2018-02-21 11:52:31 +01:00
|
|
|
# Generated by roxygen2: do not edit by hand
|
|
|
|
|
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(as.data.frame,ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(as.data.frame,atc)
|
2019-05-29 19:56:17 +02:00
|
|
|
S3method(as.data.frame,freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(as.data.frame,mo)
|
|
|
|
|
S3method(as.double,mic)
|
|
|
|
|
S3method(as.integer,mic)
|
|
|
|
|
S3method(as.numeric,mic)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(as.rsi,data.frame)
|
|
|
|
|
S3method(as.rsi,default)
|
|
|
|
|
S3method(as.rsi,disk)
|
|
|
|
|
S3method(as.rsi,mic)
|
2019-05-29 19:56:17 +02:00
|
|
|
S3method(as.vector,freq)
|
|
|
|
|
S3method(as_tibble,freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(barplot,mic)
|
|
|
|
|
S3method(barplot,rsi)
|
2019-05-29 19:56:17 +02:00
|
|
|
S3method(boxplot,freq)
|
|
|
|
|
S3method(diff,freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(droplevels,mic)
|
|
|
|
|
S3method(droplevels,rsi)
|
2019-05-29 19:56:17 +02:00
|
|
|
S3method(format,freq)
|
|
|
|
|
S3method(hist,freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(kurtosis,data.frame)
|
|
|
|
|
S3method(kurtosis,default)
|
|
|
|
|
S3method(kurtosis,matrix)
|
2019-05-29 19:56:17 +02:00
|
|
|
S3method(plot,freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(plot,mic)
|
|
|
|
|
S3method(plot,resistance_predict)
|
|
|
|
|
S3method(plot,rsi)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(print,ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(print,atc)
|
2019-03-26 14:24:03 +01:00
|
|
|
S3method(print,catalogue_of_life_version)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(print,disk)
|
2019-05-29 19:56:17 +02:00
|
|
|
S3method(print,freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(print,frequency_tbl)
|
|
|
|
|
S3method(print,mic)
|
|
|
|
|
S3method(print,mo)
|
2019-02-28 13:56:28 +01:00
|
|
|
S3method(print,mo_renamed)
|
|
|
|
|
S3method(print,mo_uncertainties)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(print,rsi)
|
2019-05-10 16:44:59 +02:00
|
|
|
S3method(pull,ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(pull,atc)
|
|
|
|
|
S3method(pull,mo)
|
2019-05-29 19:56:17 +02:00
|
|
|
S3method(select,freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
S3method(skewness,data.frame)
|
|
|
|
|
S3method(skewness,default)
|
|
|
|
|
S3method(skewness,matrix)
|
|
|
|
|
S3method(summary,mic)
|
|
|
|
|
S3method(summary,mo)
|
|
|
|
|
S3method(summary,rsi)
|
|
|
|
|
export("%like%")
|
|
|
|
|
export(ab_atc)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(ab_atc_group1)
|
|
|
|
|
export(ab_atc_group2)
|
|
|
|
|
export(ab_cid)
|
|
|
|
|
export(ab_ddd)
|
|
|
|
|
export(ab_group)
|
2019-05-16 22:07:31 +02:00
|
|
|
export(ab_info)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(ab_name)
|
|
|
|
|
export(ab_official)
|
|
|
|
|
export(ab_property)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(ab_synonyms)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(ab_tradenames)
|
|
|
|
|
export(abname)
|
|
|
|
|
export(age)
|
|
|
|
|
