dagitty和ggdag的对比

dag <- dagitty(
"
dag {
y <- x <- z1 <- v -> z2 -> y
z1 <- w1 <-> w2 -> z2
x <- w1 -> y
x <- w2 -> y
x [exposure]
y [outcome]
}
"
)

## Error in `dagitty()`:
## ! could not find function "dagitty"

tidy_dag <- tidy_dagitty(dag)

## Error in `tidy_dagitty()`:
## ! could not find function "tidy_dagitty"

tidy_dag

## Error:
## ! object 'tidy_dag' not found

ggdag(tidy_dag)

## Error in `ggdag()`:
## ! could not find function "ggdag"

• 这里的代码，类似于 @DiagrammeR 开发的包DiagrammeR。
• <->表示双向箭头。

tidy_ggdag <-
  ggdag::dagify(
    y ~ x + z2 + w2 + w1,
    x ~ z1 + w1,
    z1 ~ w1 + v,
    z2 ~ w2 + v,
    w1 ~~ w2, # bidirected path
    exposure = "x",
    outcome = "y"
    ) %>%
  tidy_dagitty()

## Error in `ggdag::dagify(y ~ x + z2 + w2 + w1, x ~ z1 + w1, z1 ~ w1 + v, z2 ~ w2 + v, w1 ~
##     (~w2), exposure = "x", outcome = "y") %>% tidy_dagitty()`:
## ! could not find function "%>%"

tidy_ggdag

## Error:
## ! object 'tidy_ggdag' not found

ggdag(tidy_ggdag)

## Error in `ggdag()`:
## ! could not find function "ggdag"

• ggdag函数是内置ggplot2的，因此非常方便。
• ~~表示双向箭头。
• y ~ x + z2 + w2 + w1表示这四个变量都导致y，类似于回归方程中，自变量和因变量的关系。
• 而且这里不需要string格式的输入。

加label

confounder_triangle是ggdag的一个内置函数， @Barrett2018 给了一个加上label的例子。

confounder_triangle(x = "Coffee", y = "Lung Cancer", z = "Smoking") %>%
  ggdag_dconnected(text = FALSE, use_labels = "label")

## Error in `confounder_triangle(x = "Coffee", y = "Lung Cancer", z = "Smoking") %>%
##     ggdag_dconnected(text = FALSE, use_labels = "label")`:
## ! could not find function "%>%"

批量label

coffee_dag <- dagify(cancer ~ smoking,
       smoking ~ addictive,
       coffee ~ addictive,
       exposure = "coffee",
       outcome = "cancer",
       labels = c("coffee" = "Coffee", "cancer" = "Lung Cancer",
                  "smoking" = "Smoking", "addictive" = "Addictive \nBehavior")) %>%
  tidy_dagitty(layout = "tree")

## Error in `dagify(cancer ~ smoking, smoking ~ addictive, coffee ~ addictive, exposure = "coffee",
##   outcome = "cancer", labels = c(coffee = "Coffee", cancer = "Lung Cancer",
##     smoking = "Smoking", addictive = "Addictive \nBehavior")) %>% tidy_dagitty(
##     layout = "tree")`:
## ! could not find function "%>%"

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

## Error in `ggdag()`:
## ! could not find function "ggdag"