From 00ba19f9a10ae0a9830471f6c45e7d06b9b8d019 Mon Sep 17 00:00:00 2001
From: Dominique Makowski <dom.mak19@gmail.com>
Date: Thu, 30 Nov 2023 16:49:43 +0000
Subject: [PATCH 01/16] Add % of variance to n_factors plot

---
 R/data_plot.R      |  3 +++
 R/plot.n_factors.R | 58 +++++++++++++++++++++++++++++++++++++---------
 2 files changed, 50 insertions(+), 11 deletions(-)

diff --git a/R/data_plot.R b/R/data_plot.R
index 8a54b9270..c4fef63f3 100644
--- a/R/data_plot.R
+++ b/R/data_plot.R
@@ -132,6 +132,9 @@ add_plot_attributes <- function(x) {
   if (!is.null(info$title)) {
     out[[length(out) + 1L]] <- ggplot2::labs(title = info$title)
   }
+  if (!is.null(info$subtitle)) {
+    out[[length(out) + 1L]] <- ggplot2::labs(subtitle = info$subtitle)
+  }
 
   out
 }
diff --git a/R/plot.n_factors.R b/R/plot.n_factors.R
index 71a967037..35655eb1f 100644
--- a/R/plot.n_factors.R
+++ b/R/plot.n_factors.R
@@ -19,8 +19,18 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
     s2[[var]] <- 1:max(x[[var]])
   }
 
+  if("Variance_Cumulative" %in% names(s1)){
+    s2$Variance_Cumulative <- NA
+  }
+
   dataplot <- rbind(s1, s2[!s2[[var]] %in% s1[[var]], ])
 
+  # Add Variance explained
+  if("Variance_Explained" %in% names(attributes(x))){
+    dataplot$Variance_Cumulative <- NULL  # Remove column and re add
+    dataplot <- merge(dataplot, attributes(x)$Variance_Explained[, c("n_Factors", "Variance_Cumulative")], by = "n_Factors")
+  }
+
   if (type == "line") {
     dataplot$x <- factor(dataplot[[var]], levels = rev(sort(levels(dataplot[[var]]))))
     dataplot$group <- "0"
@@ -37,19 +47,31 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
   dataplot$y <- dataplot$n_Methods / sum(dataplot$n_Methods)
   rownames(dataplot) <- NULL
 
+  # Labels and titles -----------------------------------------------------
+  n_max <- sum(dataplot$n_Methods)
+  axis_lab <- paste0("% of methods (out of ", n_max, ")")
+
+  # Inverse xlab and ylab for line plot
   if (type == "line") {
     attr(dataplot, "info") <- list(
       "ylab" = paste("Number of", lab),
-      "xlab" = "Consensus between methods",
-      "title" = paste("How many", lab, "to retain")
+      "xlab" = axis_lab
     )
   } else {
     attr(dataplot, "info") <- list(
       "xlab" = paste("Number of", lab),
-      "ylab" = "Consensus between methods",
-      "title" = paste("How many", lab, "to retain")
+      "ylab" = axis_lab
     )
   }
+  # Title
+
+  attr(dataplot, "info")$title <-  paste("How many", lab, "to retain")
+  attr(dataplot, "info")$subtitle <- paste0("Number of ", lab, " considered optimal by various algorithm")
+  if("Variance_Cumulative" %in% names(dataplot) && type != "line"){
+    attr(dataplot, "info")$subtitle <- paste0(
+      attr(dataplot, "info")$subtitle,
+      ". The dashed line represent the cumulative percentage of variance explained")
+  }
 
   class(dataplot) <- unique(c("data_plot", "see_n_factors", class(dataplot)))
   dataplot
@@ -83,7 +105,10 @@ data_plot.n_clusters <- data_plot.n_factors
 #' data(mtcars)
 #' result <- n_factors(mtcars, type = "PCA")
 #' result
+#'
+#' plot(result)  # type = "bar" by default
 #' plot(result, type = "line")
+#' plot(result, type = "area")
 #'
 #' @export
 plot.see_n_factors <- function(x,
@@ -105,8 +130,9 @@ plot.see_n_factors <- function(x,
     )
   }
 
+  # Base plot
   if (type == "area") {
-    ggplot(x, aes(x = .data$x, y = .data$y)) +
+    p <- ggplot(x, aes(x = .data$x, y = .data$y)) +
       geom_area(fill = flat_colors("grey")) +
       geom_segment(
         aes(
@@ -115,32 +141,42 @@ plot.see_n_factors <- function(x,
           y = 0,
           yend = max(.data$y)
         ),
-        color = flat_colors("red"),
-        linetype = "dashed"
+        color = flat_colors("red")
       ) +
       geom_point(aes(x = .data$x[which.max(.data$y)], y = max(.data$y)),
         color = flat_colors("red")
       ) +
-      scale_y_continuous(labels = .percents) +
       scale_x_continuous(breaks = 1:max(x$x)) +
       add_plot_attributes(x)
   } else if (type == "line") {
-    ggplot(x, aes(y = .data$x, x = .data$y, colour = .data$group)) +
+    p <- ggplot(x, aes(y = .data$x, x = .data$y, colour = .data$group)) +
       geom_segment(aes(x = 0, yend = .data$x, xend = .data$y), linewidth = size) +
       geom_point(size = 2 * size) +
       guides(colour = "none") +
       scale_x_continuous(labels = .percents) +
       scale_color_manual(values = unname(flat_colors(c("grey", "red")))) +
       add_plot_attributes(x)
+    # If line, return plot as variance explained cannot be added due to the horizontal orientation of the plot
+    return(p)
   } else {
-    ggplot(x, aes(x = .data$x, y = .data$y, fill = .data$fill)) +
+    p <- ggplot(x, aes(x = .data$x, y = .data$y, fill = .data$fill)) +
       geom_bar(stat = "identity", width = size) +
       guides(fill = "none") +
-      scale_y_continuous(labels = .percents) +
       add_plot_attributes(x) +
       scale_x_continuous(breaks = 1:max(x$x)) +
       scale_fill_manual(values = unname(flat_colors(c("grey", "red"))))
   }
+
+  # Add variance explained
+  if("Variance_Cumulative" %in% names(x)) {
+    x$Varex_scaled <- x$Variance_Cumulative * max(x$y)
+    p <- p +
+      geom_line(data=x, aes(x = .data$x, y = .data$Varex_scaled, group=1), linetype="dashed") +
+      scale_y_continuous(labels = .percents, sec.axis = sec_axis(~ . / max(x$y), name = "% of variance explained", labels = .percents))
+  } else {
+    p <- p + scale_y_continuous(labels = .percents)
+  }
+  p
 }
 