export(age_groups)
|
|
|
|
|
export(anti_join_microorganisms)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(as.ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(as.atc)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(as.disk)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(as.mic)
|
|
|
|
|
export(as.mo)
|
|
|
|
|
export(as.rsi)
|
|
|
|
|
export(atc_name)
|
|
|
|
|
export(atc_official)
|
|
|
|
|
export(atc_online_ddd)
|
|
|
|
|
export(atc_online_groups)
|
|
|
|
|
export(atc_online_property)
|
|
|
|
|
export(atc_property)
|
|
|
|
|
export(atc_tradenames)
|
|
|
|
|
export(atc_trivial_nl)
|
|
|
|
|
export(availability)
|
|
|
|
|
export(brmo)
|
2019-02-20 00:04:48 +01:00
|
|
|
export(catalogue_of_life_version)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(count_I)
|
|
|
|
|
export(count_IR)
|
|
|
|
|
export(count_R)
|
|
|
|
|
export(count_S)
|
|
|
|
|
export(count_SI)
|
|
|
|
|
export(count_all)
|
|
|
|
|
export(count_df)
|
|
|
|
|
export(eucast_exceptional_phenotypes)
|
|
|
|
|
export(eucast_rules)
|
|
|
|
|
export(facet_rsi)
|
2019-03-05 22:47:42 +01:00
|
|
|
export(filter_1st_cephalosporins)
|
|
|
|
|
export(filter_2nd_cephalosporins)
|
|
|
|
|
export(filter_3rd_cephalosporins)
|
|
|
|
|
export(filter_4th_cephalosporins)
|
|
|
|
|
export(filter_ab_class)
|
|
|
|
|
export(filter_aminoglycosides)
|
|
|
|
|
export(filter_carbapenems)
|
|
|
|
|
export(filter_cephalosporins)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(filter_first_isolate)
|
|
|
|
|
export(filter_first_weighted_isolate)
|
2019-03-05 22:47:42 +01:00
|
|
|
export(filter_fluoroquinolones)
|
|
|
|
|
export(filter_glycopeptides)
|
|
|
|
|
export(filter_macrolides)
|
|
|
|
|
export(filter_tetracyclines)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(first_isolate)
|
|
|
|
|
export(freq)
|
|
|
|
|
export(frequency_tbl)
|
|
|
|
|
export(full_join_microorganisms)
|
|
|
|
|
export(g.test)
|
|
|
|
|
export(geom_rsi)
|
|
|
|
|
export(get_locale)
|
|
|
|
|
export(get_mo_source)
|
|
|
|
|
export(ggplot_rsi)
|
|
|
|
|
export(ggplot_rsi_predict)
|
|
|
|
|
export(guess_ab_col)
|
|
|
|
|
export(header)
|
|
|
|
|
export(inner_join_microorganisms)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(is.ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(is.atc)
|
2019-05-10 16:44:59 +02:00
|
|
|
export(is.disk)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(is.mic)
|
|
|
|
|
export(is.mo)
|
|
|
|
|
export(is.rsi)
|
|
|
|
|
export(is.rsi.eligible)
|
|
|
|
|
export(key_antibiotics)
|
|
|
|
|
export(key_antibiotics_equal)
|
|
|
|
|
export(kurtosis)
|
|
|
|
|
export(labels_rsi_count)
|
|
|
|
|
export(left_join_microorganisms)
|
|
|
|
|
export(like)
|
2019-05-23 16:58:59 +02:00
|
|
|
export(mdr_tb)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mdro)
|
|
|
|
|
export(mo_authors)
|
|
|
|
|
export(mo_class)
|
|
|
|
|
export(mo_failures)
|
|
|
|
|
export(mo_family)
|
|
|
|
|
export(mo_fullname)
|
|
|
|
|
export(mo_genus)
|
|
|
|
|
export(mo_gramstain)
|
2019-06-11 14:18:25 +02:00
|
|
|
export(mo_info)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mo_kingdom)
