Merge pull request #161 from r-causal/tidyup

Tidy up a little
r-causal · Jul 22, 2024 · 46d7ca8 · 46d7ca8
2 parents ef31d5f + 4eeb506
commit 46d7ca8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,8 +11,7 @@ Description: Tidy, analyze, and plot directed acyclic graphs (DAGs).
     'ggplot2' and 'ggraph', as well as common analytic and graphical
     functions, such as determining adjustment sets and node relationships.
 License: MIT + file LICENSE
-URL: https://github.com/r-causal/ggdag,
-    https://r-causal.github.io/ggdag/
+URL: https://github.com/r-causal/ggdag, https://r-causal.github.io/ggdag/
 BugReports: https://github.com/r-causal/ggdag/issues
 Depends: 
     R (>= 3.4.0)
@@ -42,8 +41,8 @@ Suggests:
     withr
 VignetteBuilder: 
     knitr
+Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-Config/testthat/edition: 3
diff --git a/R/adjustment_sets.R b/R/adjustment_sets.R
@@ -73,32 +73,31 @@ extract_sets <- function(sets) {
 #' @rdname adjustment_sets
 #' @export
 ggdag_adjustment_set <- function(
-  .tdy_dag,
-  exposure = NULL,
-  outcome = NULL,
-  ...,
-  shadow = TRUE,
-  size = 1,
-  node_size = 16,
-  text_size = 3.88,
-  label_size = text_size,
-  text_col = "white",
-  label_col = "black",
-  edge_width = 0.6,
-  edge_cap = 10,
-  arrow_length = 5,
-  use_edges = TRUE,
-  use_nodes = TRUE,
-  use_stylized = FALSE,
-  use_text = TRUE,
-  use_labels = FALSE,
-  label = NULL,
-  text = NULL,
-  node = deprecated(),
-  stylized = deprecated(),
-  expand_x = expansion(c(0.25, 0.25)),
-  expand_y = expansion(c(0.2, 0.2))
-) {
+    .tdy_dag,
+    exposure = NULL,
+    outcome = NULL,
+    ...,
+    shadow = TRUE,
+    size = 1,
+    node_size = 16,
+    text_size = 3.88,
+    label_size = text_size,
+    text_col = "white",
+    label_col = "black",
+    edge_width = 0.6,
+    edge_cap = 10,
+    arrow_length = 5,
+    use_edges = TRUE,
+    use_nodes = TRUE,
+    use_stylized = FALSE,
+    use_text = TRUE,
+    use_labels = FALSE,
+    label = NULL,
+    text = NULL,
+    node = deprecated(),
+    stylized = deprecated(),
+    expand_x = expansion(c(0.25, 0.25)),
+    expand_y = expansion(c(0.2, 0.2))) {
   .tdy_dag <- if_not_tidy_daggity(.tdy_dag) %>%
     dag_adjustment_sets(exposure = exposure, outcome = outcome, ...)
 
@@ -223,30 +222,29 @@ adjust_for <- control_for
 #' @rdname control_for
 #' @export
 ggdag_adjust <- function(
-  .tdy_dag,
-  var = NULL,
-  ...,
-  size = 1,
-  edge_type = c("link_arc", "link", "arc", "diagonal"),
-  node_size = 16,
-  text_size = 3.88,
-  label_size = text_size,
-  text_col = "white",
-  label_col = "black",
-  edge_width = 0.6,
-  edge_cap = 10,
-  arrow_length = 5,
-  use_edges = TRUE,
-  use_nodes = TRUE,
-  use_stylized = FALSE,
-  use_text = TRUE,
-  use_labels = FALSE,
-  text = NULL,
-  label = NULL,
-  node = deprecated(),
-  stylized = deprecated(),
-  collider_lines = TRUE
-) {
+    .tdy_dag,
+    var = NULL,
+    ...,
+    size = 1,
+    edge_type = c("link_arc", "link", "arc", "diagonal"),
+    node_size = 16,
+    text_size = 3.88,
+    label_size = text_size,
+    text_col = "white",
+    label_col = "black",
+    edge_width = 0.6,
+    edge_cap = 10,
+    arrow_length = 5,
+    use_edges = TRUE,
+    use_nodes = TRUE,
+    use_stylized = FALSE,
+    use_text = TRUE,
+    use_labels = FALSE,
+    text = NULL,
+    label = NULL,
+    node = deprecated(),
+    stylized = deprecated(),
+    collider_lines = TRUE) {
   .tdy_dag <- if_not_tidy_daggity(.tdy_dag, ...)
   if (!is.null(var)) {
     .tdy_dag <- .tdy_dag %>% control_for(var)

diff --git a/R/canonical.R b/R/canonical.R
@@ -32,24 +32,23 @@ node_canonical <- function(.dag, ...) {
 #' @rdname canonicalize
 #' @export
 ggdag_canonical <- function(
-  .tdy_dag,
-  ...,
-  edge_type = "link_arc",
-  node_size = 16,
-  text_size = 3.88,
-  label_size = text_size,
-  text_col = "white",
-  label_col = text_col,
-  use_edges = TRUE,
-  use_nodes = TRUE,
-  use_stylized = FALSE,
-  use_text = TRUE,
-  use_labels = NULL,
-  label = NULL,
-  text = NULL,
-  node = deprecated(),
-  stylized = deprecated()
-) {
+    .tdy_dag,
+    ...,
+    edge_type = "link_arc",
+    node_size = 16,
+    text_size = 3.88,
+    label_size = text_size,
+    text_col = "white",
+    label_col = text_col,
+    use_edges = TRUE,
+    use_nodes = TRUE,
+    use_stylized = FALSE,
+    use_text = TRUE,
+    use_labels = NULL,
+    label = NULL,
+    text = NULL,
+    node = deprecated(),
+    stylized = deprecated()) {
   if_not_tidy_daggity(.tdy_dag, ...) %>%
     node_canonical() %>%
     ggdag(

diff --git a/R/colliders.R b/R/colliders.R
@@ -50,28 +50,27 @@ node_collider <- function(.dag, as_factor = TRUE, ...) {
 #' @rdname colliders
 #' @export
 ggdag_collider <- function(
-  .tdy_dag,
-  ...,
-  size = 1,
-  edge_type = c("link_arc", "link", "arc", "diagonal"),
-  node_size = 16,
-  text_size = 3.88,
-  label_size = text_size,
-  text_col = "white",
-  label_col = "black",
-  edge_width = 0.6,
-  edge_cap = 8,
-  arrow_length = 5,
-  use_edges = TRUE,
-  use_nodes = TRUE,
-  use_stylized = FALSE,
-  use_text = TRUE,
-  use_labels = FALSE,
-  text = NULL,
-  label = NULL,
-  node = deprecated(),
-  stylized = deprecated()
-) {
+    .tdy_dag,
+    ...,
+    size = 1,
+    edge_type = c("link_arc", "link", "arc", "diagonal"),
+    node_size = 16,
+    text_size = 3.88,
+    label_size = text_size,
+    text_col = "white",
+    label_col = "black",
+    edge_width = 0.6,
+    edge_cap = 8,
+    arrow_length = 5,
+    use_edges = TRUE,
+    use_nodes = TRUE,
+    use_stylized = FALSE,
+    use_text = TRUE,
+    use_labels = FALSE,
+    text = NULL,
+    label = NULL,
+    node = deprecated(),
+    stylized = deprecated()) {
   p <- if_not_tidy_daggity(.tdy_dag, ...) %>%
     node_collider() %>%
     dplyr::mutate(colliders = forcats::fct_rev(colliders)) %>%