 #' @export

From f444f767376af407a1c3ff83611f5345a1eae47a Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Fri, 1 Dec 2023 09:16:17 +0100
Subject: [PATCH 02/16] lintrs, news, desc

---
 DESCRIPTION                   |  2 +-
 NEWS.md                       |  7 ++++
 R/geom_binomdensity.R         |  2 +-
 R/geom_from_list.R            | 50 +++++++++++++++++-----------
 R/plot.n_factors.R            | 62 +++++++++++++++++++++--------------
 R/plot.parameters_brms_meta.R | 18 +++++-----
 6 files changed, 85 insertions(+), 56 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d18611b18..052aed07a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: see
 Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2'
-Version: 0.8.1
+Version: 0.8.1.1
 Authors@R: 
     c(person(given = "Daniel",
              family = "Lüdecke",
diff --git a/NEWS.md b/NEWS.md
index 3971c6217..caaa42dc4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# see 0.8.2
+
+## Minor Changes
+
+* `plot.n_factors()` now shows a dashed line over the bars, indicating the
+  cumulate explained variance by the number of factors.
+
 # see 0.8.1
 
 ## Major Changes
diff --git a/R/geom_binomdensity.R b/R/geom_binomdensity.R
index e430baecb..ab951c513 100644
--- a/R/geom_binomdensity.R
+++ b/R/geom_binomdensity.R
@@ -62,7 +62,7 @@ geom_binomdensity <- function(data,
 
   # Other parameters
   data$.side <- ifelse(data[[y]] == y_levels[1], "top", "bottom")
-  data$.justification <- as.numeric(!(data[[y]] == y_levels[1]))
+  data$.justification <- as.numeric(data[[y]] != y_levels[1])
   data$.scale <- .geom_binomdensity_scale(data, x, y, scale)
 
   # ggdist geom
diff --git a/R/geom_from_list.R b/R/geom_from_list.R
index 52a9186a4..65a78a0f2 100644
--- a/R/geom_from_list.R
+++ b/R/geom_from_list.R
@@ -114,58 +114,68 @@
 #' @export
 geom_from_list <- function(x, ...) {
   # Additional parameters ------------------------------------------------------
-  args <- x[!names(x) %in% c("geom", "aes", "data", "width", "height", "position", "show.legend")]
+  arguments <- x[!names(x) %in% c("geom", "aes", "data", "width", "height", "position", "show.legend")]
 
   if (is.null(x$geom)) {
     return(NULL)
   }
 
   if (inherits(x$geom, "function")) {
-    return(do.call(x$geom, args))
+    return(do.call(x$geom, args = arguments))
   }
 
   if (x$geom %in% c("density_2d", "density_2d_filled", "density_2d_polygon")) {
-    if (!"contour" %in% names(args)) args$contour <- TRUE
-    if (!"contour_var" %in% names(args)) args$contour_var <- "density"
+    if (!"contour" %in% names(arguments)) arguments$contour <- TRUE
+    if (!"contour_var" %in% names(arguments)) arguments$contour_var <- "density"
   }
 
   # If they are not geoms, return immediately
   if (x$geom == "labs") {
-    return(do.call(ggplot2::labs, args))
+    return(do.call(ggplot2::labs, args = arguments))
   }
   if (x$geom == "guides") {
-    return(do.call(ggplot2::guides, args))
+    return(do.call(ggplot2::guides, args = arguments))
   }
   if (x$geom == "coord_flip") {
-    return(do.call(ggplot2::coord_flip, args))
+    return(do.call(ggplot2::coord_flip, args = arguments))
   }
   if (x$geom == "facet_wrap") {
-    return(do.call(ggplot2::facet_wrap, args))
+    return(do.call(ggplot2::facet_wrap, args = arguments))
   }
   if (x$geom == "facet_grid") {
-    return(do.call(ggplot2::facet_grid, args))
+    return(do.call(ggplot2::facet_grid, args = arguments))
   }
   if (x$geom == "smooth") {
-    if (!is.null(x$aes)) args$mapping <- do.call(ggplot2::aes, lapply(x$aes, .str_to_sym))
-    if (!"method" %in% names(args)) args$method <- "loess"
-    if (!"formula" %in% names(args)) args$formula <- "y ~ x"
-    return(do.call(ggplot2::geom_smooth, args))
+    if (!is.null(x$aes)) {
+      arguments$mapping <- do.call(ggplot2::aes, args = lapply(x$aes, .str_to_sym))
+    }
+    if (!"method" %in% names(arguments)) {
+      arguments$method <- "loess"
+    }
+    if (!"formula" %in% names(arguments)) {
+      arguments$formula <- "y ~ x"
+    }
+    return(do.call(ggplot2::geom_smooth, args = arguments))
   }
 
   if (startsWith(x$geom, "scale_") || startsWith(x$geom, "theme") || startsWith(x$geom, "see_")) {
-    return(do.call(x$geom, args))
+    return(do.call(x$geom, args = arguments))
   }
 
   if (startsWith(x$geom, "ggside::")) {
     insight::check_if_installed("ggside")
-    if (!is.null(x$aes)) args$mapping <- do.call(ggplot2::aes, lapply(x$aes, .str_to_sym))
-    return(do.call(eval(parse(text = x$geom)), args))
+    if (!is.null(x$aes)) {
+      arguments$mapping <- do.call(ggplot2::aes, args = lapply(x$aes, .str_to_sym))
+    }
+    return(do.call(eval(parse(text = x$geom)), args = arguments))
   }
 
   if (startsWith(x$geom, "ggraph::")) {
     insight::check_if_installed("ggraph")
-    if (!is.null(x$aes)) args$mapping <- do.call(ggplot2::aes, lapply(x$aes, .str_to_sym))
-    return(do.call(eval(parse(text = x$geom)), args))
+    if (!is.null(x$aes)) {
+      arguments$mapping <- do.call(ggplot2::aes, args = lapply(x$aes, .str_to_sym))
+    }
+    return(do.call(eval(parse(text = x$geom)), args = arguments))
   }
 
