diff --git a/R/get_confidence_set.R b/R/get_confidence_set.R index 556c6ae..9b99f30 100644 --- a/R/get_confidence_set.R +++ b/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( diff --git a/R/lago_optimization.R b/R/lago_optimization.R index ef9cb93..7664afe 100644 --- a/R/lago_optimization.R +++ b/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 diff --git a/R/lago_report.R b/R/lago_report.R index 669e0b0..11d98c8 100644 --- a/R/lago_report.R +++ b/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, diff --git a/R/visualize_cost.R b/R/visualize_cost.R index 211adda..d578807 100644 --- a/R/visualize_cost.R +++ b/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 diff --git a/README.md b/README.md index d49474f..4ccc0ea 100644 --- a/README.md +++ b/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. + +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. diff --git a/_pkgdown.yml b/_pkgdown.yml index 6290dc4..ea0207a 100644 --- a/_pkgdown.yml +++ b/_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. diff --git a/man/get_confidence_set.Rd b/man/get_confidence_set.Rd index c067227..711761a 100644 --- a/man/get_confidence_set.Rd +++ b/man/get_confidence_set.Rd @@ -218,4 +218,13 @@ opt$rec_int head(cs$cs) } +\seealso{ +[lago_optimization()] + +Other LAGO functions: +\code{\link[=lago_optimization]{lago_optimization()}}, +\code{\link[=lago_report]{lago_report()}}, +\code{\link[=visualize_cost]{visualize_cost()}} +} +\concept{LAGO functions} \keyword{internal} diff --git a/man/lago_optimization.Rd b/man/lago_optimization.Rd index 87468ce..1610d26 100644 --- a/man/lago_optimization.Rd +++ b/man/lago_optimization.Rd @@ -373,3 +373,12 @@ lago_optimization( } } +\seealso{ +[get_confidence_set()], [visualize_cost()], [lago_report()] + +Other LAGO functions: +\code{\link[=get_confidence_set]{get_confidence_set()}}, +\code{\link[=lago_report]{lago_report()}}, +\code{\link[=visualize_cost]{visualize_cost()}} +} +\concept{LAGO functions} diff --git a/man/lago_report.Rd b/man/lago_report.Rd index ebd4f40..aefe013 100644 --- a/man/lago_report.Rd +++ b/man/lago_report.Rd @@ -69,3 +69,12 @@ report_path <- lago_report(result) } } +\seealso{ +[lago_optimization()] + +Other LAGO functions: +\code{\link[=get_confidence_set]{get_confidence_set()}}, +\code{\link[=lago_optimization]{lago_optimization()}}, +\code{\link[=visualize_cost]{visualize_cost()}} +} +\concept{LAGO functions} diff --git a/man/visualize_cost.Rd b/man/visualize_cost.Rd index f3728ae..49de629 100644 --- a/man/visualize_cost.Rd +++ b/man/visualize_cost.Rd @@ -71,3 +71,12 @@ visualize_cost( ) } } +\seealso{ +[lago_optimization()] + +Other LAGO functions: +\code{\link[=get_confidence_set]{get_confidence_set()}}, +\code{\link[=lago_optimization]{lago_optimization()}}, +\code{\link[=lago_report]{lago_report()}} +} +\concept{LAGO functions} diff --git a/pkgdown/favicon/apple-touch-icon.png b/pkgdown/favicon/apple-touch-icon.png new file mode 100644 index 0000000..09e61cd Binary files /dev/null and b/pkgdown/favicon/apple-touch-icon.png differ diff --git a/pkgdown/favicon/favicon-96x96.png b/pkgdown/favicon/favicon-96x96.png new file mode 100644 index 0000000..321d5ad Binary files /dev/null and b/pkgdown/favicon/favicon-96x96.png differ diff --git a/pkgdown/favicon/favicon.ico b/pkgdown/favicon/favicon.ico new file mode 100644 index 0000000..491f2ec Binary files /dev/null and b/pkgdown/favicon/favicon.ico differ diff --git a/pkgdown/favicon/favicon.svg b/pkgdown/favicon/favicon.svg new file mode 100644 index 0000000..a9a69a8 --- /dev/null +++ b/pkgdown/favicon/favicon.svg @@ -0,0 +1,21 @@ +RealFaviconGeneratorhttps://realfavicongenerator.netLAGO R package logoA blue hex sticker with an ascending stage path ending at an orange target above the LAGO wordmark. + + + + + + + + + + + + + + + + + + + LAGO + \ No newline at end of file diff --git a/pkgdown/favicon/site.webmanifest b/pkgdown/favicon/site.webmanifest new file mode 100644 index 0000000..4ebda26 --- /dev/null +++ b/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" +} \ No newline at end of file diff --git a/pkgdown/favicon/web-app-manifest-192x192.png b/pkgdown/favicon/web-app-manifest-192x192.png new file mode 100644 index 0000000..4f19e00 Binary files /dev/null and b/pkgdown/favicon/web-app-manifest-192x192.png differ diff --git a/pkgdown/favicon/web-app-manifest-512x512.png b/pkgdown/favicon/web-app-manifest-512x512.png new file mode 100644 index 0000000..f29df7d Binary files /dev/null and b/pkgdown/favicon/web-app-manifest-512x512.png differ