|
2019-05-13 12:21:57 +02:00
|
|
|
export(mo_name)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mo_order)
|
|
|
|
|
export(mo_phylum)
|
|
|
|
|
export(mo_property)
|
2019-02-22 22:12:10 +01:00
|
|
|
export(mo_rank)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mo_ref)
|
|
|
|
|
export(mo_renamed)
|
|
|
|
|
export(mo_shortname)
|
|
|
|
|
export(mo_species)
|
|
|
|
|
export(mo_subspecies)
|
2019-06-16 21:42:40 +02:00
|
|
|
export(mo_synonyms)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mo_taxonomy)
|
|
|
|
|
export(mo_type)
|
|
|
|
|
export(mo_uncertainties)
|
2019-02-20 00:04:48 +01:00
|
|
|
export(mo_url)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(mo_year)
|
|
|
|
|
export(mrgn)
|
|
|
|
|
export(n_rsi)
|
|
|
|
|
export(p.symbol)
|
|
|
|
|
export(portion_I)
|
|
|
|
|
export(portion_IR)
|
|
|
|
|
export(portion_R)
|
|
|
|
|
export(portion_S)
|
|
|
|
|
export(portion_SI)
|
|
|
|
|
export(portion_df)
|
|
|
|
|
export(ratio)
|
|
|
|
|
export(read.4D)
|
|
|
|
|
export(resistance_predict)
|
|
|
|
|
export(right_join_microorganisms)
|
2019-06-13 14:28:46 +02:00
|
|
|
export(rsi_df)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(rsi_predict)
|
|
|
|
|
export(scale_rsi_colours)
|
2019-06-08 23:50:06 +02:00
|
|
|
export(scale_type.ab)
|
|
|
|
|
export(scale_type.mo)
|
2019-02-10 09:13:06 +01:00
|
|
|
export(scale_y_percent)
|
|
|
|
|
export(semi_join_microorganisms)
|
|
|
|
|
export(set_mo_source)
|
|
|
|
|
export(skewness)
|
|
|
|
|
export(theme_rsi)
|
|
|
|
|
export(top_freq)
|
2019-05-10 16:44:59 +02:00
|
|
|
exportMethods(as.data.frame.ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(as.data.frame.atc)
|
2019-05-29 19:56:17 +02:00
|
|
|
exportMethods(as.data.frame.freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(as.data.frame.mo)
|
|
|
|
|
exportMethods(as.double.mic)
|
|
|
|
|
exportMethods(as.integer.mic)
|
|
|
|
|
exportMethods(as.numeric.mic)
|
2019-05-29 19:56:17 +02:00
|
|
|
exportMethods(as.vector.freq)
|
|
|
|
|
exportMethods(as_tibble.freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(barplot.mic)
|
|
|
|
|
exportMethods(barplot.rsi)
|
2019-05-29 19:56:17 +02:00
|
|
|
exportMethods(boxplot.freq)
|
|
|
|
|
exportMethods(diff.freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(droplevels.mic)
|
|
|
|
|
exportMethods(droplevels.rsi)
|
2019-05-29 19:56:17 +02:00
|
|
|
exportMethods(format.freq)
|
|
|
|
|
exportMethods(hist.freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(kurtosis)
|
|
|
|
|
exportMethods(kurtosis.data.frame)
|
|
|
|
|
exportMethods(kurtosis.default)
|
|
|
|
|
exportMethods(kurtosis.matrix)
|
2019-05-29 19:56:17 +02:00
|
|
|
exportMethods(plot.freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(plot.mic)
|
|
|
|
|
exportMethods(plot.rsi)
|
2019-05-10 16:44:59 +02:00
|
|
|
exportMethods(print.ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(print.atc)
|
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)
|
2019-05-29 19:56:17 +02:00
|
|
|
exportMethods(print.freq)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(print.frequency_tbl)
|
|
|
|
|
