Causal Pitchfork - The Data

Data-based Storytelling

Introduction

This document deals with a fundamental question of causal inference: Which variables should be included in a causal model? (see Cinelli, Forney, and Pearl 2020) To answer this question two points need to be clear:

1. In general each causal model only investigates the causal effect of a single independent variable, \(x_k\), on the dependent variable \(y\). The coefficients associated with all other variables, \(x_{j\neq k}\), cannot (automatically) be interpreted as causal relationships. As regression coefficients are commonly presented in a single table, it is often unclear to the reader which coefficients can be interpreted as causal (see Westreich and Greenland 2013).
2. Statistical significance (or any other statistical test) does not give us any idea about the causal model. To illustrate this, the following figure shows three statistically significant relationships between the variables \(x\) and \(y\) (all t-stats \(> 9\)). However, by construction there is no causal relationship between them in two of these examples. Even more concerning: In one case the exclusion of a control variable leads to spurious correlation (leftmost plot) while in the other the inclusion of the control variable does the same (rightmost plot).

Code

library(tidyverse)
library(patchwork)
set.seed(11)
## Fork
# n ... number of observations
n <- 500
# d ... binary confounder
d <- rbinom(n, 1, 0.5)
x <- 1.5 * d + rnorm(n)
y <- 0.4 + 2 * d + rnorm(n)
data_fork <- data.frame(x, y, d = factor(d, levels = c(0, 1), labels = c("Yes", "No")))
plt_fork <- ggplot(data_fork, aes(x, y)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal() +
  ggtitle("Relation due to omitted confounder")
## Pipe
set.seed(11)
x <- 1 * rnorm(n)
z <- rbinom(n, 1, boot::inv.logit(2 * x + rnorm(n)))
y <- 2 * z + rnorm(n)
data_pipe <- data.frame(x, z = factor(z, levels = c(0, 1), labels = c("Yes", "No")), y)
plt_pipe <- ggplot(data_pipe, aes(x, y)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal() +
  ggtitle("Relation through mediator")
## Collider
set.seed(11)
x <- rnorm(n)
y <- rnorm(n)
a <- rbinom(n, 1, boot::inv.logit(9 * x - 9 * y + rnorm(n)))
data_collider <- data.frame(x, y, a = factor(a, levels = c(0, 1), labels = c("No", "Yes")))
data_collider$x_a <- resid(lm(x ~ 0 + a))
data_collider$y_a <- resid(lm(y ~ 0 + a))
plt_collider <- ggplot(data_collider, aes(x_a, y_a)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal() +
  labs(x = "x", y = "y") +
  theme(legend.position = "top") +
  ggtitle("Relation due to included collider")
plt_fork + plt_pipe + plt_collider

The Fork (Good control)

Code

set.seed(42)
library(ggdag)
library(gt)
library(dagitty)
confounder <- dagify(x ~ d, y ~ d,
  coords = list(
    x = c(x = 1, y = 2, d = 1.5),
    y = c(x = 1, y = 2, d = 2)
  )
) |>
  tidy_dagitty() |>
  mutate(fill = ifelse(name == "d", "Confounder", "variables of interest")) |>
  ggplot(aes(x = x, y = y, xend = xend, yend = yend)) +
  geom_dag_point(size = 7, aes(color = fill)) +
  geom_dag_edges(show.legend = FALSE) +
  geom_dag_text() +
  theme_dag() +
  theme(
    legend.title = element_blank(),
    legend.position = "top"
  )
confounder

A typical dataset with a confounder will exhibit correlation between the treatment \(X\) and outcome \(y.\) This relationship is not causal! In the example below we have a binary confounder \(d\) (Yes/No) that is d-connected with both \(X\) and \(y\) (\(X\) and \(y\) are not d-connected)

Code

set.seed(11)
# n ... number of observations
n <- 500
# d ... binary confounder
d <- rbinom(n, 1, 0.5)
x <- 1.5 * d + rnorm(n)
y <- 0.4 + 2 * d + rnorm(n)
data_fork <- data.frame(x, y, d = factor(d, levels = c(0, 1), labels = c("Yes", "No")))
ggplot(data_fork, aes(x, y)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal()

Code

lm(y ~ x) |>
  broom::tidy() |>
  gt() |>
  fmt_number(
    columns = estimate:p.value,
    decimals = 4
  )

term	estimate	std.error	statistic	p.value
(Intercept)	1.0086	0.0671	15.0351	0.0000
x	0.4672	0.0464	10.0576	0.0000

However once we take the confounder into account the association vanishes which reflects the lack of a causal relationship in this case (note that for simplicity the regression lines in the plot are not the same as the model output shown).

