Package index • ggdag

Create and Tidy Dags

tidy_dagitty(): Tidy a dagitty object

as_tidy_dagitty(): Convert objects into tidy_dagitty objects

dagify(): Create a dagitty DAG using R-like syntax

dag(): Create a dagitty DAG

coords2df() coords2list(): Manipulate DAG coordinates

time_ordered_coords(): Create a time-ordered coordinate data frame

`label<-`() dag_label() label() has_labels(): DAG labels

simulate_data(): Simulate Data from Structural Equation Model

pull_dag() pull_dag_data() `update_dag_data<-`() update_dag() `update_dag<-`(): Pull components from DAG objects

Analyzing and Plotting DAGs

node_canonical() ggdag_canonical(): Canonicalize a DAG

node_collider() ggdag_collider(): Find colliders

node_dconnected() node_dseparated() node_drelationship() ggdag_drelationship() ggdag_dseparated() ggdag_dconnected(): D-relationship between variables

node_equivalent_dags() ggdag_equivalent_dags() node_equivalent_class() ggdag_equivalent_class(): Generating Equivalent Models

node_exogenous() ggdag_exogenous(): Find Exogenous Variables

node_instrumental() ggdag_instrumental(): Find Instrumental Variables

node_status() ggdag_status(): Find variable status

node_children() node_parents() node_ancestors() node_descendants() node_markov_blanket() node_adjacent() ggdag_children() ggdag_parents() ggdag_ancestors() ggdag_descendants() ggdag_markov_blanket() ggdag_adjacent(): Familial relationships between variables

dag_adjustment_sets() ggdag_adjustment_set(): Covariate Adjustment Sets

dag_saturate() dag_prune(): Saturate or prune an existing DAG

`label<-`() dag_label() label() has_labels(): DAG labels

dag_paths() ggdag_paths() ggdag_paths_fan(): Find Open Paths Between Variables

edge_backdoor(): Classify DAG edges as backdoor or direct

control_for() adjust_for() ggdag_adjust(): Adjust for variables and activate any biasing paths that result

ggdag(): Quickly plot a DAG in ggplot2

ggdag_classic(): Quickly plot a DAG in ggplot2

query_conditional_independence() test_conditional_independence() ggdag_conditional_independence(): Query and Test Conditional Independence in a DAG

m_bias() butterfly_bias() confounder_triangle() collider_triangle() mediation_triangle() quartet_collider() quartet_confounder() quartet_mediator() quartet_m_bias() quartet_time_collider() ggdag_m_bias() ggdag_butterfly_bias() ggdag_confounder_triangle() ggdag_collider_triangle() ggdag_mediation_triangle() ggdag_quartet_collider() ggdag_quartet_confounder() ggdag_quartet_mediator() ggdag_quartet_m_bias() ggdag_quartet_time_collider(): Quickly create a DAGs with common structures of bias

activate_collider_paths(): Activate paths opened by stratifying on a collider

is_collider() is_downstream_collider(): Detecting colliders in DAGs

is_confounder(): Assess if a variable confounds a relationship

is_acyclic() is_adjustment_set() is_d_separated() is_d_connected(): Test DAG properties

is_exogenous() is_instrumental() is_exposure() is_outcome() is_latent(): Test node properties

is_parent() is_child() is_ancestor() is_descendant() is_adjacent(): Test node relationships

is.tidy_dagitty(): Test for object class for tidy_dagitty

Query Functions

Direct analytical queries that return tibbles

query_adjustment_sets(): Query Adjustment Sets

query_ancestors(): Query Node Ancestors

query_children(): Query Node Children

query_colliders(): Query Collider Nodes

query_conditional_independence() test_conditional_independence() ggdag_conditional_independence(): Query and Test Conditional Independence in a DAG

