adding more changes from posit course

.Rbuildignore

@@ -6,11 +6,11 @@
 ^doc$
 ^docs$
 ^figures$
+^\.github$
 ^Ideas for Future Work$
 ^Meta$
 ^pkgdown$
 ^README_files$
 ^README\.Rmd$
 ^residuals.Rmd$
 ^tests.R$
-^\.github$

R/plot_auxindex.R

@@ -27,7 +27,13 @@ plot_auxindex <- function(resid, smoother, theme, axis.text.size, title.text.siz
   # If smoother is set to true, add it to the plot
   if (smoother == TRUE){
     plot <- plot +
-      geom_smooth(method = "loess", se = FALSE, color = "red", size = 0.5)
+      geom_smooth(
+        method = "loess", 
+        se = FALSE, 
+        color = "red", 
+        linewidth = 0.5,
+        formula = 'y ~ x'
+      )
   }
 
   # Add theme to plot

R/plot_auxqq.R

@@ -38,7 +38,7 @@ plot_auxqq <- function(resid, theme, axis.text.size, title.text.size, title.opt,
 
   # Add a line if requested
   if(qqline == TRUE){
-    plot <- plot + stat_qq_line(color = "blue", size = .5)
+    plot <- plot + stat_qq_line(color = "blue", linewidth = .5)
   }
 
   # Add theme to plot

R/plot_constlev.R

@@ -78,8 +78,8 @@ plot_constlev <- function(model, type, theme, axis.text.size, title.text.size, t
       na.rm = TRUE
     ) +
     geom_point(aes(group = {Data}), alpha = alpha) +
-    #geom_line(aes(x = {Lowess.x}, y = {Lowess.y}), color = "red", size = 0.5) +
-    geom_abline(slope = 0, intercept = 0, color = "blue", size = 0.5) +
+    #geom_line(aes(x = {Lowess.x}, y = {Lowess.y}), color = "red", linewidth = 0.5) +
+    geom_abline(slope = 0, intercept = 0, color = "blue", linewidth = 0.5) +
     xlab("Factor Level Combinations") +
     ylab("Standardized Residuals")
 

R/plot_index.R

@@ -38,7 +38,13 @@ plot_index <- function(model, type, smoother, theme, axis.text.size, title.text.
   # If smoother is set to true, add it to the plot
   if (smoother == TRUE){
     plot <- plot +
-      geom_smooth(method = "loess", se = FALSE, color = "red", size = 0.5)
+      geom_smooth(
+        method = "loess", 
+        se = FALSE, 
+        color = "red", 
+        linewidth = 0.5,
+        formula = 'y ~ x'
+      )
   }
 
   # Add theme to plot

R/plot_lev.R

@@ -180,13 +180,14 @@ plot_lev <- function(model, type, smoother, theme, axis.text.size, title.text.si
     # no sense
     if (smoother == TRUE){
       plot <- plot #+
-        #geom_smooth(data = model_values,
+        # geom_smooth(data = model_values,
         #            aes(x = {Leverage}, y = {Std_Res}),
         #            na.rm = TRUE,
         #            method = "loess",
         #            se = FALSE,
         #            color = "red",
-        #            size = 0.5)
+        #            size = 0.5,
+        #            formula = 'y ~ x')
     }
 
     # Add Cook's D lines if they are inside the limits of the plot

R/plot_ls.R

@@ -90,7 +90,13 @@ plot_ls <- function(model, type, smoother, theme, axis.text.size, title.text.siz
   # If smoother is set to true, do not add it to the plot
   if (smoother == TRUE){
     plot <- plot #+
-    #  geom_smooth(method = "loess", se = FALSE, color = "red", size = 0.5)
+      # geom_smooth(
+      #   method = "loess", 
+      #   se = FALSE, 
+      #   color = "red", 
+      #   linewidth = 0.5, 
+      #   formula = 'y ~ x'
+      # )
   }
 
   # Add theme to plot

R/plot_qq.R

@@ -75,7 +75,7 @@ plot_qq <- function(model, type, theme, axis.text.size, title.text.size, title.o
 
   # Add a line if requested
   if (qqline == TRUE) {
-    plot <- plot + stat_qq_line(color = "blue", size = .5)
+    plot <- plot + stat_qq_line(color = "blue", linewidth = .5)
   }
 
   # Add theme to plot

R/plot_resid.R

@@ -42,7 +42,13 @@ plot_resid <- function(model, type, smoother, theme, axis.text.size,
   # If smoother is set to true, add it to the plot
   if (smoother == TRUE){
    plot <- plot +
-     geom_smooth(method = "loess", se = FALSE, color = "red", size = 0.5)
+     geom_smooth(
+       method = "loess", 
+       se = FALSE, 
+       color = "red", 
+       linewidth = 0.5,
+       formula = 'y ~ x'
+      )
   }
 
   # Add theme to plot

R/resid_xpanel.R

@@ -197,7 +197,15 @@ create_predictor_plots <- function(x_column_number, y_column_number,
 
   # Add a smoother to the plots if requested
   if(smoother == TRUE){
-    plot <- plot + geom_smooth(method = "loess", se = FALSE, color = "red", size = 0.5)
+    plot <- 
+      plot + 
+      geom_smooth(
+        method = "loess", 
+        se = FALSE, 
+        color = "red", 
+        linewidth = 0.5,
+        formula = 'y ~ x'
+      )
   }
 
   # Add theme to plot

inst/ideas-for-future-work.md

@@ -5,7 +5,6 @@
 - Write up list of questions
 - Work through Mark's examples
 - Check in with Mark
-- Work in updates from posit course
 - Clean up old to do list
 - Ask Katie about changing her email address
 - Work through list of issues on GitLab