   # Default parameters
@@ -212,7 +222,7 @@ geom_from_list <- function(x, ...) {
 
   # Aesthetics
   if ("aes" %in% names(x)) {
-    aes_list <- do.call(ggplot2::aes, lapply(x$aes, .str_to_sym))
+    aes_list <- do.call(ggplot2::aes, args = lapply(x$aes, .str_to_sym))
   } else {
     aes_list <- NULL
   }
@@ -231,7 +241,7 @@ geom_from_list <- function(x, ...) {
     geom = x$geom,
     mapping = aes_list,
     data = x$data,
-    params = args,
+    params = arguments,
     show.legend = show.legend,
     ...
   )
diff --git a/R/plot.n_factors.R b/R/plot.n_factors.R
index 35655eb1f..a58af6888 100644
--- a/R/plot.n_factors.R
+++ b/R/plot.n_factors.R
@@ -3,43 +3,47 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
   s1 <- summary(x)
 
   if ("n_Factors" %in% names(x)) {
-    var <- "n_Factors"
+    variable <- "n_Factors"
     lab <- "factors"
   } else {
-    var <- "n_Clusters"
+    variable <- "n_Clusters"
     lab <- "clusters"
   }
 
-  s2 <- data.frame(n_Methods = rep(0, max(x[[var]])))
+  s2 <- data.frame(n_Methods = rep(0, max(x[[variable]])))
 
   if (type == "line") {
-    s1[[var]] <- as.factor(s1[[var]])
-    s2[[var]] <- factor(1:max(x[[var]]))
+    s1[[variable]] <- as.factor(s1[[variable]])
+    s2[[variable]] <- factor(1:max(x[[variable]]))
   } else {
-    s2[[var]] <- 1:max(x[[var]])
+    s2[[variable]] <- 1:max(x[[variable]])
   }
 
-  if("Variance_Cumulative" %in% names(s1)){
+  if ("Variance_Cumulative" %in% names(s1)) {
     s2$Variance_Cumulative <- NA
   }
 
-  dataplot <- rbind(s1, s2[!s2[[var]] %in% s1[[var]], ])
+  dataplot <- rbind(s1, s2[!s2[[variable]] %in% s1[[variable]], ])
 
   # Add Variance explained
-  if("Variance_Explained" %in% names(attributes(x))){
+  if ("Variance_Explained" %in% names(attributes(x))) {
     dataplot$Variance_Cumulative <- NULL  # Remove column and re add
-    dataplot <- merge(dataplot, attributes(x)$Variance_Explained[, c("n_Factors", "Variance_Cumulative")], by = "n_Factors")
+    dataplot <- merge(
+      dataplot,
+      attributes(x)$Variance_Explained[, c("n_Factors", "Variance_Cumulative")],
+      by = "n_Factors"
+    )
   }
 
   if (type == "line") {
-    dataplot$x <- factor(dataplot[[var]], levels = rev(sort(levels(dataplot[[var]]))))
+    dataplot$x <- factor(dataplot[[variable]], levels = rev(sort(levels(dataplot[[variable]]))))
     dataplot$group <- "0"
     dataplot$group[which.max(dataplot$n_Methods)] <- "1"
   } else if (type == "area") {
-    dataplot$x <- dataplot[[var]]
+    dataplot$x <- dataplot[[variable]]
   } else {
-    dataplot <- dataplot[order(dataplot[[var]]), ]
-    dataplot$x <- dataplot[[var]]
+    dataplot <- dataplot[order(dataplot[[variable]]), ]
+    dataplot$x <- dataplot[[variable]]
     dataplot$fill <- "Not-optimal"
     dataplot$fill[which.max(dataplot$n_Methods)] <- "Optimal"
   }
@@ -54,23 +58,24 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
   # Inverse xlab and ylab for line plot
   if (type == "line") {
     attr(dataplot, "info") <- list(
-      "ylab" = paste("Number of", lab),
-      "xlab" = axis_lab
+      ylab = paste("Number of", lab),
+      xlab = axis_lab
     )
   } else {
     attr(dataplot, "info") <- list(
-      "xlab" = paste("Number of", lab),
-      "ylab" = axis_lab
+      xlab = paste("Number of", lab),
+      ylab = axis_lab
     )
   }
   # Title
 
   attr(dataplot, "info")$title <-  paste("How many", lab, "to retain")
   attr(dataplot, "info")$subtitle <- paste0("Number of ", lab, " considered optimal by various algorithm")
-  if("Variance_Cumulative" %in% names(dataplot) && type != "line"){
+  if ("Variance_Cumulative" %in% names(dataplot) && type != "line") {
     attr(dataplot, "info")$subtitle <- paste0(
       attr(dataplot, "info")$subtitle,
-      ". The dashed line represent the cumulative percentage of variance explained")
+      ". The dashed line represent the cumulative percentage of variance explained"
+    )
   }
 
   class(dataplot) <- unique(c("data_plot", "see_n_factors", class(dataplot)))
@@ -124,8 +129,8 @@ plot.see_n_factors <- function(x,
 
   if (missing(size)) {
     size <- switch(type,
-      "bar" = 0.7,
-      "line" = 1,
+      bar = 0.7,
+      line = 1,
       1
     )
   }
@@ -168,11 +173,18 @@ plot.see_n_factors <- function(x,
   }
 
