From 79c1d454bd3a9a681f6c0807ed1c600bb0a814ec Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sat, 3 Aug 2024 18:38:24 +0200
Subject: [PATCH 1/7] Add plot-method for `check_dag()`

---
 DESCRIPTION           |  3 +-
 NAMESPACE             |  1 +
 NEWS.md               |  6 +++
 R/plot.check_dag.R    | 99 +++++++++++++++++++++++++++++++++++++++++++
 man/plot.check_dag.Rd | 41 ++++++++++++++++++
 5 files changed, 149 insertions(+), 1 deletion(-)
 create mode 100644 R/plot.check_dag.R
 create mode 100644 man/plot.check_dag.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 12410928e..965ef4d4f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: see
 Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2'
-Version: 0.8.5
+Version: 0.8.5.1
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -78,6 +78,7 @@ Suggests:
     DHARMa,
     emmeans,
     factoextra,
+    ggdag,
     ggdist,
     ggraph,
     ggrepel,
diff --git a/NAMESPACE b/NAMESPACE
index 7dcf77601..3f72afdc2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -23,6 +23,7 @@ S3method(data_plot,performance_pp_check)
 S3method(data_plot,point_estimate)
 S3method(data_plot,rope)
 S3method(data_plot,see_compare_parameters)
+S3method(plot,check_dag)
 S3method(plot,datawizard_table)
 S3method(plot,datawizard_tables)
 S3method(plot,see_bayesfactor_models)
diff --git a/NEWS.md b/NEWS.md
index 271dd7251..4c3592757 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# see (dev)
+
+## Canges
+
+- New `plot()` method for `performance::check_dag()`.
+
 # see 0.8.5
 
 ## Major Changes
diff --git a/R/plot.check_dag.R b/R/plot.check_dag.R
new file mode 100644
index 000000000..080935db2
--- /dev/null
+++ b/R/plot.check_dag.R
@@ -0,0 +1,99 @@
+#' Plot method for check DAGs
+#'
+#' The `plot()` method for the `performance::check_dag()` function.
+#'
+#' @param x A `check_dag` object.
+#' @param size_point Numeric value specifying size of point geoms.
+#' @param colors Character vector of length five, indicating the colors (in
+#' hex-format) for different types of variables.
+#' @param which Character string indicating which plot to show. Can be either
+#' `"all"`, `"current"` or `"required"`.
+#' @param ... Not used.
+#'
+#' @return A ggplot2-object.
+#'
+#' @examplesIf require("ggdag", quietly = TRUE)
+#' library(performance)
+#' # incorrect adjustment
+#' dag <- check_dag(
+#'   y ~ x + b + c,
+#'   x ~ b,
+#'   outcome = "y",
+#'   exposure = "x"
+#' )
+#' dag
+#' plot(dag)
+#' @export
+plot.check_dag <- function(x, size_point = 15, colors = NULL, which = "all", ...) {
+  .data <- NULL
+  insight::check_if_installed(c("ggdag", "ggplot2"))
+  which <- match.arg(which, choices = c("all", "current", "required"))
+
+  p1 <- suppressWarnings(ggdag::ggdag_adjust(x, stylized = TRUE))
+  p2 <- suppressWarnings(ggdag::ggdag_adjustment_set(x, shadow = TRUE, stylized = TRUE))
+
+  # tweak data
+  p1$data$type <- as.character(p1$data$adjusted)
+  p1$data$type[vapply(p1$data$name, ggdag::is_collider, logical(1), .dag = x)] <- "collider"
+  p1$data$type[p1$data$name == attributes(x)$outcome] <- "outcome"
+  p1$data$type[p1$data$name %in% attributes(x)$exposure] <- "exposure"
+  p1$data$type <- factor(p1$data$type, levels = c("outcome", "exposure", "adjusted", "unadjusted", "collider"))
+
+  p2$data$type <- as.character(p2$data$adjusted)
+  p2$data$type[vapply(p2$data$name, ggdag::is_collider, logical(1), .dag = x)] <- "collider"
+  p2$data$type[p2$data$name == attributes(x)$outcome] <- "outcome"
+  p2$data$type[p2$data$name %in% attributes(x)$exposure] <- "exposure"
+  p2$data$type <- factor(p2$data$type, levels = c("outcome", "exposure", "adjusted", "unadjusted", "collider"))
+
+  if (is.null(colors)) {
+    point_colors <- see_colors(c("yellow", "cyan", "blue grey", "red", "orange"))
+  } else if (length(colors) != 5) {
+    insight::format_error("`colors` must be a character vector with five color-values.")
+  } else {
+    point_colors <- colors
+  }
+  names(point_colors) <- c("outcome", "exposure", "adjusted", "unadjusted", "collider")
+
+  plot1 <- ggplot2::ggplot(p1$data, ggplot2::aes(x = .data$x, y = .data$y)) +
+    geom_point_borderless(ggplot2::aes(fill = .data$type), size = size_point) +
+    ggdag::geom_dag_edges(
+      ggplot2::aes(
+        xend = .data$xend,
+        yend = .data$yend,
+        edge_alpha = .data$adjusted
+      )
+    ) +
+    ggdag::scale_adjusted() +
+    ggdag::geom_dag_label(ggplot2::aes(label = .data$name)) +
+    ggdag::theme_dag() +
+    ggplot2::scale_fill_manual(values = point_colors) +
+    ggplot2::ggtitle("Current model") +
+    ggplot2::guides(edge_alpha = "none")
+
+  plot2 <- ggplot2::ggplot(p2$data, ggplot2::aes(x = .data$x, y = .data$y)) +
+    geom_point_borderless(ggplot2::aes(fill = .data$type), size = size_point) +
+    ggdag::geom_dag_edges(
+      ggplot2::aes(
+        xend = .data$xend,
+        yend = .data$yend,
+        edge_alpha = .data$adjusted
+      )
+    ) +
+    ggdag::scale_adjusted() +
+    ggdag::geom_dag_label(ggplot2::aes(label = .data$name)) +
+    ggdag::theme_dag() +
+    ggplot2::scale_fill_manual(values = point_colors) +
+    ggplot2::ggtitle("Required model") +
+    ggplot2::guides(edge_alpha = "none")
+
+  if (which == "all") {
+    # fix legends
+    plot2 <- plot2 + ggplot2::theme(legend.position = "none")
+    # plot
+    plots(plot1, plot2, n_rows = 1)
+  } else if (which == "current") {
+    plot1
+  } else {
+    plot2
+  }
+}
diff --git a/man/plot.check_dag.Rd b/man/plot.check_dag.Rd
new file mode 100644
index 000000000..8148b812e
--- /dev/null
+++ b/man/plot.check_dag.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.check_dag.R
+\name{plot.check_dag}
+\alias{plot.check_dag}
+\title{Plot method for check DAGs}
+\usage{
+\method{plot}{check_dag}(x, size_point = 15, colors = NULL, which = "all", ...)
+}
+\arguments{
+\item{x}{A \code{check_dag} object.}
+
+\item{size_point}{Numeric value specifying size of point geoms.}
+
+\item{colors}{Character vector of length five, indicating the colors (in
+hex-format) for different types of variables.}
+
+\item{which}{Character string indicating which plot to show. Can be either
+\code{"all"}, \code{"current"} or \code{"required"}.}
+
+\item{...}{Not used.}
+}
+\value{
+A ggplot2-object.
+}
+\description{
+The \code{plot()} method for the \code{performance::check_dag()} function.
+}
+\examples{
+\dontshow{if (require("ggdag", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+library(performance)
+# incorrect adjustment
+dag <- check_dag(
+  y ~ x + b + c,
+  x ~ b,
+  outcome = "y",
+  exposure = "x"
+)
+dag
+plot(dag)
+\dontshow{\}) # examplesIf}
+}

