(v3.0.1.9047) fix #272

man/amr-tidymodels.Rd

@@ -73,7 +73,6 @@ These steps integrate with \code{recipes::recipe()} and work like standard prepr
 }
 \examples{
 if (require("tidymodels")) {
-
   # The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703
   # Presence of ESBL genes was predicted based on raw MIC values.
 
@@ -92,13 +91,10 @@ if (require("tidymodels")) {
 
   # Create and prep a recipe with MIC log2 transformation
   mic_recipe <- recipe(esbl ~ ., data = training_data) \%>\%
-
     # Optionally remove non-predictive variables
     remove_role(genus, old_role = "predictor") \%>\%
-
     # Apply the log2 transformation to all MIC predictors
     step_mic_log2(all_mic_predictors()) \%>\%
-
     # And apply the preparation steps
     prep()
 
@@ -119,13 +115,15 @@ if (require("tidymodels")) {
     bind_cols(out_testing)
 
   # Evaluate predictions using standard classification metrics
-  our_metrics <- metric_set(accuracy,
-                            recall,
-                            precision,
-                            sensitivity,
-                            specificity,
-                            ppv,
-                            npv)
+  our_metrics <- metric_set(
+    accuracy,
+    recall,
+    precision,
+    sensitivity,
+    specificity,
+    ppv,
+    npv
+  )
   metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
 
   # Show performance

man/pca.Rd

@@ -79,12 +79,12 @@ if (require("dplyr")) {
 
 # new ggplot2 plotting method using this package:
 if (require("dplyr") && require("ggplot2")) {
-    ggplot_pca(pca_result)
+  ggplot_pca(pca_result)
 }
 if (require("dplyr") && require("ggplot2")) {
-    ggplot_pca(pca_result) +
-      scale_colour_viridis_d() +
-      labs(title = "Title here")
+  ggplot_pca(pca_result) +
+    scale_colour_viridis_d() +
+    labs(title = "Title here")
 }
 }
 }

man/plot.Rd

@@ -321,7 +321,7 @@ if (require("ggplot2")) {
     theme_minimal() +
     geom_boxplot(fill = NA, colour = "grey30") +
     geom_jitter(width = 0.25)
-    labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
+  labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
 
   mic_sir_plot
 }