inst/doc/intro-to-dags.R

In ggdag: Analyze and Create Elegant Directed Acyclic Graphs

## ----setup, include = FALSE---------------------------------------------------
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
  dpi <- 320
} else {
  dpi <- 72
}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 4,
  fig.align = "center",
  fig.dpi = dpi,
  warning = FALSE,
  message = FALSE
)
set.seed(2939)

## ----set_theme----------------------------------------------------------------
#  set theme of all DAGs to `theme_dag()`
library(ggdag)
library(ggplot2)
theme_set(theme_dag())

## ----fig.width = 4------------------------------------------------------------
dagify(y ~ x) %>%
  ggdag()

## ----fig.width = 4------------------------------------------------------------
dagify(y ~ ~x) %>%
  ggdag()

## ----fig.width = 4------------------------------------------------------------
#  canonicalize the DAG: Add the latent variable in to the graph
dagify(y ~ ~x) %>%
  ggdag_canonical()

## ----fig.width = 4------------------------------------------------------------
dagify(
  y ~ x,
  x ~ a,
  a ~ y
) %>%
  ggdag()

## -----------------------------------------------------------------------------
smoking_ca_dag <- dagify(cardiacarrest ~ cholesterol,
  cholesterol ~ smoking + weight,
  smoking ~ unhealthy,
  weight ~ unhealthy,
  labels = c(
    "cardiacarrest" = "Cardiac\n Arrest",
    "smoking" = "Smoking",
    "cholesterol" = "Cholesterol",
    "unhealthy" = "Unhealthy\n Lifestyle",
    "weight" = "Weight"
  ),
  latent = "unhealthy",
  exposure = "smoking",
  outcome = "cardiacarrest"
)

ggdag(smoking_ca_dag, text = FALSE, use_labels = "label")

## -----------------------------------------------------------------------------
ggdag_paths(smoking_ca_dag, text = FALSE, use_labels = "label", shadow = TRUE)

## -----------------------------------------------------------------------------
ggdag_adjustment_set(smoking_ca_dag, text = FALSE, use_labels = "label", shadow = TRUE)

## ----fig.width = 4------------------------------------------------------------
fever_dag <- collider_triangle(
  x = "Influenza",
  y = "Chicken Pox",
  m = "Fever"
)

ggdag(fever_dag, text = FALSE, use_labels = "label")

## -----------------------------------------------------------------------------
ggdag_dseparated(fever_dag, text = FALSE, use_labels = "label")

## -----------------------------------------------------------------------------
ggdag_dseparated(fever_dag,
  controlling_for = "m",
  text = FALSE, use_labels = "label"
)

## -----------------------------------------------------------------------------
dagify(fever ~ flu + pox,
  acetaminophen ~ fever,
  labels = c(
    "flu" = "Influenza",
    "pox" = "Chicken Pox",
    "fever" = "Fever",
    "acetaminophen" = "Acetaminophen"
  )
) %>%
  ggdag_dseparated(
    from = "flu", to = "pox", controlling_for = "acetaminophen",
    text = FALSE, use_labels = "label"
  )

## -----------------------------------------------------------------------------
ggdag_dseparated(smoking_ca_dag,
  controlling_for = c("weight", "cholesterol"),
  text = FALSE, use_labels = "label", collider_lines = FALSE
)