From 3ce461ec93b6525d849c48dfe030f68bc2aaac5d Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sat, 3 Aug 2024 18:42:24 +0200
Subject: [PATCH 2/7] update class

---
 NAMESPACE                                        | 2 +-
 R/plot.check_dag.R                               | 2 +-
 man/{plot.check_dag.Rd => plot.see_check_dag.Rd} | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename man/{plot.check_dag.Rd => plot.see_check_dag.Rd} (87%)

diff --git a/NAMESPACE b/NAMESPACE
index 3f72afdc2..7f5dce91b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -23,7 +23,6 @@ S3method(data_plot,performance_pp_check)
 S3method(data_plot,point_estimate)
 S3method(data_plot,rope)
 S3method(data_plot,see_compare_parameters)
-S3method(plot,check_dag)
 S3method(plot,datawizard_table)
 S3method(plot,datawizard_tables)
 S3method(plot,see_bayesfactor_models)
@@ -31,6 +30,7 @@ S3method(plot,see_bayesfactor_parameters)
 S3method(plot,see_bayesfactor_savagedickey)
 S3method(plot,see_binned_residuals)
 S3method(plot,see_check_collinearity)
+S3method(plot,see_check_dag)
 S3method(plot,see_check_distribution)
 S3method(plot,see_check_distribution_numeric)
 S3method(plot,see_check_heteroscedasticity)
diff --git a/R/plot.check_dag.R b/R/plot.check_dag.R
index 080935db2..67809ece2 100644
--- a/R/plot.check_dag.R
+++ b/R/plot.check_dag.R
@@ -24,7 +24,7 @@
 #' dag
 #' plot(dag)
 #' @export
-plot.check_dag <- function(x, size_point = 15, colors = NULL, which = "all", ...) {
+plot.see_check_dag <- function(x, size_point = 15, colors = NULL, which = "all", ...) {
   .data <- NULL
   insight::check_if_installed(c("ggdag", "ggplot2"))
   which <- match.arg(which, choices = c("all", "current", "required"))
diff --git a/man/plot.check_dag.Rd b/man/plot.see_check_dag.Rd
similarity index 87%
rename from man/plot.check_dag.Rd
rename to man/plot.see_check_dag.Rd
index 8148b812e..829ac91a8 100644
--- a/man/plot.check_dag.Rd
+++ b/man/plot.see_check_dag.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/plot.check_dag.R
-\name{plot.check_dag}
-\alias{plot.check_dag}
+\name{plot.see_check_dag}
+\alias{plot.see_check_dag}
 \title{Plot method for check DAGs}
 \usage{
-\method{plot}{check_dag}(x, size_point = 15, colors = NULL, which = "all", ...)
+\method{plot}{see_check_dag}(x, size_point = 15, colors = NULL, which = "all", ...)
 }
 \arguments{
 \item{x}{A \code{check_dag} object.}