   # Add variance explained
-  if("Variance_Cumulative" %in% names(x)) {
+  if ("Variance_Cumulative" %in% names(x)) {
     x$Varex_scaled <- x$Variance_Cumulative * max(x$y)
     p <- p +
-      geom_line(data=x, aes(x = .data$x, y = .data$Varex_scaled, group=1), linetype="dashed") +
-      scale_y_continuous(labels = .percents, sec.axis = sec_axis(~ . / max(x$y), name = "% of variance explained", labels = .percents))
+      geom_line(
+        data = x,
+        aes(x = .data$x, y = .data$Varex_scaled, group = 1),
+        linetype = "dashed"
+      ) +
+      scale_y_continuous(
+        labels = .percents,
+        sec.axis = sec_axis(~ . / max(x$y), name = "% of variance explained", labels = .percents)
+      )
   } else {
     p <- p + scale_y_continuous(labels = .percents)
   }
diff --git a/R/plot.parameters_brms_meta.R b/R/plot.parameters_brms_meta.R
index 7558d83ad..f97e20d44 100644
--- a/R/plot.parameters_brms_meta.R
+++ b/R/plot.parameters_brms_meta.R
@@ -59,11 +59,11 @@ data_plot.parameters_brms_meta <- function(x, data = NULL, normalize_height = TR
 
   attr(dataplot, "summary") <- summary
   attr(dataplot, "info") <- list(
-    "xlab" = "Standardized Mean Difference",
-    "ylab" = NULL,
-    "legend_fill" = NULL,
-    "legend_color" = NULL,
-    "title" = "Bayesian Meta-Analysis"
+    xlab = "Standardized Mean Difference",
+    ylab = NULL,
+    legend_fill = NULL,
+    legend_color = NULL,
+    title = "Bayesian Meta-Analysis"
   )
 
   class(dataplot) <- unique(c("data_plot", "see_parameters_brms_meta", class(dataplot)))
@@ -212,12 +212,12 @@ plot.see_parameters_brms_meta <- function(x,
     theme_lucid() +
     ggplot2::scale_y_discrete() +
     ggplot2::scale_fill_manual(values = c(
-      "Study" = unname(metro_colors("light blue")),
-      "Overall" = unname(metro_colors("amber"))
+      Study = unname(metro_colors("light blue")),
+      Overall = unname(metro_colors("amber"))
     )) +
     ggplot2::scale_colour_manual(values = c(
-      "Study" = unname(metro_colors("light blue")),
-      "Overall" = unname(metro_colors("amber"))
+      Study = unname(metro_colors("light blue")),
+      Overall = unname(metro_colors("amber"))
     )) +
     ggplot2::guides(fill = "none", colour = "none") +
     add_plot_attributes(x)

From 905cde5d4142683e81c31f5d6ca727d779d5194b Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Fri, 1 Dec 2023 09:19:48 +0100
Subject: [PATCH 03/16] lintr

---
 R/plot.check_collinearity.R       | 50 +++++++++++++++----------------
 R/plot.check_heteroscedasticity.R | 24 +++++++--------
 2 files changed, 35 insertions(+), 39 deletions(-)

diff --git a/R/plot.check_collinearity.R b/R/plot.check_collinearity.R
index 594c556ec..cf84d66e2 100644
--- a/R/plot.check_collinearity.R
+++ b/R/plot.check_collinearity.R
@@ -69,11 +69,11 @@ plot.see_check_collinearity <- function(x,
   xlim <- nrow(x)
   if (ylim < 10) ylim <- 10
 
-  if (!is.null(ci_data)) {
-    x <- cbind(x, ci_data)
-  } else {
+  if (is.null(ci_data)) {
     x$VIF_CI_low <- NA_real_
     x$VIF_CI_high <- NA_real_
+  } else {
+    x <- cbind(x, ci_data)
   }
 
   # make sure legend is properly sorted
@@ -119,31 +119,29 @@ plot.see_check_collinearity <- function(x,
       color = NA,
       alpha = 0.15
     ) +
-    {
-      if (!is.null(ci_data)) {
-        list(
-          ggplot2::geom_linerange(
-            linewidth = size_line,
-            na.rm = TRUE
+    if (!is.null(ci_data)) {
+      list(
+        ggplot2::geom_linerange(
+          linewidth = size_line,
+          na.rm = TRUE
+        ),
+        ggplot2::geom_segment(
+          data = x[x$VIF_CI_high > ylim * 1.15, ],
+          mapping = aes(
+            x = .data$x,
+            xend = .data$x,
+            y = .data$y,
+            yend = .data$VIF_CI_high
+          ),
+          lineend = "round",
+          linejoin = "round",
+          arrow = ggplot2::arrow(
+            ends = "last", type = "closed",
+            angle = 20, length = ggplot2::unit(0.03, "native")
           ),
-          ggplot2::geom_segment(
-            data = x[x$VIF_CI_high > ylim * 1.15, ],
-            mapping = aes(
-              x = .data$x,
-              xend = .data$x,
-              y = .data$y,
-              yend = .data$VIF_CI_high
-            ),
-            lineend = "round",
-            linejoin = "round",
-            arrow = ggplot2::arrow(
-              ends = "last", type = "closed",
-              angle = 20, length = ggplot2::unit(0.03, "native")
-            ),
-            show.legend = FALSE
-          )
+          show.legend = FALSE
         )
-      }
+      )
     } +
     geom_point2(
       size = size_point,
diff --git a/R/plot.check_heteroscedasticity.R b/R/plot.check_heteroscedasticity.R
index 53cd814c2..18c9b9260 100644
--- a/R/plot.check_heteroscedasticity.R
+++ b/R/plot.check_heteroscedasticity.R
@@ -24,21 +24,19 @@ plot.see_check_heteroscedasticity <- function(x, data = NULL, ...) {
 