Code

# options(scipen = 10)
ggplot(data_fork, aes(x, y, color = d)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal() +
  theme(legend.position = "top")

Code

lm(y ~ x * d, data_fork) |>
  broom::tidy() |>
  gt() |>
  fmt_number(
    columns = estimate:p.value,
    decimals = 4
  )

term	estimate	std.error	statistic	p.value
(Intercept)	0.4426	0.0633	6.9879	0.0000
x	0.0526	0.0617	0.8519	0.3947
dNo	1.9350	0.1364	14.1815	0.0000
x:dNo	−0.0616	0.0914	−0.6741	0.5006

The Pipe (Bad control)

Code

med <- dagify(z ~ x, y ~ z,
  coords = list(x = c(x = 1, z = 1.5, y = 2), y = c(x = 1, y = 1, z = 1))
) |>
  tidy_dagitty() |>
  mutate(fill = ifelse(name == "z", "Mediator", "variables of interest")) |>
  ggplot(aes(x = x, y = y, xend = xend, yend = yend)) +
  geom_dag_point(size = 7, aes(color = fill)) +
  geom_dag_edges(show.legend = FALSE) +
  geom_dag_text() +
  theme_dag() +
  theme(
    legend.title = element_blank(),
    legend.position = "top"
  )
med

If we have a mediator in our data the picture looks very similar to the previous one. In addition, taking the mediator into account also has a similar effect: we remove the association between \(X\) and \(y\). However, in this case that is not what we want since \(X\) and \(y\) are d-connected. \(X\) causes \(y\) through \(z\) (note that for simplicity the regression lines in the second plot are not the same as the model output shown).

Code

set.seed(11)
x <- 1 * rnorm(n)
z <- rbinom(n, 1, boot::inv.logit(2 * x + rnorm(n)))
y <- 2 * z + rnorm(n)
data_pipe <- data.frame(x, z = factor(z, levels = c(0, 1), labels = c("Yes", "No")), y)
ggplot(data_pipe, aes(x, y)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal()

Code

lm(y ~ x) |>
  broom::tidy() |>
  gt() |>
  fmt_number(
    columns = estimate:p.value,
    decimals = 4
  )

term	estimate	std.error	statistic	p.value
(Intercept)	0.9028	0.0586	15.4170	0.0000
x	0.5804	0.0593	9.7944	0.0000

Code

ggplot(data_pipe, aes(x, y, color = z)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal() +
  theme(legend.position = "top")

Code

lm(y ~ x * z) |>
  broom::tidy() |>
  gt() |>
  fmt_number(
    columns = estimate:p.value,
    decimals = 4
  )

term	estimate	std.error	statistic	p.value
(Intercept)	−0.0393	0.0755	−0.5205	0.6029
x	−0.0185	0.0787	−0.2349	0.8143
z	2.0562	0.1137	18.0855	0.0000
x:z	−0.0324	0.1146	−0.2826	0.7776

The Collider (Bad control)

Code

dagify(a ~ x, a ~ y,
  coords = list(x = c(x = 1, y = 2, a = 1.5), y = c(x = 1, y = 0,  a = 0))
) |>
  tidy_dagitty() |>
  mutate(fill = ifelse(name == "a", "Collider", "variables of interest")) |>
  ggplot(aes(x = x, y = y, xend = xend, yend = yend)) +
  geom_dag_point(size = 7, aes(color = fill)) +
  geom_dag_edges(show.legend = FALSE) +
  geom_dag_text() +
  theme_dag() +
  theme(
    legend.title = element_blank(),
    legend.position = "top"
  )

The collider is a special case. There is no association between \(X\) and \(y\) as long as we do not account for the collider in the model. However, by accounting for the collider we implicitly learn about \(y\) as well (we use \(X\) as the predictor). Since the collider is caused by \(X\) and \(y\), we can figure out what \(y\) must be once we know \(X\) and the collider similar to solving a simple equation you would see in high-school.

