knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
medltmle
Estimation for Natural Mediation Effect in Longitudinal Data
Authors: Ivana Malenica, Wenjing Zheng and Mark van der Laan
medltmle
estimates the natural mediation effect for a longitudinal setting
with time-varying mediators. This R package implements several estimators of the
data dependent parameter (SE) and non-data dependent parameter (NE) for direct
and indirect mediation effects over multiple time points, adjusting for measured
time-varying confounding and informative right-censoring. The theoretical
justifications for using either of the aforementioned parameters are outlined in
the vignette.
Currently available estimators include
Future releases will support longitudinal data in long format and will integrate
with the stremr
package in order to handle
more elaborate longitudinal data structures.
You can install the most recent stable release from GitHub via
devtools
with:
devtools::install_github("podTockom/medltmle")
If you encounter any bugs or have any specific feature requests, please file an issue.
To get an idea of how medltmle
works, let's try using it with a simple
simulated data set:
# setup suppressMessages(library(medltmle)) set.seed(67394) # simulation parameters end.time = 2 n <- 400 # simulate data data <- GenerateData(n = n, end.time = end.time)
Next, we can generate simple models for conditional densities and iterative expectations, and define counterfactual exposures:
# define models spec <- make.sim.spec(2) # define counterfactuals abar <- 1 abar.prime <- 0
Having gone through the above steps, we can now obtain IPTW and TMLE estimates of the natural mediation effect:
# let's fit the longitudinal TMLE for the mediation parameter result_10 <- suppressMessages( medltmle(data = data, Anodes = names(data)[grep("^A", names(data))], Cnodes = names(data)[grep("^C", names(data))], Znodes = names(data)[grep("^Z", names(data))], Lnodes = names(data)[grep("^L", names(data))], Ynodes = names(data)[grep("^Y", names(data))], survivalOutcome = TRUE, QLform = spec$QL.c, QZform = spec$QZ.c, gform = spec$g.c, qzform = spec$qz.c, qLform = spec$qL.c, abar = rep(abar, end.time), abar.prime = rep(abar.prime, end.time), CSE = TRUE, time.end = end.time ) )
After using the medltmle R package, please cite the following:
@software{malenica2018medltmle, author = {Malenica, Ivana and Zheng, Wenjing and {van der Laan}, Mark J}, title = {{medltmle}: Natural mediation effect for a longitudinal setting with time-varying mediators}, year = {2018}, doi = {}, url = {https://github.com/imalenica/medltmle}, note = {R package version 0.1.0} }
© 2018 Ivana Malenica
The contents of this repository are distributed under the MIT license. See below for details:
The MIT License (MIT) Copyright (c) 2018 Ivana Malenica 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, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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