 +01:00
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exportMethods(droplevels.mic)
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exportMethods(droplevels.rsi)
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2019-08-27 22:41:09 +02:00
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exportMethods(format.bug_drug_combinations)
|
2019-07-29 13:33:48 +02:00
|
|
|
exportMethods(freq.mo)
|
|
|
|
|
exportMethods(freq.rsi)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(kurtosis)
|
|
|
|
|
exportMethods(kurtosis.data.frame)
|
|
|
|
|
exportMethods(kurtosis.default)
|
|
|
|
|
exportMethods(kurtosis.matrix)
|
|
|
|
|
exportMethods(plot.mic)
|
|
|
|
|
exportMethods(plot.rsi)
|
2019-05-10 16:44:59 +02:00
|
|
|
exportMethods(print.ab)
|
2019-08-27 22:41:09 +02:00
|
|
|
exportMethods(print.bug_drug_combinations)
|
2019-03-26 14:24:03 +01:00
|
|
|
exportMethods(print.catalogue_of_life_version)
|
2019-05-10 16:44:59 +02:00
|
|
|
exportMethods(print.disk)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(print.mic)
|
|
|
|
|
exportMethods(print.mo)
|
2019-02-28 13:56:28 +01:00
|
|
|
exportMethods(print.mo_renamed)
|
|
|
|
|
exportMethods(print.mo_uncertainties)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(print.rsi)
|
2019-06-07 22:47:37 +02:00
|
|
|
exportMethods(scale_type.ab)
|
|
|
|
|
exportMethods(scale_type.mo)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(skewness)
|
|
|
|
|
exportMethods(skewness.data.frame)
|
|
|
|
|
exportMethods(skewness.default)
|
|
|
|
|
exportMethods(skewness.matrix)
|
|
|
|
|
exportMethods(summary.mic)
|
|
|
|
|
exportMethods(summary.mo)
|
|
|
|
|
exportMethods(summary.rsi)
|
2020-03-14 14:05:43 +01:00
|
|
|
importFrom(R6,R6Class)
|
2019-11-03 22:24:42 +01:00
|
|
|
importFrom(cleaner,freq)
|
|
|
|
|
importFrom(cleaner,freq.default)
|
|
|
|
|
importFrom(cleaner,percentage)
|
|
|
|
|
importFrom(cleaner,top_freq)
|
2018-10-17 17:32:34 +02:00
|
|
|
importFrom(crayon,bgGreen)
|
|
|
|
|
importFrom(crayon,bgRed)
|
|
|
|
|
importFrom(crayon,bgYellow)
|
|
|
|
|
importFrom(crayon,black)
|
|
|
|
|
importFrom(crayon,blue)
|
|
|
|
|
importFrom(crayon,bold)
|
|
|
|
|
importFrom(crayon,green)
|
2018-11-01 20:23:33 +01:00
|
|
|
importFrom(crayon,italic)
|
2018-12-06 14:36:39 +01:00
|
|
|
importFrom(crayon,magenta)
|
2019-08-20 11:40:54 +02:00
|
|
|
importFrom(crayon,make_style)
|
2018-10-18 12:10:10 +02:00
|
|
|
importFrom(crayon,red)
|
|
|
|
|
importFrom(crayon,silver)
|
2018-11-08 16:10:03 +01:00
|
|
|
importFrom(crayon,strip_style)
|
2019-03-18 14:29:41 +01:00
|
|
|
importFrom(crayon,underline)
|
2019-03-26 14:24:03 +01:00
|
|
|
importFrom(crayon,white)
|
2019-02-28 13:56:28 +01:00
|
|
|
importFrom(crayon,yellow)
|
2018-09-24 23:33:29 +02:00
|
|
|
importFrom(data.table,as.data.table)
|
|
|
|
|
importFrom(data.table,data.table)
|
|
|
|
|
importFrom(data.table,setkey)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,"%>%")
|
2018-10-19 13:53:31 +02:00
|
|
|
importFrom(dplyr,all_vars)
|
|
|
|
|
importFrom(dplyr,any_vars)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,arrange)
|
|
|
|
|
importFrom(dplyr,arrange_at)
|
|
|
|
|
