mirror of https://github.com/msberends/AMR.git
391 lines
8.3 KiB
Plaintext
Executable File
391 lines
8.3 KiB
Plaintext
Executable File
# Generated by roxygen2: do not edit by hand
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S3method("!",mic)
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S3method("!=",ab_selector)
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S3method("!=",mic)
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S3method("%%",mic)
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S3method("%/%",mic)
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S3method("&",ab_selector)
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S3method("&",mic)
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S3method("*",mic)
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S3method("+",mic)
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S3method("-",mic)
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S3method("/",mic)
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S3method("<",mic)
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S3method("<=",mic)
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S3method("==",ab_selector)
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S3method("==",mic)
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S3method(">",mic)
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S3method(">=",mic)
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S3method("[",ab)
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S3method("[",av)
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S3method("[",disk)
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S3method("[",mic)
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S3method("[",mo)
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S3method("[<-",ab)
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S3method("[<-",av)
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S3method("[<-",disk)
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S3method("[<-",mic)
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S3method("[<-",mo)
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S3method("[<-",rsi)
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S3method("[[",ab)
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S3method("[[",av)
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S3method("[[",disk)
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S3method("[[",mic)
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S3method("[[",mo)
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S3method("[[<-",ab)
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S3method("[[<-",av)
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S3method("[[<-",disk)
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S3method("[[<-",mic)
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S3method("[[<-",mo)
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S3method("[[<-",rsi)
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S3method("^",mic)
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S3method("|",ab_selector)
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S3method("|",mic)
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S3method(abs,mic)
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S3method(acos,mic)
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S3method(acosh,mic)
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S3method(all,ab_selector)
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S3method(all,ab_selector_any_all)
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S3method(all,mic)
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S3method(any,ab_selector)
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S3method(any,ab_selector_any_all)
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S3method(any,mic)
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S3method(as.data.frame,ab)
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S3method(as.data.frame,av)
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S3method(as.data.frame,mo)
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S3method(as.double,mic)
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S3method(as.list,custom_eucast_rules)
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S3method(as.list,custom_mdro_guideline)
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S3method(as.matrix,mic)
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S3method(as.numeric,mic)
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S3method(as.rsi,data.frame)
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S3method(as.rsi,default)
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S3method(as.rsi,disk)
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S3method(as.rsi,mic)
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S3method(asin,mic)
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S3method(asinh,mic)
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S3method(atan,mic)
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S3method(atanh,mic)
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S3method(barplot,disk)
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S3method(barplot,mic)
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S3method(barplot,rsi)
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S3method(c,ab)
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S3method(c,ab_selector)
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S3method(c,av)
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S3method(c,custom_eucast_rules)
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S3method(c,custom_mdro_guideline)
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S3method(c,disk)
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S3method(c,mic)
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S3method(c,mo)
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S3method(c,rsi)
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S3method(ceiling,mic)
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S3method(close,progress_bar)
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S3method(cos,mic)
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S3method(cosh,mic)
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S3method(cospi,mic)
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S3method(cummax,mic)
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S3method(cummin,mic)
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S3method(cumprod,mic)
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S3method(cumsum,mic)
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S3method(digamma,mic)
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S3method(droplevels,mic)
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S3method(droplevels,rsi)
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S3method(exp,mic)
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S3method(expm1,mic)
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S3method(floor,mic)
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S3method(format,bug_drug_combinations)
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S3method(gamma,mic)
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S3method(hist,mic)
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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(lgamma,mic)
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S3method(log,mic)
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S3method(log10,mic)
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S3method(log1p,mic)
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S3method(log2,mic)
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S3method(max,mic)
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S3method(mean,mic)
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S3method(mean_amr_distance,data.frame)
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S3method(mean_amr_distance,default)
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S3method(mean_amr_distance,disk)
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S3method(mean_amr_distance,mic)
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S3method(mean_amr_distance,rsi)
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S3method(median,mic)
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S3method(min,mic)
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S3method(plot,disk)
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S3method(plot,mic)
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S3method(plot,resistance_predict)
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S3method(plot,rsi)
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S3method(print,ab)
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S3method(print,av)
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S3method(print,bug_drug_combinations)
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S3method(print,custom_eucast_rules)
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S3method(print,custom_mdro_guideline)
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S3method(print,disk)
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S3method(print,mic)
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S3method(print,mo)
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S3method(print,mo_renamed)
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S3method(print,mo_uncertainties)
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S3method(print,pca)
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S3method(print,rsi)
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S3method(prod,mic)
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S3method(quantile,mic)
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S3method(range,mic)
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S3method(rep,ab)
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S3method(rep,av)
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S3method(rep,disk)
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S3method(rep,mic)
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S3method(rep,mo)
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S3method(rep,rsi)
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S3method(round,mic)
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S3method(sign,mic)
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S3method(signif,mic)
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S3method(sin,mic)
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S3method(sinh,mic)
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S3method(sinpi,mic)
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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(sort,mic)
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S3method(sqrt,mic)
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S3method(sum,mic)
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S3method(summary,mic)
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S3method(summary,mo)
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S3method(summary,pca)
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S3method(summary,rsi)
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S3method(tan,mic)
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S3method(tanh,mic)
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S3method(tanpi,mic)
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S3method(trigamma,mic)
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S3method(trunc,mic)
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S3method(unique,ab)
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S3method(unique,av)
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S3method(unique,disk)
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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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export("%like%")
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export("%like_case%")
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export("%unlike%")
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export("%unlike_case%")
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export(NA_disk_)
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export(NA_mic_)
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export(NA_rsi_)
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export(ab_atc)
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export(ab_atc_group1)
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export(ab_atc_group2)
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export(ab_cid)
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export(ab_class)
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export(ab_ddd)
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export(ab_ddd_units)
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export(ab_from_text)
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export(ab_group)
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export(ab_info)
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export(ab_loinc)
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export(ab_name)
