Nothing
.plot_diag_outliers_new <- function(x,
na.rm = TRUE,
ref.color = "darkgray",
ref.linetype = "dashed",
show_labels = TRUE,
size_line = NULL,
size_point = 2,
size_text = NULL,
size_axis_title = base_size,
size_title = 12,
theme_style = theme_lucid,
base_size = 10,
colors = unname(social_colors(c("green", "blue grey", "red"))),
dot_alpha_level = 0.8,
show_dots = TRUE) {
size_line <- size_line %||% 0.7
size_text <- size_text %||% 3
plot_data <- x
cook.levels <- attributes(x)$cook_levels
n_params <- attributes(x)$n_params
min_cook_level <- min(cook.levels, na.rm = TRUE)
n_above <- sum(plot_data$Cooks_Distance >= min_cook_level, na.rm = TRUE)
label.n <- pmax(n_above, 5)
p <- ggplot(plot_data, aes(x = .data$Hat, .data$Std_Residuals))
if (isTRUE(show_dots)) {
p <- p + geom_point2(
aes(colour = .data$Influential),
na.rm = na.rm,
alpha = dot_alpha_level,
size = size_point
)
}
p <- p +
geom_vline(
xintercept = 0,
color = ref.color,
linetype = ref.linetype
) +
geom_hline(
yintercept = 0,
color = ref.color,
linetype = ref.linetype
) +
stat_smooth(
formula = y ~ x,
method = "loess",
na.rm = na.rm,
se = FALSE,
color = colors[1],
linewidth = size_line
) +
scale_colour_manual(values = c(OK = colors[2], Influential = colors[3])) +
(if (isTRUE(show_labels)) {
if (requireNamespace("ggrepel", quietly = TRUE)) {
ggrepel::geom_text_repel(
data = plot_data[order(plot_data$Cooks_Distance, decreasing = TRUE)[1:label.n], ],
aes(label = .data$Index, colour = .data$Influential),
size = size_text
)
} else {
geom_text(
data = plot_data[order(plot_data$Cooks_Distance, decreasing = TRUE)[1:label.n], ],
aes(label = .data$Index, colour = .data$Influential),
size = size_text, position = position_nudge(
x = diff(range(plot_data$Hat)) / 40,
y = diff(range(plot_data$Std_Residuals)) / 20
)
)
}
}) +
labs(
x = expression("Leverage (" * h[ii] * ")"),
y = "Std. Residuals",
title = "Influential Observations",
subtitle = "Points should be inside the contour lines",
colour = NULL
)
if (length(cook.levels)) {
.hat <- sort(plot_data$Hat)
.cook_ref <- lapply(cook.levels, function(crit) {
sqrt(crit * n_params * (1 - .hat) / .hat)
})
.hat80 <- min(.hat) + diff(range(.hat)) * 0.8
.cook_labels <- c("Cook's D = ", rep("", length(cook.levels) - 1))
.cook_lines <- c(
lapply(seq_along(cook.levels), function(.level) {
annotate(
geom = "line",
x = .hat,
y = .cook_ref[[.level]],
color = colors[1],
linetype = ref.linetype,
linewidth = size_line
)
}),
lapply(seq_along(cook.levels), function(.level) {
annotate(
geom = "line",
x = .hat,
y = -1 * .cook_ref[[.level]],
color = colors[1],
linetype = ref.linetype,
linewidth = size_line
)
}),
lapply(seq_along(cook.levels), function(.level) {
annotate(
geom = "text",
label = insight::format_value(cook.levels[.level], digits = 1),
x = .hat80,
y = sqrt(cook.levels[.level] * n_params * (1 - .hat80) / .hat80),
hjust = "right",
vjust = -1,
color = colors[1],
size = size_text
)
}),
lapply(seq_along(cook.levels), function(.level) {
annotate(
geom = "text",
label = insight::format_value(cook.levels[.level], digits = 1),
x = .hat80,
y = -1 * sqrt(cook.levels[.level] * n_params * (1 - .hat80) / .hat80),
color = colors[1],
hjust = "right",
vjust = 1.5,
size = size_text
)
})
)
p <- p +
.cook_lines +
theme_style(
base_size = base_size,
plot.title.space = 3,
axis.title.space = 5,
plot.title.size = size_title,
axis.title.size = size_axis_title
) +
guides(colour = "none", text = "none")
}
p
}
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