In nhejazi/medoutcon: Efficient Natural and Interventional Causal Mediation Analysis

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R/`medoutcon`

Efficient Causal Mediation Analysis for the Natural and Interventional Effects

Authors: Nima Hejazi, Iván Díaz, and Kara Rudolph

What's `medoutcon`?

The medoutcon R package provides facilities for efficient estimation of path-specific (in)direct effects that measure the impact of a treatment variable $A$ on an outcome variable $Y$, through a direct path (through $A$ only) and an indirect path (through a set of mediators $M$ only). In the presence of an intermediate mediator-outcome confounder $Z$, itself affected by the treatment $A$, these correspond to the interventional (in)direct effects described by @diaz2020nonparametric, though similar (yet less general) effect definitions and/or estimation strategies have appeared in @vanderweele2014effect, @rudolph2017robust, @zheng2017longitudinal, and @benkeser2020nonparametric. When no intermediate confounders are present, these effect definitions simplify to the well-studied natural (in)direct effects, and our estimators are analogs of those formulated by @zheng2012targeted. Both an efficient one-step bias-corrected estimator with cross-fitting [@pfanzagl1985contributions; @zheng2011cross; @chernozhukov2018double] and a cross-validated targeted minimum loss estimator (TMLE) [@vdl2011targeted; @zheng2011cross] are made available. medoutcon integrates with the sl3 R package [@coyle-gh-sl3] to leverage statistical machine learning in the estimation procedure.

Installation

Install the most recent stable release from GitHub via remotes:

remotes::install_github("nhejazi/medoutcon")

Example

To illustrate how medoutcon may be used to estimate stochastic interventional (in)direct effects of the exposure (A) on the outcome (Y) in the presence of mediator(s) (M) and a mediator-outcome confounder (Z), consider the following example:

library(data.table)
library(stringr)
library(medoutcon)
set.seed(02138)

# produces a simple data set based on ca causal model with mediation
make_example_data <- function(n_obs = 1000) {
  ## baseline covariates
  w_1 <- rbinom(n_obs, 1, prob = 0.6)
  w_2 <- rbinom(n_obs, 1, prob = 0.3)
  w_3 <- rbinom(n_obs, 1, prob = pmin(0.2 + (w_1 + w_2) / 3, 1))
  w <- cbind(w_1, w_2, w_3)
  w_names <- paste("W", seq_len(ncol(w)), sep = "_")

  ## exposure
  a <- as.numeric(rbinom(n_obs, 1, plogis(rowSums(w) - 2)))

  ## mediator-outcome confounder affected by treatment
  z <- rbinom(n_obs, 1, plogis(rowMeans(-log(2) + w - a) + 0.2))

  ## mediator -- could be multivariate
  m <- rbinom(n_obs, 1, plogis(rowSums(log(3) * w[, -3] + a - z)))
  m_names <- "M"

  ## outcome
  y <- rbinom(n_obs, 1, plogis(1 / (rowSums(w) - z + a + m)))

  ## construct output
  dat <- as.data.table(cbind(w = w, a = a, z = z, m = m, y = y))
  setnames(dat, c(w_names, "A", "Z", m_names, "Y"))
  return(dat)
}

# set seed and simulate example data
example_data <- make_example_data(n_obs = 5000L)
w_names <- str_subset(colnames(example_data), "W")
m_names <- str_subset(colnames(example_data), "M")

# quick look at the data
head(example_data)

# compute one-step estimate of the interventional direct effect
os_de <- medoutcon(
  W = example_data[, ..w_names],
  A = example_data$A,
  Z = example_data$Z,
  M = example_data[, ..m_names],
  Y = example_data$Y,
  effect = "direct",
  estimator = "onestep"
)
os_de

# compute targeted minimum loss estimate of the interventional direct effect
tmle_de <- medoutcon(
  W = example_data[, ..w_names],
  A = example_data$A,
  Z = example_data$Z,
  M = example_data[, ..m_names],
  Y = example_data$Y,
  effect = "direct",
  estimator = "tmle"
)
tmle_de

For details on how to use data adaptive regression (machine learning) techniques in the estimation of nuisance parameters, consider consulting the vignette that accompanies the package.

Issues

If you encounter any bugs or have any specific feature requests, please file an issue.

Contributions

Contributions are very welcome. Interested contributors should consult our contribution guidelines prior to submitting a pull request.

Citation

After using the medoutcon R package, please cite the following:

    @article{diaz2020nonparametric,
      title={Non-parametric efficient causal mediation with intermediate
        confounders},
      author={D{\'\i}az, Iv{\'a}n and Hejazi, Nima S and Rudolph, Kara E
        and {van der Laan}, Mark J},
      year={2020},
      url = {https://arxiv.org/abs/1912.09936},
      doi = {10.1093/biomet/asaa085},
      journal={Biometrika},
      volume = {108},
      number = {3},
      pages = {627--641},
      publisher={Oxford University Press}
    }

    @article{hejazi2022medoutcon-joss,
      author = {Hejazi, Nima S and Rudolph, Kara E and D{\'\i}az,
        Iv{\'a}n},
      title = {{medoutcon}: Nonparametric efficient causal mediation
        analysis with machine learning in {R}},
      year = {2022},
      doi = {10.21105/joss.03979},
      url = {https://doi.org/10.21105/joss.03979},
      journal = {Journal of Open Source Software},
      publisher = {The Open Journal}
    }

    @software{hejazi2022medoutcon-rpkg,
      author={Hejazi, Nima S and D{\'\i}az, Iv{\'a}n and Rudolph, Kara E},
      title = {{medoutcon}: Efficient natural and interventional causal
        mediation analysis},
      year  = {2024},
      doi = {10.5281/zenodo.5809519},
      url = {https://github.com/nhejazi/medoutcon},
      note = {R package version 0.2.3}
    }

License

The contents of this repository are distributed under the MIT license. See below for details:

MIT License

Copyright (c) 2020-2024 Nima S. Hejazi

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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