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deps fix
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193
NAMESPACE
193
NAMESPACE
@ -1,192 +1,5 @@
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# Generated by roxygen2: do not edit by hand
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S3method(as.data.frame,atc)
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S3method(as.data.frame,frequency_tbl)
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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.vector,frequency_tbl)
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S3method(as_tibble,frequency_tbl)
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S3method(barplot,mic)
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S3method(barplot,rsi)
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S3method(diff,frequency_tbl)
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S3method(droplevels,mic)
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S3method(droplevels,rsi)
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S3method(format,frequency_tbl)
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S3method(hist,frequency_tbl)
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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(plot,frequency_tbl)
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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,atc)
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S3method(print,frequency_tbl)
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S3method(print,mic)
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S3method(print,mo)
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S3method(print,rsi)
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S3method(pull,atc)
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S3method(pull,mo)
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S3method(select,frequency_tbl)
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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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export("%like%")
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export(EUCAST_rules)
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export(ab_atc)
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export(ab_certe)
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export(ab_name)
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export(ab_official)
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export(ab_property)
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export(ab_tradenames)
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export(ab_trivial_nl)
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export(ab_umcg)
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export(abname)
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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.atc)
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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_certe)
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export(atc_ddd)
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export(atc_groups)
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export(atc_name)
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export(atc_official)
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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(atc_property)
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export(atc_tradenames)
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export(atc_trivial_nl)
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export(atc_umcg)
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export(brmo)
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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(eucast_exceptional_phenotypes)
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export(eucast_rules)
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export(facet_rsi)
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export(filter_first_isolate)
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export(filter_first_weighted_isolate)
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export(first_isolate)
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export(freq)
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export(frequency_tbl)
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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(guess_atc)
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export(guess_mo)
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export(header)
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export(inner_join_microorganisms)
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export(interpretive_reading)
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export(is.atc)
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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(mdro)
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export(mo_TSN)
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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_kingdom)
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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_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_subkingdom)
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export(mo_subspecies)
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export(mo_taxonomy)
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export(mo_type)
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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(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(ratio)
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export(read.4D)
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export(resistance_predict)
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export(right_join_microorganisms)
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export(rsi)
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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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export(theme_rsi)
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export(top_freq)
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exportMethods(as.data.frame.atc)
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exportMethods(as.data.frame.frequency_tbl)
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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(as.vector.frequency_tbl)
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exportMethods(as_tibble.frequency_tbl)
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exportMethods(barplot.mic)
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exportMethods(barplot.rsi)
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exportMethods(diff.frequency_tbl)
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exportMethods(droplevels.mic)
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exportMethods(droplevels.rsi)
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exportMethods(format.frequency_tbl)
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exportMethods(hist.frequency_tbl)
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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.frequency_tbl)
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exportMethods(plot.mic)
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exportMethods(plot.rsi)
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exportMethods(print.atc)
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exportMethods(print.frequency_tbl)
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exportMethods(print.mic)
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exportMethods(print.mo)
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exportMethods(print.rsi)
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exportMethods(pull.atc)
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exportMethods(pull.mo)
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exportMethods(select.frequency_tbl)
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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(crayon,bgGreen)
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importFrom(crayon,bgRed)
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importFrom(crayon,bgYellow)
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@ -199,7 +12,6 @@ importFrom(crayon,magenta)
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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(curl,nslookup)
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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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@ -253,10 +65,6 @@ importFrom(graphics,plot)
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importFrom(graphics,text)
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importFrom(hms,is.hms)
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importFrom(knitr,kable)
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importFrom(rvest,html_children)
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importFrom(rvest,html_node)
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importFrom(rvest,html_nodes)
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importFrom(rvest,html_table)
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importFrom(stats,complete.cases)
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importFrom(stats,fivenum)
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importFrom(stats,glm)
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@ -267,4 +75,3 @@ importFrom(stats,predict)
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importFrom(stats,sd)
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importFrom(utils,browseVignettes)
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importFrom(utils,installed.packages)
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importFrom(xml2,read_html)
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@ -56,9 +56,6 @@
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#' @export
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#' @rdname atc_online
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#' @importFrom dplyr %>% progress_estimated
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#' @importFrom xml2 read_html
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#' @importFrom rvest html_children html_node html_nodes html_table
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#' @importFrom curl nslookup
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#' @source \url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
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#' @examples
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#' \donttest{
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@ -94,7 +91,7 @@ atc_online_property <- function(atc_code,
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!is.null(curl::nslookup(url, error = FALSE))
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}
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# check for connection using the ATC of amoxicillin
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if (!has_internet(url = url)) {
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if (!curl::has_internet(url = url)) {
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message("The URL could not be reached.")
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return(rep(NA, length(atc_code)))
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}
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