From 58a09bf128eaf23ded66ad77b4e41ced37ade6e1 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sat, 3 Aug 2024 19:13:24 +0200
Subject: [PATCH 3/7] use PR

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 965ef4d4f..034c4dc60 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -120,3 +120,4 @@ Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/Needs/website: easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
+Remotes: easystats/performance#761

From 2ad1d616ec8c48314ed233a2335bda23d3904188 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sat, 3 Aug 2024 19:34:28 +0200
Subject: [PATCH 4/7] docs

---
 R/plot.check_dag.R        | 3 +++
 man/plot.see_check_dag.Rd | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/R/plot.check_dag.R b/R/plot.check_dag.R
index 67809ece2..8d91f5185 100644
--- a/R/plot.check_dag.R
+++ b/R/plot.check_dag.R
@@ -23,6 +23,9 @@
 #' )
 #' dag
 #' plot(dag)
+#'
+#' # plot only model with required adjustments
+#' plot(dag, which = "required")
 #' @export
 plot.see_check_dag <- function(x, size_point = 15, colors = NULL, which = "all", ...) {
   .data <- NULL
diff --git a/man/plot.see_check_dag.Rd b/man/plot.see_check_dag.Rd
index 829ac91a8..5866cba81 100644
--- a/man/plot.see_check_dag.Rd
+++ b/man/plot.see_check_dag.Rd
@@ -37,5 +37,8 @@ dag <- check_dag(
 )
 dag
 plot(dag)
+
+# plot only model with required adjustments
+plot(dag, which = "required")
 \dontshow{\}) # examplesIf}
 }

From a5fc90687cc6c41e0728909adaa716f46a43c76e Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sat, 3 Aug 2024 20:31:08 +0200
Subject: [PATCH 5/7] update

---
 R/plot.check_dag.R        | 28 +++++++++++++++++++++++-----
 man/plot.see_check_dag.Rd | 12 +++++++++++-
 2 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/R/plot.check_dag.R b/R/plot.check_dag.R
index 8d91f5185..74bd3cc06 100644
--- a/R/plot.check_dag.R
+++ b/R/plot.check_dag.R
@@ -8,6 +8,8 @@
 #' hex-format) for different types of variables.
 #' @param which Character string indicating which plot to show. Can be either
 #' `"all"`, `"current"` or `"required"`.
+#' @param check_colliders Logical indicating whether to highlight colliders.
+#' Set to `FALSE` if the algorithm to detect colliders is very slow.
 #' @param ... Not used.
 #'
 #' @return A ggplot2-object.
@@ -27,23 +29,39 @@
 #' # plot only model with required adjustments
 #' plot(dag, which = "required")
 #' @export
-plot.see_check_dag <- function(x, size_point = 15, colors = NULL, which = "all", ...) {
+plot.see_check_dag <- function(x,
+                               size_point = 15,
+                               colors = NULL,
+                               which = "all",
+                               check_colliders = TRUE,
+                               ...) {
   .data <- NULL
   insight::check_if_installed(c("ggdag", "ggplot2"))
   which <- match.arg(which, choices = c("all", "current", "required"))
 
-  p1 <- suppressWarnings(ggdag::ggdag_adjust(x, stylized = TRUE))
-  p2 <- suppressWarnings(ggdag::ggdag_adjustment_set(x, shadow = TRUE, stylized = TRUE))
+  # get plot data
+  p1 <- p2 <- suppressWarnings(ggdag::dag_adjustment_sets(x))
+  adjusted_for <- attributes(x)$adjusted
+
+  # for current plot, we need to update the "adjusted" column
+  p1$data$adjusted <- "unadjusted"
+  if (!is.null(adjusted_for)) {
+    p1$data$adjusted[p1$data$name %in% adjusted_for] <- "adjusted"
+  }
 