importFrom(dplyr,between)
|
2018-08-12 22:34:03 +02:00
|
|
|
importFrom(dplyr,bind_rows)
|
2018-07-28 09:34:03 +02:00
|
|
|
importFrom(dplyr,case_when)
|
2019-07-29 17:34:57 +02:00
|
|
|
importFrom(dplyr,desc)
|
2019-02-27 14:22:07 +01:00
|
|
|
importFrom(dplyr,distinct)
|
2018-08-12 22:34:03 +02:00
|
|
|
importFrom(dplyr,everything)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,filter)
|
2018-10-19 13:53:31 +02:00
|
|
|
importFrom(dplyr,filter_all)
|
2018-11-08 16:10:03 +01:00
|
|
|
importFrom(dplyr,filter_at)
|
2018-10-19 13:53:31 +02:00
|
|
|
importFrom(dplyr,funs)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,group_by)
|
|
|
|
|
importFrom(dplyr,group_by_at)
|
2018-08-12 22:34:03 +02:00
|
|
|
importFrom(dplyr,group_vars)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,if_else)
|
|
|
|
|
importFrom(dplyr,lag)
|
|
|
|
|
importFrom(dplyr,left_join)
|
|
|
|
|
importFrom(dplyr,mutate)
|
2018-10-19 13:53:31 +02:00
|
|
|
importFrom(dplyr,mutate_all)
|
2018-10-18 12:10:10 +02:00
|
|
|
importFrom(dplyr,mutate_at)
|
2018-12-22 22:39:34 +01:00
|
|
|
importFrom(dplyr,n)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,n_distinct)
|
2019-01-15 12:45:24 +01:00
|
|
|
importFrom(dplyr,n_groups)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,pull)
|
2019-08-25 22:53:22 +02:00
|
|
|
importFrom(dplyr,rename)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,row_number)
|
|
|
|
|
importFrom(dplyr,select)
|
2018-08-22 00:02:26 +02:00
|
|
|
importFrom(dplyr,select_if)
|
2018-02-21 12:10:00 +01:00
|
|
|
importFrom(dplyr,slice)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,summarise)
|
2018-08-11 21:30:00 +02:00
|
|
|
importFrom(dplyr,summarise_if)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,tibble)
|
2019-01-15 16:38:54 +01:00
|
|
|
importFrom(dplyr,transmute)
|
2019-07-29 17:34:57 +02:00
|
|
|
importFrom(dplyr,ungroup)
|
2018-10-18 12:10:10 +02:00
|
|
|
importFrom(dplyr,vars)
|
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)
|
2019-06-18 19:28:26 +02:00
|
|
|
importFrom(graphics,par)
|
2018-02-21 11:52:31 +01:00
|
|
|
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)
|
2019-10-11 17:21:02 +02:00
|
|
|
importFrom(knitr,kable)
|
2019-04-05 18:47:39 +02:00
|
|
|
importFrom(microbenchmark,microbenchmark)
|
2019-08-07 15:37:39 +02:00
|
|
|
importFrom(pillar,pillar_shaft)
|
2019-01-29 20:20:09 +01:00
|
|
|
importFrom(rlang,as_label)
|
2019-01-28 11:20:32 +01:00
|
|
|
importFrom(rlang,enquos)
|
2020-03-07 21:48:21 +01:00
|
|
|
importFrom(rlang,eval_tidy)
|
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)
|
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)
|
|
|
|
|
importFrom(stats,var)
|
2019-11-11 10:46:39 +01:00
|
|
|
importFrom(tidyr,pivot_longer)
|
|
|
|
|
importFrom(tidyr,pivot_wider)
|
2019-11-15 15:25:03 +01:00
|
|
|
importFrom(utils,adist)
|
2019-02-22 22:12:10 +01:00
|
|
|
importFrom(utils,browseURL)
|
2019-08-06 15:57:51 +02:00
|
|
|
importFrom(utils,menu)
|
2020-03-14 14:05:43 +01:00
|
|
|
importFrom(vctrs,vec_cast)
|
|
|
|
|
importFrom(vctrs,vec_ptype2)
|
|
|
|
|
importFrom(vctrs,vec_ptype_abbr)
|
|
|
|
|
importFrom(vctrs,vec_ptype_full)
|
