refactor: replace deprecated aes_string

Author: Quentin62

R/dataPlot.R

@@ -90,8 +90,8 @@ plotData <- function(data, group = NULL, col = NULL, addId = TRUE, addBorder = T
 
   p <- ggplot() +
     geom_rect(data = d_graph,
-              mapping = aes_string(xmin = "t_start", xmax = "t_end", ymin = "position - 0.5",
-                                   ymax = "position + 0.5", fill = "state"),
+              mapping = aes(xmin = .data$t_start, xmax = .data$t_end, ymin = .data$position - 0.5,
+                            ymax = .data$position + 0.5, fill = .data$state),
               color = ifelse(addBorder, "black", NA)) +
     scale_x_continuous(name = "Time") +
     labs(fill = "State")

R/plotEncoding.R

@@ -85,7 +85,7 @@ plotEncodingCI <- function(fdmat, variance, coeff = 2, states = NULL, harm = 1,
       State = factor(rep(colnames(fdmat$y)[i], each = nrow(fdmat$y)), levels = colnames(fdmat$y))
     )
     p <- p + geom_ribbon(
-      data = df, aes_string(ymin = "ymin", ymax = "ymax", x = "time", fill = "State"),
+      data = df, aes(ymin = .data$ymin, ymax = .data$ymax, x = .data$time, fill = .data$State),
       colour = NA, alpha = 0.8
     )
   }
@@ -98,7 +98,7 @@ plotEncodingCI <- function(fdmat, variance, coeff = 2, states = NULL, harm = 1,
   df <- df[df$State %in% states, ]
 
   p <- p +
-    geom_line(data = df, mapping = aes_string(x = "x", y = "y", group = "State", colour = "State"), alpha = 1) +
+    geom_line(data = df, mapping = aes(x = .data$x, y = .data$y, group = .data$State, colour = .data$State), alpha = 1) +
     scale_colour_hue(l = 30, drop = FALSE)
 
   p <- p +
@@ -123,7 +123,7 @@ plotEncoding <- function(fdmat, states = NULL, harm = 1, col = NULL) {
   )
 
   df <- df[df$State %in% states, ]
-  p <- ggplot(df, aes_string(x = "x", y = "y", group = "State", colour = "State")) +
+  p <- ggplot(df, aes(x = .data$x, y = .data$y, group = .data$State, colour = .data$State)) +
     geom_line()
 
   p <- p +
@@ -292,12 +292,12 @@ plotComponent <- function(x, comp = c(1, 2), addNames = TRUE, nudge_x = 0.1, nud
   df <- as.data.frame(Re(x$pc))
   df$name <- rownames(x$pc)
 
-  p <- ggplot(df, aes_string(x = paste0("V", comp[1]), y = paste0("V", comp[2]))) +
+  p <- ggplot(df, aes(x = .data[[paste0("V", comp[1])]], y = .data[[paste0("V", comp[2])]])) +
     geom_point(...) +
     labs(x = paste0("Comp ", comp[1]), y = paste0("Comp ", comp[2]))
 
   if (addNames) {
-    p <- p + geom_text(aes_string(label = "name"), nudge_x = nudge_x, nudge_y = nudge_y, size = size)
+    p <- p + geom_text(aes(label = .data$name), nudge_x = nudge_x, nudge_y = nudge_y, size = size)
   }
 
   p
@@ -366,7 +366,7 @@ plotEigenvalues <- function(x, cumulative = FALSE, normalize = FALSE, ...) {
 
   df <- data.frame(eigenvalues = eigenv, component = comp)
 
-  p <- ggplot(df, aes_string(x = "component", y = "eigenvalues")) +
+  p <- ggplot(df, aes(x = .data$component, y = .data$eigenvalues)) +
     geom_point(...) +
     geom_step() +
     labs(

R/stat.R

@@ -97,7 +97,7 @@ compute_time_spent_intern <- function(data, labels) {
 #' @export
 boxplot.timeSpent <- function(x, col = NULL, ...) {
   df <- data.frame(timeSpent = as.vector(x), state = factor(rep(colnames(x), each = nrow(x)), levels = colnames(x)))
-  p <- ggplot(df, aes_string(x = "state", y = "timeSpent", fill = "state")) +
+  p <- ggplot(df, aes(x = .data$state, y = .data$timeSpent, fill = .data$state)) +
     geom_boxplot(...) +
     labs(x = "State", y = "Time Spent", fill = "State")
 
@@ -189,7 +189,7 @@ hist.duration <- function(x, breaks = NULL, ...) {
   defaultParam <- list(fill = "lightblue", color = "black", bins = breaks)
   param <- c(extraParam, defaultParam[which(!(names(defaultParam) %in% names(extraParam)))])
 
-  ggplot(data.frame(duration = as.vector(x)), aes_string(x = "duration")) +
+  ggplot(data.frame(duration = as.vector(x)), aes(x = .data$duration)) +
     do.call(geom_histogram, param) +
     labs(x = "Duration", y = "Frequency")
 }
@@ -426,7 +426,7 @@ plot_pt_classic <- function(pt, col = NULL) {
     time = rep(pt$t, nrow(pt$pt))
   )
 
-  p <- ggplot(plot_data, aes_string(x = "time", y = "proba", group = "State", colour = "State")) +
+  p <- ggplot(plot_data, aes(x = .data$time, y = .data$proba, group = .data$State, colour = .data$State)) +
     geom_line() +
     ylim(0, 1) +
     labs(x = "Time", y = "p(t)", title = "P(X(t) = x)")
@@ -460,12 +460,14 @@ plot_pt_ribbon <- function(pt, col = NULL, addBorder = TRUE) {
 
   p <- ggplot(plot_data)
   for (i in seq_len(nState)) {
-    p <- p + geom_ribbon(aes_string(
-      ymin = paste0("`", labels[i], "`"),
-      ymax = paste0("`", labels[i + 1], "`"), x = "time",
-      fill = shortLabels[i]
-    ),
-    colour = ifelse(addBorder, "black", NA), alpha = 0.8
+    p <- p + geom_ribbon(
+      aes(
+        ymin = .data[[paste0("`", labels[i], "`")]],
+        ymax = .data[[paste0("`", labels[i + 1], "`")]],
+        x = .data$time,
+        fill = .data[[shortLabels[i]]]
+      ),
+      colour = ifelse(addBorder, "black", NA), alpha = 0.8
     )
   }
 
@@ -575,7 +577,7 @@ hist.njump <- function(x, breaks = NULL, ...) {
   defaultParam <- list(fill = "lightblue", color = "black", bins = breaks, center = 0)
   param <- c(extraParam, defaultParam[which(!(names(defaultParam) %in% names(extraParam)))])
 
-  ggplot(data.frame(njump = as.vector(x)), aes_string(x = "njump")) +
+  ggplot(data.frame(njump = as.vector(x)), aes(x = .data$njump)) +
     do.call(geom_histogram, param) +
     labs(x = "Number of jumps", y = "Frequency") +
     scale_x_continuous(breaks = function(x) pretty(seq(ceiling(x[1]), floor(x[2]), by = 1)))