Code

set.seed(11)
x <- rnorm(n)
y <- rnorm(n)
a <- rbinom(n, 1, boot::inv.logit(9 * x - 9 * y + rnorm(n)))
data_collider <- data.frame(x, y, a = factor(a, levels = c(0, 1), labels = c("No", "Yes")))
ggplot(data_collider, aes(x, y)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal()

Code

lm(y ~ x) |>
  broom::tidy() |>
  gt() |>
  fmt_number(columns = estimate:p.value, decimals = 4)

term	estimate	std.error	statistic	p.value
(Intercept)	0.0203	0.0449	0.4519	0.6515
x	0.0307	0.0455	0.6754	0.4997

Code

data_collider$x_a <- resid(lm(x ~ 0 + a))
data_collider$y_a <- resid(lm(y ~ 0 + a))
ggplot(data_collider, aes(x_a, y_a)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +
  theme_minimal() +
  labs(x = "x after accounting for a", y = "y after accounting for a") +
  theme(legend.position = "top")

Code

lm(y ~ x + a, data_collider) |>
  broom::tidy() |>
  gt() |>
  fmt_number(columns = estimate:p.value, decimals = 4)

term	estimate	std.error	statistic	p.value
(Intercept)	0.8614	0.0538	16.0142	0.0000
x	0.5328	0.0422	12.6293	0.0000
aYes	−1.6663	0.0834	−19.9822	0.0000

Connections to related concepts

Omitted Variable Bias (OVB)

Recall that variables that influence both the outcome and other independent variables will bias the coefficients of those other independent variables if left out of a model. This bias is referred to as “Omitted Variable Bias” (short OVB) since it occurs due to the omission of a crucial variable. OVB occurs whenever a confounder (see The Fork) is left out of the model. The magnitude of the bias depends on how strongly correlated the confounder is with the included variable \(x\). To illustrate this take a look at the equations representing the situation in The Fork:

\[ \begin{aligned} x &= \alpha_0 + \alpha_1 d + \varepsilon_x \\ y &= \beta_0 + \beta_1 d + \varepsilon_y \end{aligned} \]

However, we might be unaware of the confounder \(d\) but still be interested in the causal effect of \(x\) on \(y\). Therefore, we might be inclined to estimate the following (misspecified) model

\[ y = \gamma_0 + \gamma_1 x + \epsilon_y \] We know (based on the equations above) that the true effect of \(x\) on \(y\) is \(0\) as it is entirely caused by \(d\). In order to investigate the magnitude of the OVB we mistakenly view \(d\) as a function of \(x\) (see Mediation analysis):

\[ d = \theta_0 + \theta_1 x + \varepsilon_d, \]

plug the incorrectly specified model for \(d\) into the correctly specified model for \(y\), and take the derivative with respect to \(x\):

\[ \begin{aligned} y &= \tilde \beta_0 + \beta_1 (\theta_0 + \theta_1 x + \varepsilon_d) + \epsilon_y \\ &= \tilde \beta_0 + \beta_1 \theta_0 + \beta_1 \theta_1 x + \beta_1 \varepsilon_d + \epsilon_y \\ {\delta \over \delta x} &= \beta_1 \theta_1 \end{aligned} \]

Note that \(\gamma_1 = \beta_1 \theta_1\).

library(stargazer)
set.seed(11)
d <- 100 * rnorm(n)
x <- -4 + 0.5 * d + 10 * rnorm(n)
y <- 25 + 10 * d + 10 * rnorm(n)
stargazer(
  lm(y ~ d + x),
  lm(y ~ x), ## gamma
  lm(y ~ d), ## beta
  lm(d ~ x), ## theta
  type = 'html')