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)
|
2019-05-10 16:44:59 +02:00
|
|
|
exportMethods(pull.ab)
|
2019-02-10 09:13:06 +01:00
|
|
|
exportMethods(pull.atc)
|
|
|
|
|
exportMethods(pull.mo)
|
2019-06-07 22:47:37 +02:00
|
|
|
exportMethods(scale_type.ab)
|
|
|
|
|
exportMethods(scale_type.mo)
|
2019-05-29 19:56:17 +02:00
|
|
|
exportMethods(select.freq)
|
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)
|
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)
|
2019-02-08 16:06:54 +01:00
|
|
|
importFrom(crayon,has_color)
|
2018-11-01 20:23:33 +01:00
|
|
|
importFrom(crayon,italic)
|
2018-12-06 14:36:39 +01:00
|
|
|
importFrom(crayon,magenta)
|
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)
|
2019-06-07 22:47:37 +02:00
|
|
|
importFrom(data.table,address)
|
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)
|
2018-06-27 15:54:56 +02:00
|
|
|
importFrom(dplyr,as_tibble)
|
2018-02-21 11:52:31 +01:00
|
|
|
importFrom(dplyr,between)
|
2019-01-28 11:20:32 +01:00
|
|
|
importFrom(dplyr,bind_cols)
|
2018-08-12 22:34:03 +02:00
|
|
|
importFrom(dplyr,bind_rows)
|
2018-07-28 09:34:03 +02:00
|
|
|
importFrom(dplyr,case_when)
|
2018-04-18 12:24:54 +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)
|
2018-09-29 21:54:32 +02:00
|
|
|
importFrom(dplyr,full_join)
|
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,progress_estimated)
|
|
|
|
|
importFrom(dplyr,pull)
|
|
|
|
|
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)
|
2018-06-20 14:47:37 +02:00
|
|
|
importFrom(dplyr,top_n)
|
2019-01-15 16:38:54 +01:00
|
|
|
importFrom(dplyr,transmute)
|
2018-11-06 16:41:59 +01:00
|
|
|
importFrom(dplyr,ungroup)
|
2018-10-18 12:10:10 +02:00
|
|
|
importFrom(dplyr,vars)
|
2018-04-18 12:24:54 +02:00
|
|
|
importFrom(grDevices,boxplot.stats)
|
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)
|
2019-05-29 19:56:17 +02:00
|
|
|
importFrom(graphics,boxplot)
|
2018-07-08 22:14:55 +02:00
|
|
|
importFrom(graphics,hist)
|
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)
|
2018-10-09 13:53:33 +02:00
|
|
|
importFrom(hms,is.hms)
|
2018-07-01 21:40:37 +02:00
|
|
|
importFrom(knitr,kable)
|
2019-04-05 18:47:39 +02:00
|
|
|
importFrom(microbenchmark,microbenchmark)
|
2019-01-29 20:20:09 +01:00
|
|
|
importFrom(rlang,as_label)
|
2019-01-28 11:20:32 +01:00
|
|
|
importFrom(rlang,enquos)
|
|
|
|
|
importFrom(rlang,eval_tidy)
|
2019-06-07 22:47:37 +02:00
|
|
|
importFrom(scales,percent)
|
2018-07-10 12:27:07 +02:00
|
|
|
importFrom(stats,complete.cases)
|
2018-04-18 12:24:54 +02:00
|
|
|
importFrom(stats,fivenum)
|
2018-07-26 16:30:42 +02:00
|
|
|
importFrom(stats,glm)
|
|
|
|
|
importFrom(stats,lm)
|
2018-07-03 11:30:40 +02:00
|
|
|
importFrom(stats,mad)
|
2018-07-01 21:40:37 +02:00
|
|
|
importFrom(stats,pchisq)
|
2018-07-26 16:30:42 +02:00
|
|
|
importFrom(stats,predict)
|
2018-04-18 12:24:54 +02:00
|
|
|
importFrom(stats,sd)
|
2019-02-22 22:12:10 +01:00
|
|
|
importFrom(utils,browseURL)
|
2018-06-20 14:47:37 +02:00
|
|
|
importFrom(utils,browseVignettes)
|
2018-11-15 12:42:35 +01:00
|
|
|
importFrom(utils,installed.packages)
|