   faminfo <- insight::model_info(model)
   r <- tryCatch(
-    {
-      if (inherits(model, "merMod")) {
-        stats::residuals(model, scaled = TRUE)
-      } else if (inherits(model, c("glmmTMB", "MixMod"))) {
-        sigma <- if (faminfo$is_mixed) {
-          sqrt(insight::get_variance_residual(model))
-        } else {
-          .sigma_glmmTMB_nonmixed(model, faminfo)
-        }
-        stats::residuals(model) / sigma
-      } else if (inherits(model, "glm")) {
-        stats::rstandard(model, type = "pearson")
+    if (inherits(model, "merMod")) {
+      stats::residuals(model, scaled = TRUE)
+    } else if (inherits(model, c("glmmTMB", "MixMod"))) {
+      sig <- if (faminfo$is_mixed) {
+        sqrt(insight::get_variance_residual(model))
       } else {
-        stats::rstandard(model)
+        .sigma_glmmTMB_nonmixed(model, faminfo)
       }
+      stats::residuals(model) / sig
+    } else if (inherits(model, "glm")) {
+      stats::rstandard(model, type = "pearson")
+    } else {
+      stats::rstandard(model)
     },
     error = function(e) {
       NULL

From 4c12bbf81bc5e4b179f9904723674d53a9403941 Mon Sep 17 00:00:00 2001
From: Dominique Makowski <dom.mak19@gmail.com>
Date: Fri, 1 Dec 2023 09:34:06 +0000
Subject: [PATCH 04/16] minor x-axis

---
 R/plot.n_factors.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/plot.n_factors.R b/R/plot.n_factors.R
index a58af6888..dd04bcfa9 100644
--- a/R/plot.n_factors.R
+++ b/R/plot.n_factors.R
@@ -58,12 +58,12 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
   # Inverse xlab and ylab for line plot
   if (type == "line") {
     attr(dataplot, "info") <- list(
-      ylab = paste("Number of", lab),
+      ylab = paste("Optimal number of", lab),
       xlab = axis_lab
     )
   } else {
     attr(dataplot, "info") <- list(
-      xlab = paste("Number of", lab),
+      xlab = paste("Optimal number of", lab),
       ylab = axis_lab
     )
   }

From bc44abd1b2e255f1d1d0cc2e465c59b0df8b8f12 Mon Sep 17 00:00:00 2001
From: Dominique Makowski <dom.mak19@gmail.com>
Date: Fri, 1 Dec 2023 09:34:24 +0000
Subject: [PATCH 05/16] Revert "minor x-axis"

This reverts commit 4c12bbf81bc5e4b179f9904723674d53a9403941.
---
 R/plot.n_factors.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/plot.n_factors.R b/R/plot.n_factors.R
index dd04bcfa9..a58af6888 100644
--- a/R/plot.n_factors.R
+++ b/R/plot.n_factors.R
@@ -58,12 +58,12 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
   # Inverse xlab and ylab for line plot
   if (type == "line") {
     attr(dataplot, "info") <- list(
-      ylab = paste("Optimal number of", lab),
+      ylab = paste("Number of", lab),
       xlab = axis_lab
     )
   } else {
     attr(dataplot, "info") <- list(
-      xlab = paste("Optimal number of", lab),
+      xlab = paste("Number of", lab),
       ylab = axis_lab
     )
   }

From 3ebc6dc2d123cc4ffa346494d70123d8bddde8db Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sun, 3 Dec 2023 13:49:46 +0100
Subject: [PATCH 06/16] remotes

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 052aed07a..713153ef4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -117,3 +117,4 @@ Config/Needs/website:
     rstudio/bslib,
     r-lib/pkgdown,
     easystats/easystatstemplate
+Remotes: easystats/parameters

From 4745e5b22d7c79a4be0b7543474f39430c289b93 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sun, 3 Dec 2023 13:52:46 +0100
Subject: [PATCH 07/16] lintr

---
 R/plot.check_collinearity.R | 48 +++++++++++++++++++------------------
 1 file changed, 25 insertions(+), 23 deletions(-)

diff --git a/R/plot.check_collinearity.R b/R/plot.check_collinearity.R
index cf84d66e2..5cf6f8d7c 100644
--- a/R/plot.check_collinearity.R
+++ b/R/plot.check_collinearity.R
@@ -118,31 +118,33 @@ plot.see_check_collinearity <- function(x,
       fill = colors[3],
       color = NA,
       alpha = 0.15
-    ) +
-    if (!is.null(ci_data)) {
-      list(
-        ggplot2::geom_linerange(
-          linewidth = size_line,
-          na.rm = TRUE
+    )
+
+  if (!is.null(ci_data)) {
+    p <- p +
+      ggplot2::geom_linerange(
+        linewidth = size_line,
+        na.rm = TRUE
+      ) +
+      ggplot2::geom_segment(
+        data = x[x$VIF_CI_high > ylim * 1.15, ],
+        mapping = aes(
+          x = .data$x,
+          xend = .data$x,
+          y = .data$y,
+          yend = .data$VIF_CI_high
         ),
-        ggplot2::geom_segment(
-          data = x[x$VIF_CI_high > ylim * 1.15, ],
-          mapping = aes(
-            x = .data$x,
-            xend = .data$x,
-            y = .data$y,
-            yend = .data$VIF_CI_high
-          ),
-          lineend = "round",
-          linejoin = "round",
-          arrow = ggplot2::arrow(
-            ends = "last", type = "closed",
-            angle = 20, length = ggplot2::unit(0.03, "native")
-          ),
-          show.legend = FALSE
-        )
+        lineend = "round",
+        linejoin = "round",
+        arrow = ggplot2::arrow(
+          ends = "last", type = "closed",
+          angle = 20, length = ggplot2::unit(0.03, "native")
+        ),
+        show.legend = FALSE
       )
-    } +
+  }
+
+  p <- p +
     geom_point2(
       size = size_point,
       na.rm = TRUE

