Cross-link the docs, add a citation section and flesh out the site

R/get_confidence_set.R

@@ -166,6 +166,8 @@
 #' head(cs$cs)
 #'
 #' @keywords internal
+#' @family LAGO functions
+#' @seealso [lago_optimization()]
 #' @export
 #'
 get_confidence_set <- function(

R/lago_optimization.R

@@ -286,6 +286,8 @@
 #' )
 #' }
 #'
+#' @family LAGO functions
+#' @seealso [get_confidence_set()], [visualize_cost()], [lago_report()]
 #' @export
 #' @importFrom utils head
 #' @import cli

R/lago_report.R

@@ -49,6 +49,8 @@
 #' report_path <- lago_report(result)
 #' }
 #'
+#' @family LAGO functions
+#' @seealso [lago_optimization()]
 #' @export
 lago_report <- function(x,
                         output_file = NULL,

R/visualize_cost.R

@@ -25,6 +25,8 @@
 #' @param intervention_upper_bounds A numeric vector of the upper bounds for
 #' each intervention component.
 #'
+#' @family LAGO functions
+#' @seealso [lago_optimization()]
 #' @export
 #' @import bslib shiny
 #' @importFrom shinyjs useShinyjs show hide runjs

README.md

@@ -414,6 +414,19 @@ See [`python/README.md`](https://github.com/correspondMerchant/LAGO-R-Package/bl
 3. [Bing A, Spiegelman D, Lok JJ. Learn-As-you-GO (LAGO) Trials: Optimizing Trials for Effectiveness and Power to Prevent Failed Trials. arXiv:2509.11479](https://arxiv.org/pdf/2509.11479)
 4. [Bui, M. T., Longenecker, C. T., Bing, A., Spiegelman, D., Webel, A. R., Bosworth, H. B., & Lok, J. J. (2026). Addressing Confounding by Indication Through (Un) Measured Centre Characteristics in Learn-As-you-GO (LAGO) Trials. arXiv preprint arXiv:2604.13276.](https://arxiv.org/abs/2604.13276)
 
+## Citation
+If you use this package, please cite both the software and the LAGO methodology.
+
+To get the software citation in R:
+```r
+citation("LAGOtrials")
+```
+
+For the methodology, please cite Bing et al. (2025):
+> Bing A, Spiegelman D, Nevo D, Lok JJ. Learn-As-you-GO (LAGO) Trials: Optimizing Treatments and Preventing Trial Failure Through Ongoing Learning. Biometrics, 81(2), ujaf061. <https://doi.org/10.1093/biomtc/ujaf061>
+
+A machine-readable citation is also provided in [CITATION.cff](CITATION.cff), which powers the "Cite this repository" button on GitHub.
+
 ## How to get help
 Before reaching out for help, please carefully review this README, examine the descriptions of the arguments in the R help files, run the `.Rmd` files in the [manual tests](https://github.com/correspondMerchant/LAGO-R-Package/tree/main/tests/manual_tests) folder, and read the relevant LAGO papers.
 

_pkgdown.yml

@@ -3,6 +3,19 @@ url: https://correspondmerchant.github.io/LAGO-R-Package/
 template:
   bootstrap: 5
 
+authors:
+  Ante Bing:
+    href: mailto:abing@bu.edu
+
+navbar:
+  structure:
+    right: [search, github]
+
+news:
+  releases:
+  - text: "Version 1.1.0"
+    href: news/index.html
+
 reference:
 - title: Optimization
   desc: Main user-facing functions.

pkgdown/favicon/site.webmanifest

@@ -0,0 +1,21 @@
+{
+  "name": "",
+  "short_name": "",
+  "icons": [
+    {
+      "src": "/web-app-manifest-192x192.png",
+      "sizes": "192x192",
+      "type": "image/png",
+      "purpose": "maskable"
+    },
+    {
+      "src": "/web-app-manifest-512x512.png",
+      "sizes": "512x512",
+      "type": "image/png",
+      "purpose": "maskable"
+    }
+  ],
+  "theme_color": "#ffffff",
+  "background_color": "#ffffff",
+  "display": "standalone"
+}