	Dependent variable:
	y			d
	(1)	(2)	(3)	(4)
d	9.996***		9.997***
	(0.023)		(0.005)
x	0.003	19.096***		1.910***
	(0.046)	(0.173)		(0.017)
Constant	24.889***	97.282***	24.878***	7.242***
	(0.488)	(8.789)	(0.456)	(0.878)
Observations	500	500	500	500
R2	1.000	0.961	1.000	0.961
Adjusted R2	1.000	0.961	1.000	0.961
Residual Std. Error	10.204 (df = 497)	195.949 (df = 498)	10.193 (df = 498)	19.576 (df = 498)
F Statistic	2,343,560.000*** (df = 2; 497)	12,212.740*** (df = 1; 498)	4,696,511.000*** (df = 1; 498)	12,242.150*** (df = 1; 498)
Note:	p<0.1; p<0.05; p<0.01

## See coef of regression y ~ x
beta1 <- coef(lm(y~d))['d']
theta1 <- coef(lm(d~x))['x']
beta1 * theta1

   d 

19.09598

Notice that without theoretical knowledge about the data it is not clear which variable should be the “outcome” and which the “independent” variable since we could estimate either direction using OLS. In the example above we know (“from theory”) that \(d\) causes \(x\) and \(y\) but we estimate models where \(x\) is the explanatory variable. As one might guess there is a clear relationship between coefficients estimated with one or the other variable on the left hand side.

theta_1 <- coef(lm(d~x))['x']
alpha_1 <- coef(lm(x~d))['d']

To be exact we have to adjust for the respective variances of the variables:

alpha_1 * var(d)/var(x)

       d 
1.910091 

theta_1

       x 
1.910091 

Mediation analysis

As the total causal effect a variable \(x\) has on the outcome \(y\) can be (partly) mediated through another variable \(m\), we cannot just include \(m\) in the model. However, we can decompose the effect into a direct and mediated part. Either of part can be \(0\) but we can easily test whether that is the case. The decomposition has two parts: First, calculate the effect the variable of interest (\(x\)) has on the mediator (\(m\)):

\[ m = \alpha_0 + \alpha_1 x + \varepsilon_m \]

Note that we use “alpha” (\(\alpha\)) for the regression coefficients to distinguish them from the parameters below. They can nonetheless be estimated using OLS.

Second, calculate the full model for the outcome (\(y\)) including both \(x\) and \(m\):

\[ y = \beta_0 + \beta_1 x + \beta_2 m + \varepsilon_y \]

Now \(\beta_1\) is the average direct effect (ADE) of \(x\) on \(y\). That is the part that is not mediated through \(m\). In The Pipe, \(\beta_1=0\) since there is no direct connection from \(x\) to \(y\). The average causal mediation effect (ACME) can be calculated as \(\alpha_1 * \beta_2\). Intuitively, “how much would a unit increase in \(x\) change \(m\)” times “how much would an increase in \(m\) change \(y\)”. The total effect of \(x\) on \(y\) can be seen more clearly by plugging in the model for \(m\) in the second equation and taking the derivative with respect to \(x\):

\[ \begin{aligned} y &= \beta_0 + \beta_1 x + \beta_2 m + \varepsilon_y \\ &= \beta_0 + \beta_1 x + \beta_2 (\alpha_0 + \alpha_1 x + \varepsilon_m) + \varepsilon_y \\ &= \beta_0 + \beta_1 x + \beta_2 \alpha_0 + \beta_2 \alpha_1 x + \beta_2 \varepsilon_m + \varepsilon_y \\ \text{total effect} := \frac{\delta y}{\delta x} &= \underbrace{\beta_1}_{\text{ADE}} + \underbrace{\beta_2 \alpha_1}_{\text{ACME}} \end{aligned} \]

Note that if we are only interested in the total effect we can omit the mediator \(m\) from the model and estimate:

\[ y = \gamma_0 + \gamma_1 x + \epsilon_y \] where \(\gamma_1 = \beta_1 + \beta_2 \alpha_1\) (again: all these equations can be estimated using OLS). In that case we are using OVB in our favor: By omitting \(m\) its effect on \(y\) is picked up by \(x\) to exactly the degree that \(x\) and \(m\) are correlated. However, in contrast to the previous example that is exactly what we want since \(m\) is caused by \(x\) as well!