From 692847a8298c4b0c2c485f4b379c02498bbc5748 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sun, 3 Dec 2023 13:55:40 +0100
Subject: [PATCH 08/16] lintr

---
 R/plot.parameters_brms_meta.R | 42 +++++++++++++++++------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/R/plot.parameters_brms_meta.R b/R/plot.parameters_brms_meta.R
index f97e20d44..b16f052b6 100644
--- a/R/plot.parameters_brms_meta.R
+++ b/R/plot.parameters_brms_meta.R
@@ -19,45 +19,45 @@ data_plot.parameters_brms_meta <- function(x, data = NULL, normalize_height = TR
   }
 
   # summary
-  summary <- x[, 1:6]
-  summary$Parameter <- attributes(x)$cleaned_parameters
-  colnames(summary)[2] <- "Estimate"
-  summary$Estimate_CI <- sprintf(
+  datasummary <- x[, 1:6]
+  datasummary$Parameter <- attributes(x)$cleaned_parameters
+  colnames(datasummary)[2] <- "Estimate"
+  datasummary$Estimate_CI <- sprintf(
     "%.2f %s",
-    summary$Estimate,
+    datasummary$Estimate,
     insight::format_ci(
-      summary$CI_low,
-      summary$CI_high,
+      datasummary$CI_low,
+      datasummary$CI_high,
       ci = NULL,
       digits = 2,
       zap_small = TRUE
     )
   )
 
-  summary$Parameter <- factor(summary$Parameter, levels = rev(unique(summary$Parameter)))
-  colnames(summary)[match("Parameter", colnames(summary))] <- "Study"
+  datasummary$Parameter <- factor(datasummary$Parameter, levels = rev(unique(datasummary$Parameter)))
+  colnames(datasummary)[match("Parameter", colnames(datasummary))] <- "Study"
 
-  summary$x <- NA_real_
-  summary$y <- NA_real_
-  summary$Color <- "Study"
-  summary$Color[summary$Study == "Overall"] <- "Overall"
+  datasummary$x <- NA_real_
+  datasummary$y <- NA_real_
+  datasummary$Color <- "Study"
+  datasummary$Color[datasummary$Study == "Overall"] <- "Overall"
 
   if ("ROPE_low" %in% names(x) && "ROPE_high" %in% names(x)) {
-    attr(summary, "rope") <- c(x$ROPE_low[1], x$ROPE_high[1])
+    attr(datasummary, "rope") <- c(x$ROPE_low[1], x$ROPE_high[1])
   }
 
   dataplot <- dataplot[dataplot$Study != "tau", ]
-  summary <- summary[summary$Study != "tau", ]
+  datasummary <- datasummary[datasummary$Study != "tau", ]
 
   dataplot$Study <- droplevels(dataplot$Study)
-  summary$Study <- droplevels(summary$Study)
+  datasummary$Study <- droplevels(datasummary$Study)
 
   dataplot$Group <- "Study"
   dataplot$Group[dataplot$Study == "Overall"] <- "Overall"
   dataplot$Color <- "Study"
   dataplot$Color[dataplot$Study == "Overall"] <- "Overall"
 
-  attr(dataplot, "summary") <- summary
+  attr(dataplot, "summary") <- datasummary
   attr(dataplot, "info") <- list(
     xlab = "Standardized Mean Difference",
     ylab = NULL,
@@ -164,7 +164,7 @@ plot.see_parameters_brms_meta <- function(x,
     x <- data_plot(x, data = model, normalize_height = normalize_height, ...)
   }
 
-  summary <- attributes(x)$summary
+  datasummary <- attributes(x)$summary
   rope <- attributes(summary)$rope
 
   p <- ggplot2::ggplot(x, mapping = ggplot2::aes(x = .data$x, y = .data$Study, height = .data$y))
@@ -192,7 +192,7 @@ plot.see_parameters_brms_meta <- function(x,
       alpha = posteriors_alpha
     ) +
     ggplot2::geom_errorbarh(
-      data = summary,
+      data = datasummary,
       mapping = ggplot2::aes(
         xmin = .data$CI_low,
         xmax = .data$CI_high,
@@ -201,7 +201,7 @@ plot.see_parameters_brms_meta <- function(x,
       linewidth = size_line
     ) +
     ggplot2::geom_point(
-      data = summary,
+      data = datasummary,
       mapping = ggplot2::aes(x = .data$Estimate, color = .data$Color),
       size = size_point,
       fill = "white",
@@ -229,7 +229,7 @@ plot.see_parameters_brms_meta <- function(x,
 
     p <- p +
       ggplot2::geom_text(
-        data = summary,
+        data = datasummary,
         mapping = ggplot2::aes(label = .data$Estimate_CI, x = Inf),
         hjust = "inward",
         size = size_text

From 34c413def82e0dc6d474e9c264c5d10cd64d0734 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sun, 3 Dec 2023 13:56:26 +0100
Subject: [PATCH 09/16] lintr

---
 R/plot.parameters_brms_meta.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/R/plot.parameters_brms_meta.R b/R/plot.parameters_brms_meta.R
index b16f052b6..34504d80e 100644
--- a/R/plot.parameters_brms_meta.R
+++ b/R/plot.parameters_brms_meta.R
@@ -150,9 +150,7 @@ plot.see_parameters_brms_meta <- function(x,
                                           ...) {
   # save model for later use
   model <- tryCatch(
-    {
-      .retrieve_data(x)
-    },
+    .retrieve_data(x),
     error = function(e) {
       priors <- FALSE
       NULL

From 228c715a0ed43043b292a2015aa813a57075c378 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 5 Dec 2023 09:55:50 +0100
Subject: [PATCH 10/16] wordlist

---
 inst/WORDLIST | 1 +
 1 file changed, 1 insertion(+)

diff --git a/inst/WORDLIST b/inst/WORDLIST
index 76cfea105..7aaeeedee 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -43,6 +43,7 @@ brms
 characterisation
 codecov
 colour
+cumulate
 datawizard
 de
 diavola

