(v1.7.1.9002) ab class selectors update

man/count.Rd

@@ -167,6 +167,12 @@ if (require("dplyr")) {
               n1 = count_all(CIP),  # the actual total; sum of all three
               n2 = n_rsi(CIP),      # same - analogous to n_distinct
               total = n())          # NOT the number of tested isolates!
+              
+  # Number of available isolates for a whole antibiotic class
+  # (i.e., in this data set columns GEN, TOB, AMK, KAN)
+  example_isolates \%>\%
+    group_by(hospital_id) \%>\%
+    summarise(across(aminoglycosides(), n_rsi))
  
   # Count co-resistance between amoxicillin/clav acid and gentamicin,
   # so we can see that combination therapy does a lot more than mono therapy.

man/plot.Rd

@@ -4,10 +4,13 @@
 \alias{plot}
 \alias{plot.mic}
 \alias{ggplot.mic}
+\alias{autoplot.mic}
 \alias{plot.disk}
 \alias{ggplot.disk}
+\alias{autoplot.disk}
 \alias{plot.rsi}
 \alias{ggplot.rsi}
+\alias{autoplot.rsi}
 \title{Plotting for Classes \code{rsi}, \code{mic} and \code{disk}}
 \usage{
 \method{plot}{mic}(
@@ -39,6 +42,21 @@
   ...
 )
 
+\method{autoplot}{mic}(
+  data,
+  mapping = NULL,
+  title = paste("MIC values of", deparse(substitute(data))),
+  ylab = "Frequency",
+  xlab = "Minimum Inhibitory Concentration (mg/L)",
+  mo = NULL,
+  ab = NULL,
+  guideline = "EUCAST",
+  colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+  language = get_locale(),
+  expand = TRUE,
+  ...
+)
+
 \method{plot}{disk}(
   x,
   main = paste("Disk zones of", deparse(substitute(x))),
@@ -68,6 +86,21 @@
   ...
 )
 
+\method{autoplot}{disk}(
+  data,
+  mapping = NULL,
+  title = paste("Disk zones of", deparse(substitute(data))),
+  ylab = "Frequency",
+  xlab = "Disk diffusion diameter (mm)",
+  mo = NULL,
+  ab = NULL,
+  guideline = "EUCAST",
+  colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+  language = get_locale(),
+  expand = TRUE,
+  ...
+)
+
 \method{plot}{rsi}(
   x,
   ylab = "Percentage",
@@ -86,6 +119,17 @@
   language = get_locale(),
   ...
 )
+
+\method{autoplot}{rsi}(
+  data,
+  mapping = NULL,
+  title = paste("Resistance Overview of", deparse(substitute(data))),
+  xlab = "Antimicrobial Interpretation",
+  ylab = "Frequency",
+  colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+  language = get_locale(),
+  ...
+)
 }
 \arguments{
 \item{x, data}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}}

man/resistance_predict.Rd

@@ -4,8 +4,9 @@
 \alias{resistance_predict}
 \alias{rsi_predict}
 \alias{plot.resistance_predict}
-\alias{ggplot.resistance_predict}
 \alias{ggplot_rsi_predict}
+\alias{ggplot.resistance_predict}
+\alias{autoplot.resistance_predict}
 \title{Predict antimicrobial resistance}
 \usage{
 resistance_predict(
@@ -40,9 +41,16 @@ rsi_predict(
 
 \method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ...)
 
+ggplot_rsi_predict(
+  x,
+  main = paste("Resistance Prediction of", x_name),
+  ribbon = TRUE,
+  ...
+)
+
 \method{ggplot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...)
 
-ggplot_rsi_predict(
+\method{autoplot}{resistance_predict}(
   x,
   main = paste("Resistance Prediction of", x_name),
   ribbon = TRUE,