Notable changes to The Pipe:

• We have both direct and indirect effects of \(x\) on \(y\)
• The mediator \(m\) is continuous instead of binary

Code

med2 <- dagify(m ~ x, y ~ m + x,
  coords = list(x = c(x = 1, m = 1.5, y = 2), y = c(x = 1, y = 1, m = 1.5))
) |>
  tidy_dagitty() |>
  mutate(fill = ifelse(name == "m", "Mediator", "variables of interest")) |>
  ggplot(aes(x = x, y = y, xend = xend, yend = yend)) +
  geom_dag_point(size = 7, aes(color = fill)) +
  geom_dag_edges(show.legend = FALSE) +
  geom_dag_text() +
  theme_dag() +
  theme(
    legend.title = element_blank(),
    legend.position = "top"
  )
med2

set.seed(11)
X <- 100 * rnorm(n)
M <- 10 + 0.5 * X + 5 * rnorm(n)
Y <- -25 + 4 * X + 3 * M + 10 * rnorm(n)
X_on_M <- lm(M ~ X)
avg_direct_effect <- lm(Y ~ X + M)
total_effect <- lm(Y ~ X)
stargazer(
  X_on_M, 
  avg_direct_effect, 
  total_effect, 
  type = 'html')

	Dependent variable:
	M	Y
	(1)	(2)	(3)
X	0.502***	3.995***	5.502***
	(0.002)	(0.046)	(0.008)
M		3.006***
		(0.091)
Constant	10.102***	-25.181***	5.182***
	(0.225)	(1.026)	(0.815)
Observations	500	500	500
R2	0.990	1.000	0.999
Adjusted R2	0.990	1.000	0.999
Residual Std. Error	5.023 (df = 498)	10.204 (df = 497)	18.218 (df = 498)
F Statistic	48,670.140*** (df = 1; 498)	710,360.500*** (df = 2; 497)	445,339.400*** (df = 1; 498)
Note:	p<0.1; p<0.05; p<0.01

avg_causal_mediation_effect <- coef(X_on_M)['X'] * coef(avg_direct_effect)['M']
total_effect_alternative <- coef(avg_direct_effect)['X'] + avg_causal_mediation_effect
proportion_mediated <- avg_causal_mediation_effect / total_effect_alternative

Code

mediation_effects <- tribble(
        ~effect,                                  ~value,
        "Average Causal Mediation Effect (ACME):", avg_causal_mediation_effect,
        "Average Direct Effect (ADE):",            coef(avg_direct_effect)['X'],
        "Total Effect:",                           coef(total_effect)['X'],
        "Total Effect (alternative):",             total_effect_alternative,
        "Proportion Mediated:",                    proportion_mediated)

gt(mediation_effects, rowname_col = 'effect')  |>
  tab_options(column_labels.hidden = TRUE) |>
  fmt_number(columns = value, decimals = 3) |>
  tab_header(title = "Causal Mediation Analysis")

Causal Mediation Analysis
Average Causal Mediation Effect (ACME):	1.508
Average Direct Effect (ADE):	3.995
Total Effect:	5.502
Total Effect (alternative):	5.502
Proportion Mediated:	0.274

Alternatively, the mediation analysis can be performed using the mediation package:

library(mediation)
mediation_result <- mediate(X_on_M, avg_direct_effect, 
                            treat = 'X', mediator = 'M',
                            boot = TRUE, sims = 1000)
summary(mediation_result)

Causal Mediation Analysis 

Nonparametric Bootstrap Confidence Intervals with the Percentile Method

               Estimate 95% CI Lower 95% CI Upper p-value    
ACME              1.508        1.421         1.60  <2e-16 ***
ADE               3.995        3.901         4.08  <2e-16 ***
Total Effect      5.502        5.486         5.52  <2e-16 ***
Prop. Mediated    0.274        0.258         0.29  <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Sample Size Used: 500 