From dab1ee208d05dd3711d88829434259d7400d299c Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 5 Dec 2023 10:01:16 +0100
Subject: [PATCH 11/16] lintr

---
 R/data_plot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/data_plot.R b/R/data_plot.R
index c4fef63f3..e9de62cc2 100644
--- a/R/data_plot.R
+++ b/R/data_plot.R
@@ -179,7 +179,7 @@ add_plot_attributes <- function(x) {
 
 #' @keywords internal
 .dynGet <- function(x,
-                    ifnotfound = stop(gettextf("%s not found", sQuote(x)), domain = NA),
+                    ifnotfound = stop(gettextf("%s not found", sQuote(x)), domain = NA, .call = FALSE),
                     minframe = 1L,
                     inherits = FALSE) {
   x <- insight::safe_deparse(x)

From eb5b5b9b85c88c2c8386fbeb3512b9308d52f7ce Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 5 Dec 2023 10:18:23 +0100
Subject: [PATCH 12/16] use GH to avoid warning

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 713153ef4..597573aa0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -117,4 +117,4 @@ Config/Needs/website:
     rstudio/bslib,
     r-lib/pkgdown,
     easystats/easystatstemplate
-Remotes: easystats/parameters
+Remotes: easystats/parameters, easystats/bayestestR

From 9746fd1aceef8e4ae58b5a714f81e9ff69c74048 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Wed, 31 Jan 2024 21:23:55 +0100
Subject: [PATCH 13/16] fix

---
 R/data_plot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/data_plot.R b/R/data_plot.R
index e9de62cc2..c88c21d5a 100644
--- a/R/data_plot.R
+++ b/R/data_plot.R
@@ -179,7 +179,7 @@ add_plot_attributes <- function(x) {
 
 #' @keywords internal
 .dynGet <- function(x,
-                    ifnotfound = stop(gettextf("%s not found", sQuote(x)), domain = NA, .call = FALSE),
+                    ifnotfound = stop(gettextf("%s not found", sQuote(x)), domain = NA, call. = FALSE),
                     minframe = 1L,
                     inherits = FALSE) {
   x <- insight::safe_deparse(x)

From 07c2a33f8480e36a9a727ffc5e7957f8a12101f2 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Wed, 31 Jan 2024 21:27:26 +0100
Subject: [PATCH 14/16] lintr

---
 R/geom_from_list.R       |  2 +-
 R/plot.check_model.R     |  4 ++--
 R/plot.check_normality.R |  2 +-
 R/plot.check_outliers.R  | 12 +++++-------
 4 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/R/geom_from_list.R b/R/geom_from_list.R
index 65a78a0f2..9196e2c90 100644
--- a/R/geom_from_list.R
+++ b/R/geom_from_list.R
@@ -189,7 +189,7 @@ geom_from_list <- function(x, ...) {
   }
 
   # Default for violin
-  if (x$geom == "violin") {
+  if (x$geom == "violin") { # nolint
     stat <- "ydensity"
     position <- "dodge"
   } else if (x$geom == "boxplot") {
diff --git a/R/plot.check_model.R b/R/plot.check_model.R
index 29c13ff02..14e0a4930 100644
--- a/R/plot.check_model.R
+++ b/R/plot.check_model.R
@@ -209,9 +209,9 @@ plot.see_check_model <- function(x,
     pw <- plots(p, n_columns = n_columns)
     .safe_print_plots(pw, ...)
     invisible(pw)
-  } else {
-    return(p)
   }
+
+  p
 }
 
 
diff --git a/R/plot.check_normality.R b/R/plot.check_normality.R
index 01c62233b..8aae47298 100644
--- a/R/plot.check_normality.R
+++ b/R/plot.check_normality.R
@@ -68,7 +68,7 @@ plot.see_check_normality <- function(x,
       alpha_level = alpha
     )
   } else {
-    if (type == "qq") {
+    if (type == "qq") { # nolint
       model_info <- attributes(x)$model_info
       if (inherits(model, c("lme", "lmerMod", "merMod", "glmmTMB", "afex_aov", "BFBayesFactor"))) {
         res_ <- suppressMessages(sort(stats::residuals(model), na.last = NA))
diff --git a/R/plot.check_outliers.R b/R/plot.check_outliers.R
index eae2b173f..8d8d0f334 100644
--- a/R/plot.check_outliers.R
+++ b/R/plot.check_outliers.R
@@ -41,9 +41,9 @@ plot.see_check_outliers <- function(x,
                                     ...) {
   type <- match.arg(type)
   influential_obs <- attributes(x)$influential_obs
-  methods <- attr(x, "methods", exact = TRUE)
+  outlier_methods <- attr(x, "methods", exact = TRUE)
 
-  if (type == "dots" && !is.null(influential_obs) && (is.null(methods) || length(methods) == 1)) {
+  if (type == "dots" && !is.null(influential_obs) && (is.null(outlier_methods) || length(outlier_methods) == 1)) {
     .plot_diag_outliers_new(
       influential_obs,
       show_labels = show_labels,
@@ -52,12 +52,10 @@ plot.see_check_outliers <- function(x,
       dot_alpha_level = dot_alpha,
       colors = colors
     )
+  } else if (length(outlier_methods) == 1) {
+    .plot_diag_outliers(x, show_labels = show_labels, size_text = size_text, rescale_distance = rescale_distance)
   } else {
-    if (length(methods == 1)) {
-      .plot_diag_outliers(x, show_labels = show_labels, size_text = size_text, rescale_distance = rescale_distance)
-    } else {
-      .plot_outliers_multimethod(x, rescale_distance)
-    }
+    .plot_outliers_multimethod(x, rescale_distance)
   }
 }
 

From 6bd6d81628ebcdc0047907b9af09a3c910fc3213 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Wed, 31 Jan 2024 21:29:38 +0100
Subject: [PATCH 15/16] lintr

---
 R/utils.R                 |  8 ++---
 R/utils_add_prior_layer.R | 62 +++++++++++++++++++--------------------
 2 files changed, 34 insertions(+), 36 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 788b05868..87cbf49ac 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -38,7 +38,7 @@
 
