--- title: "The built-in application" author: "Muhammad Yaseen" date: last-modified format: html: self-contained: true number-sections: true toc: true toc-depth: 3 highlight-style: pygments code-tools: true html-math-method: mathjax vignette: > %\VignetteIndexEntry{The built-in application} %\VignetteEngine{quarto::html} %\VignetteEncoding{UTF-8} execute: echo: true warning: false message: false --- {{< include _bayesammi-macros.txt >}} ```{r setup, include = FALSE} # HTML figures are drawn as PNG and kept as WebP: lossless (the same pixels in about half the space of PNG), or # lossy at quality 90 when that is less than half the size, as for traces and densities of thousands of draws. The # PDF figures stay vector graphics. Any failure of magick (not installed, no WebP, or a broken installation whose # system libraries are missing) keeps the PNG webp <- function(path) { if (knitr::is_latex_output() || !grepl(pattern = "[.]png$", x = path)) return(path) tryCatch( { if (!requireNamespace("magick", quietly = TRUE) || !isTRUE(magick::magick_config()$webp)) return(path) img <- magick::image_read(path) out <- sub(pattern = "[.]png$", replacement = ".webp", x = path) tmp <- tempfile(fileext = ".webp") magick::image_write( image = img , path = out , format = "webp" , quality = 100 , defines = c(`webp:lossless` = "true") ) magick::image_write(image = img, path = tmp, format = "webp", quality = 90) if (file.size(tmp) < file.size(out) / 2) file.copy(from = tmp, to = out, overwrite = TRUE) unlink(c(path, tmp)) out } , error = function(e) path ) } knitr::opts_chunk$set(collapse = FALSE, comment = "", fig.width = 7, fig.height = 4.2, dev = if (knitr::is_latex_output()) "cairo_pdf" else "ragg_png", dpi = 96, fig.process = webp) if (requireNamespace("bayesammi", quietly = TRUE)) library(bayesammi) else pkgload::load_all(export_all = FALSE, helpers = FALSE, quiet = TRUE) ``` # Abstract `bam_app()` opens an application in the web browser that runs every analysis of the package without code. This vignette describes its pages and how it keeps its results reproducible. # Starting the application ```{r launch, eval = FALSE} bam_app( launch.browser = TRUE ) ``` The application needs the suggested packages **shiny**, **bslib** and **DT**. **magick** with WebP support is optional: with it the plots are sent to the browser as lossless WebP images, about half the size of the same PNG. ```{r webp} isTRUE(tryCatch(requireNamespace("magick", quietly = TRUE) && isTRUE(magick::magick_config()$webp), error = function(e) FALSE)) ``` `TRUE` means WebP is available. A magick installation that no longer loads, because the ImageMagick libraries of the system were removed or upgraded, gives `FALSE`, and the application then sends PNG images; reinstalling magick restores WebP. # The pages | Page | What it does | |---|---| | Home | what the application does and the order of the pages | | Data | the `Maiz` example or a CSV file with one row per plot; choice of the response, genotype, environment and replicate columns | | Model | AMMI or GGE, number of terms, common or environment-specific variances, iterations, burn-in, thinning, chains, seed and priors; then the summary, traces and densities | | Biplot | the biplot with HPD regions, for genotypes, environments or both | | Decisions | winners, probabilities of superior performance, ranks, stability and predictions | | Stability | Bayesian Eberhart-Russell, Finlay-Wilkinson and Shukla models; classical and AMMI-based stability indices | | Model choice | posterior predictive checks and a comparison of the fits of the session | Every result page has the same tabs: * **Interpretation** gives the plain-language reading of `bam_interpret()`, with a button that copies it, and the sources of the method. * **Plot** shows the figure, which can be saved as PNG, PDF or WebP. * **Table** shows the numbers, rounded, in a sortable table with buttons to copy them or save them as CSV or Excel. * **Output** shows the printed result as text, with a button that copies it. The model page has a further tab, **R code**, with the code that reproduces the fit outside the application. The model page after a fit, with the interpretation tab open: ```{r shot-model, echo = FALSE, out.width = "100%"} knitr::include_graphics(path = if (knitr::is_latex_output()) "figures/app-model.jpg" else "figures/app-model.webp") ``` The plot tab of the Bayesian Eberhart-Russell model on the Stability menu: ```{r shot-stab, echo = FALSE, out.width = "100%"} knitr::include_graphics(path = if (knitr::is_latex_output()) "figures/app-stability.jpg" else "figures/app-stability.webp") ``` The screenshots are lossless WebP in the HTML version: `r round(file.size("figures/app-model.webp") / 1024)` KB for the first, against `r round(file.size("figures/app-model.jpg") / 1024)` KB for the lossy JPEG of the PDF version. # Reproducibility For the default settings with environment-specific variances, the R code tab shows: ```{r code} settings <- list( .y = "y" , .gen = "entry" , .env = "site" , .rep = "rep" , .nIter = 3000 , .k = 2 , .burnin = 500 , .thin = 1 , .chains = 2 , .priors = bam_priors( mu_mean = 0 , mu_var = 1e+8 , tau_mean = 0 , tau_var = 1e+8 , delta_mean = 0 , delta_var = 1e+8 , lambda_mean = 0 , lambda_var = 1e+8 , nu = 1 , s2 = NULL ) , .level = 0.95 , .seed = 1 , .model = "AMMI" , .het = TRUE ) cat(bayesammi:::.bam_app_code(a = settings, source = "maiz")) ``` The seed fixes the draws, so the code returns the same numbers as the application. # Deploying `bam_app_object()` returns the application object without running it, for a server: ```{r deploy, eval = FALSE} # app.R on a Shiny server bayesammi::bam_app_object() ``` # References Crossa, J., Perez-Elizalde, S., Jarquin, D., Cotes, J. M., Viele, K., Liu, G. and Cornelius, P. L. (2011). Bayesian estimation of the additive main effects and multiplicative interaction model. *Crop Science*, 51(4), 1458--1469. doi:10.2135/cropsci2010.06.0343