Simulations: 1000 

Estimation using Process

In research settings the PROCESS macro by Andrew Hayes is very popular. The following code should download and source the macro for you but will definitely break in the future (try changing the v42 part of the link to v43 or v44 etc. or obtain a new link from the website if it does):

## Download and source the PROCESS macro by Andrew F. Hayes
temp <- tempfile()
process_macro_dl <- "https://www.afhayes.com/public/processv43.zip"
download.file(process_macro_dl,temp)
files <- unzip(temp, list = TRUE)
fname <- files$Name[endsWith(files$Name, "process.R")]
source(unz(temp, fname))
unlink(temp)
rm(files)
rm(fname)
rm(process_macro_dl)
rm(temp)

Alternatively download the program from here and source the process.R file manually.

PROCESS model 4 (not run):

process(data.frame(Y, X, M), y = 'Y', x = 'X', m = 'M', model = 4)

Appendix: How the sausage is made

The fork, mediator, and collider were generated as binary variables to make visualization easier. Binary variables can be drawn from a so-called Bernoulli distribution which is a special case of the binomial distribution with size = 1. The distribution takes the probability of getting a \(1\) as input.

The Fork

## Make code reproducible
set.seed(11)
## Number of observations
n <- 1500
## Random draw from Bernoulli with p(1) = 0.5, p(0) = 0.5
d <- rbinom(n, 1, 0.5)
## X is caused by d
x <- 2 * d + rnorm(n)
## y is caused by d
y <- 0.4 + 2.5 * d + rnorm(n)
fork <- data.frame(x, y, d = factor(d,
  levels = c(0, 1),
  labels = c("No", "Yes")
))
ggplot(fork, aes(x, y, color = d)) +
  geom_point() +
  theme_minimal() +
  theme(legend.position = "top")

The Pipe

Code

## Generate random X
x <- rnorm(n)
## inv.logit ensures that values are between 0 and 1
ggplot(data.frame()) +
  stat_function(fun = boot::inv.logit, xlim = c(-10, 10)) +
  theme_minimal() +
  labs(title = "Inverse Logit function", x = "x", y = "inv.logit(x)")

Code

## z is caused by X
z <- rbinom(n, 1, boot::inv.logit(2 * x + rnorm(n)))
## y is caused by z
y <- 2 * z + rnorm(n)
pipe <- data.frame(x, y, z = factor(z,
  levels = c(0, 1),
  labels = c("Yes", "No")
))
ggplot(pipe, aes(x, y, color = z)) +
  geom_point() +
  theme_minimal() +
  theme(legend.position = "top")

The Collider

Code

## Generate random x
x <- rnorm(n)
## Generate random y
y <- rnorm(n)
## a is caused by both X and y
a <- rbinom(n, 1, boot::inv.logit(9 * x - 9 * y + rnorm(n)))
collider <- data.frame(x, y, a = factor(a,
  levels = c(0, 1),
  labels = c("No", "Yes")
))
ggplot(collider, aes(x, y)) +
  geom_point() +
  theme_minimal()

In order to get the partial correlation of \(X\) and \(y\) after accounting for \(a\) we first regress both \(X\) and \(y\) on \(a\) and use the unexplained part (residual) in the plot. This is equivalent to a regression that has both \(X\) and \(a\) as explanatory variables.

Code

collider$x_a <- residuals(lm(x ~ 0 + a))
collider$y_a <- residuals(lm(y ~ 0 + a))
ggplot(collider, aes(x_a, y_a)) +
  geom_point() +
  theme_minimal() +
  labs(x = "x after accounting for a", y = "y after accounting for a")

References

Cinelli, Carlos, Andrew Forney, and Judea Pearl. 2020. “A Crash Course in Good and Bad Controls.” SSRN 3689437.

Westreich, Daniel, and Sander Greenland. 2013. “The Table 2 Fallacy: Presenting and Interpreting Confounder and Modifier Coefficients.” American Journal of Epidemiology 177 (4): 292–98.