Replace RSI with SIR

NAMESPACE

@@ -28,6 +28,7 @@ S3method("[<-",disk)
 S3method("[<-",mic)
 S3method("[<-",mo)
 S3method("[<-",rsi)
+S3method("[<-",sir)
 S3method("[[",ab)
 S3method("[[",av)
 S3method("[[",disk)
@@ -39,6 +40,7 @@ S3method("[[<-",disk)
 S3method("[[<-",mic)
 S3method("[[<-",mo)
 S3method("[[<-",rsi)
+S3method("[[<-",sir)
 S3method("^",mic)
 S3method("|",ab_selector)
 S3method("|",mic)
@@ -63,6 +65,10 @@ S3method(as.rsi,data.frame)
 S3method(as.rsi,default)
 S3method(as.rsi,disk)
 S3method(as.rsi,mic)
+S3method(as.sir,data.frame)
+S3method(as.sir,default)
+S3method(as.sir,disk)
+S3method(as.sir,mic)
 S3method(asin,mic)
 S3method(asinh,mic)
 S3method(atan,mic)
@@ -70,6 +76,7 @@ S3method(atanh,mic)
 S3method(barplot,disk)
 S3method(barplot,mic)
 S3method(barplot,rsi)
+S3method(barplot,sir)
 S3method(c,ab)
 S3method(c,ab_selector)
 S3method(c,av)
@@ -79,6 +86,7 @@ S3method(c,disk)
 S3method(c,mic)
 S3method(c,mo)
 S3method(c,rsi)
+S3method(c,sir)
 S3method(ceiling,mic)
 S3method(close,progress_bar)
 S3method(cos,mic)
@@ -91,6 +99,7 @@ S3method(cumsum,mic)
 S3method(digamma,mic)
 S3method(droplevels,mic)
 S3method(droplevels,rsi)
+S3method(droplevels,sir)
 S3method(exp,mic)
 S3method(expm1,mic)
 S3method(floor,mic)
@@ -111,13 +120,14 @@ S3method(mean_amr_distance,data.frame)
 S3method(mean_amr_distance,default)
 S3method(mean_amr_distance,disk)
 S3method(mean_amr_distance,mic)
-S3method(mean_amr_distance,rsi)
+S3method(mean_amr_distance,sir)
 S3method(median,mic)
 S3method(min,mic)
 S3method(plot,disk)
 S3method(plot,mic)
 S3method(plot,resistance_predict)
 S3method(plot,rsi)
+S3method(plot,sir)
 S3method(print,ab)
 S3method(print,av)
 S3method(print,bug_drug_combinations)
@@ -130,6 +140,7 @@ S3method(print,mo_renamed)
 S3method(print,mo_uncertainties)
 S3method(print,pca)
 S3method(print,rsi)
+S3method(print,sir)
 S3method(prod,mic)
 S3method(quantile,mic)
 S3method(range,mic)
@@ -139,6 +150,7 @@ S3method(rep,disk)
 S3method(rep,mic)
 S3method(rep,mo)
 S3method(rep,rsi)
+S3method(rep,sir)
 S3method(round,mic)
 S3method(sign,mic)
 S3method(signif,mic)
@@ -155,6 +167,7 @@ S3method(summary,mic)
 S3method(summary,mo)
 S3method(summary,pca)
 S3method(summary,rsi)
+S3method(summary,sir)
 S3method(tan,mic)
 S3method(tanh,mic)
 S3method(tanpi,mic)
@@ -166,6 +179,7 @@ S3method(unique,disk)
 S3method(unique,mic)
 S3method(unique,mo)
 S3method(unique,rsi)
+S3method(unique,sir)
 export("%like%")
 export("%like_case%")
 export("%unlike%")
@@ -173,6 +187,7 @@ export("%unlike_case%")
 export(NA_disk_)
 export(NA_mic_)
 export(NA_rsi_)
+export(NA_sir_)
 export(ab_atc)
 export(ab_atc_group1)
 export(ab_atc_group2)
@@ -210,6 +225,7 @@ export(as.disk)
 export(as.mic)
 export(as.mo)
 export(as.rsi)
+export(as.sir)
 export(atc_online_ddd)
 export(atc_online_ddd_units)
 export(atc_online_groups)
@@ -255,18 +271,22 @@ export(eucast_dosage)
 export(eucast_exceptional_phenotypes)
 export(eucast_rules)
 export(facet_rsi)
+export(facet_sir)
 export(filter_first_isolate)
 export(first_isolate)
 export(fluoroquinolones)
 export(full_join_microorganisms)
 export(g.test)
 export(geom_rsi)
+export(geom_sir)
 export(get_AMR_locale)
 export(get_episode)
 export(get_mo_source)
 export(ggplot_pca)
 export(ggplot_rsi)
 export(ggplot_rsi_predict)
+export(ggplot_sir)
+export(ggplot_sir_predict)
 export(glycopeptides)
 export(guess_ab_col)
 export(inner_join_microorganisms)
@@ -277,12 +297,15 @@ export(is.mic)
 export(is.mo)
 export(is.rsi)
 export(is.rsi.eligible)
+export(is.sir)
 export(is_new_episode)
+export(is_sir_eligible)
 export(italicise_taxonomy)
 export(italicize_taxonomy)
 export(key_antimicrobials)
 export(kurtosis)
 export(labels_rsi_count)
+export(labels_sir_count)
 export(left_join_microorganisms)
 export(like)
 export(lincosamides)
@@ -333,6 +356,7 @@ export(mo_url)
 export(mo_year)
 export(mrgn)
 export(n_rsi)
+export(n_sir)
 export(not_intrinsic_resistant)
 export(oxazolidinones)
 export(pca)
@@ -348,25 +372,30 @@ export(quinolones)
 export(random_disk)
 export(random_mic)
 export(random_rsi)
+export(random_sir)
 export(reset_AMR_locale)
 export(resistance)
 export(resistance_predict)
 export(right_join_microorganisms)
-export(rsi_confidence_interval)
 export(rsi_df)
-export(rsi_interpretation_history)
 export(rsi_predict)
 export(scale_rsi_colours)
+export(scale_sir_colours)
 export(scale_y_percent)
 export(semi_join_microorganisms)
 export(set_AMR_locale)
 export(set_ab_names)
 export(set_mo_source)
+export(sir_confidence_interval)
+export(sir_df)
+export(sir_interpretation_history)
+export(sir_predict)
 export(skewness)
 export(streptogramins)
 export(susceptibility)
 export(tetracyclines)
 export(theme_rsi)
+export(theme_sir)
 export(translate_AMR)
 export(trimethoprims)
 export(ureidopenicillins)