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export(ab_property)
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export(ab_selector)
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export(ab_synonyms)
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export(ab_tradenames)
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export(ab_url)
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export(add_custom_antimicrobials)
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export(add_custom_microorganisms)
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export(administrable_iv)
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export(administrable_per_os)
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export(age)
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export(age_groups)
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export(all_antimicrobials)
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export(aminoglycosides)
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export(aminopenicillins)
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export(amr_distance_from_row)
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export(anti_join_microorganisms)
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export(antifungals)
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export(antimicrobials_equal)
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export(antimycobacterials)
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export(as.ab)
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export(as.av)
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export(as.disk)
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export(as.mic)
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export(as.mo)
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export(as.rsi)
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export(atc_online_ddd)
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export(atc_online_ddd_units)
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export(atc_online_groups)
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export(atc_online_property)
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export(av_atc)
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export(av_cid)
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export(av_ddd)
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export(av_ddd_units)
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export(av_from_text)
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export(av_group)
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export(av_info)
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export(av_loinc)
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export(av_name)
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export(av_property)
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export(av_synonyms)
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export(av_tradenames)
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export(av_url)
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export(availability)
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export(betalactams)
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export(brmo)
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export(bug_drug_combinations)
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export(carbapenems)
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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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export(clear_custom_antimicrobials)
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export(clear_custom_microorganisms)
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export(count_I)
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export(count_IR)
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export(count_R)
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export(count_S)
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export(count_SI)
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export(count_all)
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export(count_df)
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export(count_resistant)
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export(count_susceptible)
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export(custom_eucast_rules)
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export(custom_mdro_guideline)
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export(eucast_dosage)
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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(first_isolate)
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export(fluoroquinolones)
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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_AMR_locale)
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export(get_episode)
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export(get_mo_source)
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export(ggplot_pca)
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export(ggplot_rsi)
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export(ggplot_rsi_predict)
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export(glycopeptides)
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export(guess_ab_col)
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export(inner_join_microorganisms)
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export(is.ab)
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export(is.av)
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export(is.disk)
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export(is.mic)
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export(is.mo)
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export(is.rsi)
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export(is.rsi.eligible)
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export(is_new_episode)
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export(italicise_taxonomy)
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export(italicize_taxonomy)
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export(key_antimicrobials)
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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(lincosamides)
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export(lipoglycopeptides)
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export(macrolides)
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export(mdr_cmi2012)
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export(mdr_tb)
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export(mdro)
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export(mean_amr_distance)
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export(mo_authors)
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export(mo_class)
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export(mo_cleaning_regex)
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export(mo_current)
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export(mo_domain)
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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_gbif)
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export(mo_genus)
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export(mo_gramstain)
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export(mo_info)
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export(mo_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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export(mo_is_yeast)
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export(mo_kingdom)
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export(mo_lpsn)
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export(mo_matching_score)
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export(mo_name)
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export(mo_order)
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export(mo_phylum)
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export(mo_property)
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export(mo_rank)
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export(mo_ref)
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export(mo_renamed)
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export(mo_reset_session)
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export(mo_shortname)
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export(mo_snomed)
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export(mo_species)
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export(mo_status)
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export(mo_subspecies)
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export(mo_synonyms)
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export(mo_taxonomy)
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export(mo_type)
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export(mo_uncertainties)
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export(mo_url)
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export(mo_year)
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export(mrgn)
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export(n_rsi)
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export(not_intrinsic_resistant)
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export(oxazolidinones)
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export(pca)
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export(penicillins)
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export(polymyxins)
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export(proportion_I)
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export(proportion_IR)
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export(proportion_R)
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export(proportion_S)
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export(proportion_SI)
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export(proportion_df)
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export(quinolones)
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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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export(reset_AMR_locale)
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export(resistance)
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export(resistance_predict)
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export(right_join_microorganisms)
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export(rsi_confidence_interval)
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export(rsi_df)
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export(rsi_interpretation_history)
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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_AMR_locale)
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export(set_ab_names)
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export(set_mo_source)
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export(skewness)
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export(streptogramins)
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export(susceptibility)
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export(tetracyclines)
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export(theme_rsi)
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export(translate_AMR)
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export(trimethoprims)
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export(ureidopenicillins)
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importFrom(graphics,arrows)
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importFrom(graphics,axis)
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importFrom(graphics,barplot)
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importFrom(graphics,hist)
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importFrom(graphics,legend)
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importFrom(graphics,mtext)
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importFrom(graphics,plot)
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importFrom(graphics,points)
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importFrom(graphics,text)
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importFrom(stats,complete.cases)
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importFrom(stats,glm)
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importFrom(stats,lm)
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importFrom(stats,median)
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importFrom(stats,pchisq)
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importFrom(stats,prcomp)
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importFrom(stats,predict)
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importFrom(stats,qchisq)
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importFrom(stats,quantile)
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importFrom(stats,var)
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