adding MCMA materials (#10)

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.gitignore

@@ -13,3 +13,4 @@ _book
 *_cache
 *.log
 site_libs
+!mathjax.html

DESCRIPTION

@@ -3,23 +3,58 @@ Type: Website
 Title: "Analysis of mechanisms"
 Version: 1.0
 URL: https://github.com/steno-aarhus/mediation-analysis-course
-Depends: 
+Depends:
     R (>= 4.0.0),
     tidyverse
 Encoding: UTF-8
 LazyData: true
 License: CC BY 4.0
-Imports: 
+Imports:
     CMAverse (>= 0.1.0),
     DiagrammeR,
     downlit,
     furrr,
     here,
     knitr,
+    quarto,
+    bbotk,
     mediation,
     NetCoupler,
     rmarkdown,
     survival,
-    xml2
-Remotes: 
-    BS1125/CMAverse
+    xml2,
+    magick,
+    pdftools,
+    svglite,
+    qpdf,
+    repr,
+    data.table,
+    mvtnorm,
+    skimr,
+    sessioninfo,
+    checkmate,
+    origami,
+    sl3,
+    medshift,
+    medoutcon,
+    lmtp,
+    lmcmtp
+Suggests:
+    nnls,
+    Rsolnp,
+    nloptr,
+    speedglm,
+    glmnet,
+    earth,
+    ranger,
+    hal9001,
+    SuperLearner,
+    mlr3extralearners
+Remotes:
+    github::BS1125/CMAverse
+    github::tlverse/sl3,
+    github::nhejazi/medshift,
+    github::nhejazi/medoutcon,
+    github::nt-williams/mlr3superlearner@Screener,
+    github::nt-williams/lcmmtp,
+    github::mlr-org/mlr3extralearners@*release

_quarto.yml

@@ -8,6 +8,8 @@ book:
     - "Daniel B. Ibsen"
     - "Omar Silverman"
     - "Jie Zhang"
+    - "Nima Hejazi"
+    - "Iván Díaz"
   site-url: "https://analysis-of-mechanisms.netlify.app"
   repo-url: "https://github.com/steno-aarhus/mediation-analysis-course"
   chapters:
@@ -25,10 +27,19 @@ book:
       - sessions/causal-mediation-analysis-survival-outcomes.qmd
       - sessions/causal-mediation-analysis-sensitivity-analysis.qmd
       - sessions/reporting-guidelines.qmd
+      - sessions/mcma_preface.qmd
+      - sessions/mcma_effects_defn.qmd
       - sessions/group_work_day2.qmd
+      - sessions/mcma_choosing_effects.qmd
+      - sessions/mcma_estim_prelims.qmd
+      - sessions/mcma_estim_natural_interv.qmd
+      - sessions/mcma_estim_walkthru.qmd
+      - sessions/mcma_longit_effects.qmd
       - sessions/NetCoupler-example.qmd
   appendices:
     - appendices/references.qmd
+    - appendices/mcma_stoch_effects.qmd
+    - appendices/mcma_addl_readings.qmd
     - LICENSE.md
   page-footer:
     center:
@@ -45,7 +56,9 @@ editor:
     canonical: true
 
 format:
-  r3-theme-html
+  r3-theme-html:
+    include-in-header:
+      - file: headers/mathjax.html
 
 execute:
   freeze: false

appendices/mcma_addl_readings.qmd

@@ -0,0 +1,63 @@
+# Appendix: Additional topics of interest
+
+The literature on mediation analysis has grown considerably in the last few
+decades and there are now many novel methods to tackle important questions with
+complex data structures. While we are unable to cover all these interesting
+methods in this workshop, here we provide a few references for further reading.
+
+This list is not meant to be comprehensive, just some of our own work and some
+work by others that we know and consider interesting.
+
+## Mediation with multiple mediators and multiple intermediate confounders
+
+Note that the [`medoutcon` `R` package](https://github.com/nhejazi/medoutcon)
+works for multiple mediators but is limited to settings with only a single,
+binary intermediate confounder. If your data scenario includes multiple
+mediators *and* *multiple* intermediate confounders, you should consider using
+the [`HDmediation` `R` package](https://github.com/nt-williams/HDmediation)
+instead.
+
+- [Practical causal mediation analysis: extending nonparametric estimators to
+  estimate the mediated effects of housing voucher receipt on adolescent risk
+  behavior](https://arxiv.org/abs/2212.08164) By Kara E. Rudolph, Nicholas
+  Williams, and Iván Díaz
+
+
+## Mediation with monotonicity of A-Z relationship
+
+- [On identification of natural direct effects when a confounder of the mediator
+  is directly affected by
+  exposure](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230499/) by Eric J.
+  Tchetgen Tchetgen and Tyler J. VanderWeele
+- [Efficient and flexible estimation of natural mediation effects under
+  intermediate confounding and monotonicity
+  constraints](https://onlinelibrary.wiley.com/doi/abs/10.1111/biom.13850) by
+  Kara E. Rudolph and Iván Díaz
+
+## Mediation with instrumental variables
+
+- [Direct and indirect treatment effects–causal chains and mediation analysis
+  with instrumental
+  variables](https://rss.onlinelibrary.wiley.com/doi/full/10.1111/rssb.12232)
+  by Markus Frolich and Martin Huber
+- [Causal mediation with instrumental
+  variables](https://arxiv.org/abs/2112.13898) by Kara E. Rudolph, Nicholas
+  Williams, and Iván Díaz
+
+## Mediation with separable effects
+
+* [An Interventionist Approach to Mediation
+  Analysis](https://dl.acm.org/doi/abs/10.1145/3501714.3501754) by James M.
+  Robins, Thomas S. Richardson, and Ilya Shpitser
+* [Conditional Separable
+  Effects](https://www.tandfonline.com/doi/abs/10.1080/01621459.2022.2071276)
+  by Mats J. Stensrud, James M. Robins, Aaron Sarvet, Eric J. Tchetgen
+  Tchetgen, and Jessica G. Young
+* [Separable Effects for Causal Inference in the Presence of Competing
+  Events](https://www.tandfonline.com/doi/abs/10.1080/01621459.2020.1765783) by
+  Mats J. Stensrud, Jessica G. Young, Vanessa Didelez, James M. Robins, and
+  Miguel A. Hernán
+* [A Generalized Theory of Separable Effects in Competing Event
+  Settings](https://link.springer.com/article/10.1007/s10985-021-09530-8) by
+  Mats J. Stensrud, Miguel A. Hernán, Eric J. Tchetgen Tchetgen, James M.
+  Robins, Vanessa Didelez, and Jessica G. Young