 .clean_parameter_names <- function(params, grid = FALSE) {
   params <- unique(params)
-  labels <- params
+  parameter_labels <- params
 
   # clean parameters names
   params <- gsub("(b_|bs_|bsp_|bcs_)(.*)", "\\2", params, perl = TRUE)
@@ -90,7 +90,7 @@
     params <- gsub("(Zero-Inflated) (Random)", "(Random, Zero-Inflated)", params, fixed = TRUE)
   }
 
-  stats::setNames(params, labels)
+  stats::setNames(params, parameter_labels)
 }
 
 
@@ -139,8 +139,8 @@
 
 .remove_intercept <- function(x, column = "Parameter", show_intercept = FALSE) {
   if (!show_intercept) {
-    remove <- which(.is_intercept(x[[column]]))
-    if (length(remove)) x <- x[-remove, ]
+    to_remove <- which(.is_intercept(x[[column]]))
+    if (length(to_remove)) x <- x[-to_remove, ]
   }
   x
 }
diff --git a/R/utils_add_prior_layer.R b/R/utils_add_prior_layer.R
index 8c2dbab76..90b0dbbac 100644
--- a/R/utils_add_prior_layer.R
+++ b/R/utils_add_prior_layer.R
@@ -17,8 +17,8 @@
       # limit xrange, to avoid overly wide plots
       x_range <- stats::median(dens$x) + 7 * stats::mad(dens$x) * c(-1, 1)
 
-      remove <- which(dens$x <= x_range[1] | dens$x >= x_range[2])
-      if (length(remove)) dens <- dens[-remove, ]
+      to_remove <- which(dens$x <= x_range[1] | dens$x >= x_range[2])
+      if (length(to_remove)) dens <- dens[-to_remove, ]
 
       # remove intercept from output, if requested
       .remove_intercept(dens, column = "Parameter", show_intercept)
@@ -60,35 +60,33 @@
           na.rm = TRUE
         )
       }
+    } else if (isTRUE(show_ridge_line)) {
+      ggridges::geom_ridgeline(
+        data = dat,
+        mapping = aes(
+          x = .data$x,
+          y = as.factor(.data$Parameter),
+          height = .data$y,
+          group = as.factor(.data$Parameter),
+          fill = "Priors"
+        ),
+        alpha = priors_alpha,
+        na.rm = TRUE
+      )
     } else {
-      if (isTRUE(show_ridge_line)) {
-        ggridges::geom_ridgeline(
-          data = dat,
-          mapping = aes(
-            x = .data$x,
-            y = as.factor(.data$Parameter),
-            height = .data$y,
-            group = as.factor(.data$Parameter),
-            fill = "Priors"
-          ),
-          alpha = priors_alpha,
-          na.rm = TRUE
-        )
-      } else {
-        ggridges::geom_ridgeline(
-          data = dat,
-          mapping = aes(
-            x = .data$x,
-            y = as.factor(.data$Parameter),
-            height = .data$y,
-            group = as.factor(.data$Parameter),
-            fill = "Priors"
-          ),
-          alpha = priors_alpha,
-          color = NA,
-          na.rm = TRUE
-        )
-      }
+      ggridges::geom_ridgeline(
+        data = dat,
+        mapping = aes(
+          x = .data$x,
+          y = as.factor(.data$Parameter),
+          height = .data$y,
+          group = as.factor(.data$Parameter),
+          fill = "Priors"
+        ),
+        alpha = priors_alpha,
+        color = NA,
+        na.rm = TRUE
+      )
     }
   }
 }
@@ -115,8 +113,8 @@
       # limit xrange, to avoid overly wide plots
       x_range <- stats::median(dens$x) + 7 * stats::mad(dens$x) * c(-1, 1)
 
-      remove <- which(dens$x <= x_range[1] | dens$x >= x_range[2])
-      if (length(remove)) dens <- dens[-remove, ]
+      to_remove <- which(dens$x <= x_range[1] | dens$x >= x_range[2])
+      if (length(to_remove)) dens <- dens[-to_remove, ]
 
       # remove intercept from output, if requested
       .remove_intercept(dens, column = "Parameter", show_intercept)

From 14edeb657cdb307b97e0c8f2d27c67af7e41c322 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Wed, 31 Jan 2024 22:15:00 +0100
Subject: [PATCH 16/16] styler

---
 R/plot.n_factors.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/plot.n_factors.R b/R/plot.n_factors.R
index a58af6888..33ef1bff5 100644
--- a/R/plot.n_factors.R
+++ b/R/plot.n_factors.R
@@ -27,7 +27,7 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
 
   # Add Variance explained
   if ("Variance_Explained" %in% names(attributes(x))) {
-    dataplot$Variance_Cumulative <- NULL  # Remove column and re add
+    dataplot$Variance_Cumulative <- NULL # Remove column and re add
     dataplot <- merge(
       dataplot,
       attributes(x)$Variance_Explained[, c("n_Factors", "Variance_Cumulative")],
@@ -69,7 +69,7 @@ data_plot.n_factors <- function(x, data = NULL, type = "bar", ...) {
   }
   # Title
 
-  attr(dataplot, "info")$title <-  paste("How many", lab, "to retain")
+  attr(dataplot, "info")$title <- paste("How many", lab, "to retain")
   attr(dataplot, "info")$subtitle <- paste0("Number of ", lab, " considered optimal by various algorithm")
   if ("Variance_Cumulative" %in% names(dataplot) && type != "line") {
     attr(dataplot, "info")$subtitle <- paste0(
@@ -111,7 +111,7 @@ data_plot.n_clusters <- data_plot.n_factors
 #' result <- n_factors(mtcars, type = "PCA")
 #' result
 #'
-#' plot(result)  # type = "bar" by default
+#' plot(result) # type = "bar" by default
 #' plot(result, type = "line")
 #' plot(result, type = "area")
 #'