   # tweak data
   p1$data$type <- as.character(p1$data$adjusted)
-  p1$data$type[vapply(p1$data$name, ggdag::is_collider, logical(1), .dag = x)] <- "collider"
+  if (check_colliders) {
+    p1$data$type[vapply(p1$data$name, ggdag::is_collider, logical(1), .dag = x)] <- "collider"
+  }
   p1$data$type[p1$data$name == attributes(x)$outcome] <- "outcome"
   p1$data$type[p1$data$name %in% attributes(x)$exposure] <- "exposure"
   p1$data$type <- factor(p1$data$type, levels = c("outcome", "exposure", "adjusted", "unadjusted", "collider"))
 
   p2$data$type <- as.character(p2$data$adjusted)
-  p2$data$type[vapply(p2$data$name, ggdag::is_collider, logical(1), .dag = x)] <- "collider"
+  if (check_colliders) {
+    p2$data$type[vapply(p2$data$name, ggdag::is_collider, logical(1), .dag = x)] <- "collider"
+  }
   p2$data$type[p2$data$name == attributes(x)$outcome] <- "outcome"
   p2$data$type[p2$data$name %in% attributes(x)$exposure] <- "exposure"
   p2$data$type <- factor(p2$data$type, levels = c("outcome", "exposure", "adjusted", "unadjusted", "collider"))
diff --git a/man/plot.see_check_dag.Rd b/man/plot.see_check_dag.Rd
index 5866cba81..0b8a0d1b4 100644
--- a/man/plot.see_check_dag.Rd
+++ b/man/plot.see_check_dag.Rd
@@ -4,7 +4,14 @@
 \alias{plot.see_check_dag}
 \title{Plot method for check DAGs}
 \usage{
-\method{plot}{see_check_dag}(x, size_point = 15, colors = NULL, which = "all", ...)
+\method{plot}{see_check_dag}(
+  x,
+  size_point = 15,
+  colors = NULL,
+  which = "all",
+  check_colliders = TRUE,
+  ...
+)
 }
 \arguments{
 \item{x}{A \code{check_dag} object.}
@@ -17,6 +24,9 @@ hex-format) for different types of variables.}
 \item{which}{Character string indicating which plot to show. Can be either
 \code{"all"}, \code{"current"} or \code{"required"}.}
 
+\item{check_colliders}{Logical indicating whether to highlight colliders.
+Set to \code{FALSE} if the algorithm to detect colliders is very slow.}
+
 \item{...}{Not used.}
 }
 \value{

From cc54a74db924e6f043d0497d79f23f7c26827236 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sat, 3 Aug 2024 20:34:24 +0200
Subject: [PATCH 6/7] docs

---
 R/plot.check_dag.R        | 12 ++++++++++++
 man/plot.see_check_dag.Rd | 12 ++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/R/plot.check_dag.R b/R/plot.check_dag.R
index 74bd3cc06..147500c89 100644
--- a/R/plot.check_dag.R
+++ b/R/plot.check_dag.R
@@ -28,6 +28,18 @@
 #'
 #' # plot only model with required adjustments
 #' plot(dag, which = "required")
+#'
+#' # collider-bias?
+#' dag <- check_dag(
+#'   y ~ x + c + d,
+#'   x ~ c + d,
+#'   b ~ x,
+#'   b ~ y,
+#'   outcome = "y",
+#'   exposure = "x",
+#'   adjusted = "c"
+#' )
+#' plot(dag)
 #' @export
 plot.see_check_dag <- function(x,
                                size_point = 15,
diff --git a/man/plot.see_check_dag.Rd b/man/plot.see_check_dag.Rd
index 0b8a0d1b4..f1b00acd4 100644
--- a/man/plot.see_check_dag.Rd
+++ b/man/plot.see_check_dag.Rd
@@ -50,5 +50,17 @@ plot(dag)
 
 # plot only model with required adjustments
 plot(dag, which = "required")
+
+# collider-bias?
+dag <- check_dag(
+  y ~ x + c + d,
+  x ~ c + d,
+  b ~ x,
+  b ~ y,
+  outcome = "y",
+  exposure = "x",
+  adjusted = "c"
+)
+plot(dag)
 \dontshow{\}) # examplesIf}
 }

From ecd59b3bdd82187644d10af07ce47fbf56080eb2 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Sat, 3 Aug 2024 20:48:22 +0200
Subject: [PATCH 7/7] typo

---
 NEWS.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 4c3592757..b9abd37bf 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,6 @@
-# see (dev)
+# see (development)
 
-## Canges
+## Changes
 
 - New `plot()` method for `performance::check_dag()`.