Website configuration

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -8,6 +8,8 @@ Imports:
 	MCMCpack,
 	doParallel,
 	foreach,
+	parallel,
+	R2jags,
 	coda (>= 0.19-4)
 License: MIT + file LICENSE
 Encoding: UTF-8
@@ -18,5 +20,6 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
-Description: This package provides tools for estimating causal effects using Bayesian Marginal Structural Models. It includes functions for Bayesian non-parametric bootstrap to calculate causal effects and for plotting the average potential outcome (APO). The package aims to facilitate the analysis of observational data with time-varying treatments, providing a user-friendly software to Bayesian causal inference methods.
+Description: This package provides tools for estimating causal effects using Bayesian Marginal Structural Models. It includes functions for estimating Bayesian weights using JAGS and for Bayesian non-parametric bootstrap to calculate causal effects.
 VignetteBuilder: knitr
+URL: https://kuan-liu-lab.github.io/bayesmsm/

R/summary.bayesmsm.R

@@ -2,7 +2,7 @@
 #'
 #' @param model A model object from bayesmsm
 #'
-#' @return
+#' @return A summary table of the results from bayesmsm.
 #' @export
 #'
 #' @examples

README.md

@@ -2,7 +2,8 @@
 
 [![pkgdown](https://img.shields.io/badge/pkgdown--blue)](https://Kuan-Liu-Lab.github.io/bayesmsm/)
 
-The `bayesmsm` package is an R package for implementing Bayesian marginal structural models.
+This package provides tools for estimating causal effects using Bayesian Marginal Structural Models. It includes functions for estimating Bayesian weights using JAGS and for Bayesian non-parametric bootstrap to calculate causal effects.
+
 
 # Reference
 
@@ -11,21 +12,89 @@ Reference paper on Bayesian marginal structural models:
 -  Saarela, O., Stephens, D. A., Moodie, E. E., & Klein, M. B. (2015). On Bayesian estimation of marginal structural models. Biometrics, 71(2), 279-288.
 
 -  Liu, K., Saarela, O., Feldman, B. M., & Pullenayegum, E. (2020). Estimation of causal effects with repeatedly measured outcomes in a Bayesian framework. Statistical methods in medical research, 29(9), 2507-2519.
-    
+
 
 # Installation
-install using `devtools` package
-```
+
+Install using `devtools` package:
+
+```r
 ## install.packages(devtools) ## make sure to have devtools installed 
 devtools::install_github("Kuan-Liu-Lab/bayesmsm")
 library(bayesmsm)
 ```
 
 # Dependency
 
-
+This package depends on the following R packages:
+-  `MCMCpack`
+-  `doParallel`
+-  `foreach`
+-  `parallel`
+-  `R2jags`
+-  `coda`
 
 
 # Examples
 
+Here are some examples demonstrating how to use the `bayesmsm` package:
+
+```r
+# Load example data
+testdata <- read.csv(system.file("extdata", "continuous_outcome_data.csv", package = "bayesmsm"))
+
+# Calculate Bayesian weights
+weights <- bayesweight(
+  trtmodel.list = list(
+    a_1 ~ w1 + w2 + L1_1 + L2_1,
+    a_2 ~ w1 + w2 + L1_1 + L2_1 + L1_2 + L2_2 + a_1
+  ),
+  data = testdata,
+  n.iter = 250,
+  n.burnin = 150,
+  n.thin = 5,
+  n.chains = 2,
+  seed = 890123,
+  parallel = TRUE
+)
+
+# Perform Bayesian non-parametric bootstrap
+model <- bayesmsm(
+  ymodel = y ~ a_1 + a_2,
+  nvisit = 2,
+  reference = c(rep(0, 2)),
+  comparator = c(rep(1, 2)),
+  family = "gaussian",
+  data = testdata,
+  wmean = weights,
+  nboot = 1000,
+  optim_method = "BFGS",
+  seed = 890123,
+  parallel = TRUE,
+  ncore = 2
+)
+
+# View model summary
+summary.bayesmsm(model)
+```
+
+
+# Documentation
+
+For comprehensive documentation and examples, visit the [pkgdown website](https://Kuan-Liu-Lab.github.io/bayesmsm/).
+
+
+# License
+
+This package is licensed under the MIT License. See the LICENSE file for details.
+
+
+# Citation
+
+If you use the `bayesmsm` package in your research, please cite the reference papers listed above.
+
+
+# Developers
 
+-  Kuan Liu
+-  Xiao Yan (Maintainer)

_pkgdown.yml

@@ -1,23 +1,21 @@
 pkgdown:
   title: bayesmsm
   destination: docs
-
 template:
   bootstrap: 5
   bootswatch: flatly
-
 navbar:
   structure:
     left:
     - home
     - reference
     - articles
   left:
-  - text: "Home"
+  - text: Home
     href: index.html
-  - text: "Reference"
+  - text: Reference
     href: reference/index.html
-  - text: "Articles"
+  - text: Articles
     href: articles/index.html
+url: https://kuan-liu-lab.github.io/bayesmsm/
 
-url: https://Kuan-Liu-Lab.github.io/bayesmsm/

docs/pkgdown.yml

@@ -3,7 +3,7 @@ pkgdown: 2.0.8
 pkgdown_sha: ~
 articles:
   vignette: vignette.html
-last_built: 2024-06-27T06:24Z
+last_built: 2024-06-27T06:32Z
 urls:
   reference: https://Kuan-Liu-Lab.github.io/bayesmsm/reference
   article: https://Kuan-Liu-Lab.github.io/bayesmsm/articles

docs/sitemap.xml

@@ -30,9 +30,6 @@
   <url>
     <loc>https://Kuan-Liu-Lab.github.io/bayesmsm/reference/calculate_effect.html</loc>
   </url>
-  <url>
-    <loc>https://Kuan-Liu-Lab.github.io/bayesmsm/reference/hello.html</loc>
-  </url>
   <url>
     <loc>https://Kuan-Liu-Lab.github.io/bayesmsm/reference/index.html</loc>
   </url>