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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2021-01-12 22:08:04 +01:00
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S3method("[",isolate_identifier)
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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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2021-01-12 22:08:04 +01:00
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S3method("[<-",isolate_identifier)
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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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2021-01-12 22:08:04 +01:00
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S3method("[[",isolate_identifier)
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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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2021-01-12 22:08:04 +01:00
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S3method("[[<-",isolate_identifier)
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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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2021-01-22 10:20:41 +01:00
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S3method(all.equal,isolate_identifier)
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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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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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2021-01-12 22:08:04 +01:00
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S3method(c,isolate_identifier)
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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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2019-02-10 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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2020-12-12 23:17:29 +01:00
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S3method(plot,disk)
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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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2021-01-17 00:26:48 +01:00
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S3method(print,custom_mdro_guideline)
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2019-05-10 16:44:59 +02:00
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S3method(print,disk)
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2021-01-12 22:08:04 +01:00
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S3method(print,isolate_identifier)
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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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2021-01-28 16:09:30 +01:00
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S3method(print,pca)
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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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2021-01-28 16:09:30 +01:00
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S3method(summary,pca)
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2019-02-10 09:13:06 +01:00
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S3method(summary,rsi)
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2020-09-25 14:44:50 +02:00
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S3method(unique,ab)
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S3method(unique,disk)
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2021-01-12 22:08:04 +01:00
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S3method(unique,isolate_identifier)
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2020-09-25 14:44:50 +02:00
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S3method(unique,mic)
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S3method(unique,mo)
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S3method(unique,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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2020-06-17 15:14:37 +02:00
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export(ab_class)
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2019-05-10 16:44:59 +02:00
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export(ab_ddd)
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2020-06-25 19:20:50 +02:00
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export(ab_from_text)
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2019-05-10 16:44:59 +02:00
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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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2020-05-22 20:15:19 +02:00
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export(ab_url)
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2019-02-10 09:13:06 +01:00
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export(age)
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export(age_groups)
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2020-06-17 01:39:30 +02:00
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export(aminoglycosides)
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2019-02-10 09:13:06 +01:00
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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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2020-06-17 01:39:30 +02:00
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export(carbapenems)
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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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2020-06-17 01:39:30 +02:00
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export(cephalosporins)
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export(cephalosporins_1st)
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export(cephalosporins_2nd)
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export(cephalosporins_3rd)
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export(cephalosporins_4th)
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export(cephalosporins_5th)
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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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2021-01-17 00:26:48 +01:00
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export(custom_mdro_guideline)
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2021-01-12 22:08:04 +01:00
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export(eucast_dosage)
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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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2021-02-08 14:18:42 +01:00
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export(filter_oxazolidinones)
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2020-06-03 11:48:00 +02:00
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export(filter_penicillins)
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2019-03-05 22:47:42 +01:00
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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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2020-06-17 01:39:30 +02:00
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export(fluoroquinolones)
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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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2020-12-27 00:07:00 +01:00
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export(get_episode)
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2019-02-10 09:13:06 +01:00
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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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2020-06-17 01:39:30 +02:00
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export(glycopeptides)
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2019-02-10 09:13:06 +01:00
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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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2020-11-17 16:57:41 +01:00
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export(is_new_episode)
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2021-01-12 22:08:04 +01:00
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export(isolate_identifier)
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2019-02-10 09:13:06 +01:00
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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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2020-06-17 01:39:30 +02:00
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export(macrolides)
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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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2020-06-22 11:18:40 +02:00
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export(mo_domain)
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2019-02-10 09:13:06 +01:00
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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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2020-11-16 11:03:24 +01:00
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export(mo_is_gram_negative)
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export(mo_is_gram_positive)
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export(mo_is_intrinsic_resistant)
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2021-01-12 22:08:04 +01:00
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export(mo_is_yeast)
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2019-02-10 09:13:06 +01:00
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export(mo_kingdom)
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2020-09-18 16:05:53 +02:00
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export(mo_matching_score)
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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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2021-02-08 14:18:42 +01:00
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export(oxazolidinones)
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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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2020-06-17 01:39:30 +02:00
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export(penicillins)
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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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2020-12-12 23:17:29 +01:00
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export(random_disk)
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export(random_mic)
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export(random_rsi)
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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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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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2020-06-17 01:39:30 +02:00
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export(tetracyclines)
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2019-02-10 09:13:06 +01:00
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export(theme_rsi)
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2019-01-15 12:45:24 +01:00
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importFrom(graphics,arrows)
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2018-03-13 15:40:10 +01:00
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importFrom(graphics,axis)
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importFrom(graphics,barplot)
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2019-06-18 19:28:26 +02:00
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importFrom(graphics,par)
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2020-09-25 14:44:50 +02:00
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importFrom(graphics,plot)
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2019-02-11 10:27:10 +01:00
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importFrom(graphics,points)
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2018-02-21 11:52:31 +01:00
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importFrom(graphics,text)
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2018-07-10 12:27:07 +02:00
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importFrom(stats,complete.cases)
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2018-07-26 16:30:42 +02:00
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importFrom(stats,glm)
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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)
|