query_dconnected(): Query D-connection

query_descendants(): Query Node Descendants

query_dseparated(): Query D-separation

query_exogenous(): Query Exogenous Variables

query_instrumental(): Query Instrumental Variables

query_markov_blanket(): Query Markov Blanket

query_parents(): Query Node Parents

query_paths(): Query Paths in a DAG

query_status(): Query Variable Status

ggplot2 geoms, themes, and scales

geom_dag(): Add common DAG layers to a ggplot

geom_dag_collider_edges(): Edges for paths activated by stratification on colliders

geom_dag_edges_link() geom_dag_edges_arc() geom_dag_edges_diagonal() geom_dag_edges_fan(): Directed DAG edges

geom_dag_edges(): Directed and bidirected DAG edges

geom_dag_label(): Node text labels

geom_dag_text(): Node text

geom_dag_node() geom_dag_point(): DAG Nodes

geom_dag_text_repel() geom_dag_label_repel() geom_dag_label_repel2() geom_dag_text_repel2(): Repulsive textual annotations

theme_dag_blank() theme_dag() theme_dag_grid(): Minimalist DAG themes

theme_dag_grey() theme_dag_gray() theme_dag_grey_grid() theme_dag_gray_grid(): Simple grey themes for DAGs

scale_adjusted() scale_dag(): Common scale adjustments for DAGs

aes_dag(): Define Aesthetics for Directed Acyclic Graphs (DAGs)

draw_key_dag_collider(): Collider pattern legend key (many-to-one)

draw_key_dag_combined(): Combined DAG legend key (horizontal node-edge-node)

draw_key_dag_edge(): DAG edge legend key (arrow only)

draw_key_dag_point(): DAG point legend key (25% size)

Common Structures of Bias

m_bias() butterfly_bias() confounder_triangle() collider_triangle() mediation_triangle() quartet_collider() quartet_confounder() quartet_mediator() quartet_m_bias() quartet_time_collider() ggdag_m_bias() ggdag_butterfly_bias() ggdag_confounder_triangle() ggdag_collider_triangle() ggdag_mediation_triangle() ggdag_quartet_collider() ggdag_quartet_confounder() ggdag_quartet_mediator() ggdag_quartet_m_bias() ggdag_quartet_time_collider(): Quickly create a DAGs with common structures of bias

Misc

as.data.frame(<tidy_dagitty>): Convert a tidy_dagitty object to data.frame

as_tbl_graph(<tidy_dagitty>) as_tbl_graph(<dagitty>): Convert DAGS to tidygraph

select(<tidy_dagitty>) filter(<tidy_dagitty>) mutate(<tidy_dagitty>) summarise(<tidy_dagitty>) arrange(<tidy_dagitty>) group_by(<tidy_dagitty>) ungroup(<tidy_dagitty>) transmute(<tidy_dagitty>) distinct(<tidy_dagitty>) full_join(<tidy_dagitty>) inner_join(<tidy_dagitty>) left_join(<tidy_dagitty>) right_join(<tidy_dagitty>) anti_join(<tidy_dagitty>) semi_join(<tidy_dagitty>) slice(<tidy_dagitty>) select_(<tidy_dagitty>) filter_(<tidy_dagitty>) mutate_(<tidy_dagitty>) summarise_(<tidy_dagitty>) arrange_(<tidy_dagitty>) slice_(<tidy_dagitty>): Dplyr verb methods for tidy_dagitty objects

expand_plot(): Quickly scale the size of a ggplot

fortify(<tidy_dagitty>) fortify(<dagitty>): Fortify a tidy_dagitty object for ggplot2

ggplot(<tidy_dagitty>) ggplot(<dagitty>): Create a new ggplot

print(<tidy_dagitty>): Print a tidy_dagitty

remove_axes() remove_grid(): Quickly remove plot axes and grids

as.tbl(<tidy_dagitty>) as_tibble(<tidy_dagitty>): Convert a tidy_dagitty object to tbl

tbl_df.tidy_dagitty(): Convert a tidy_dagitty object to tbl_df