---
title: "Tables for papers and the interactive 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{Tables for papers and the interactive application}
  %\VignetteEngine{quarto::html}
  %\VignetteEncoding{UTF-8}
execute:
  echo: true
  warning: false
  message: false
---

{{< include _DiallelAnalysisR-macros.txt >}}

```{r setup, include = FALSE}
knitr::opts_chunk$set(collapse = FALSE, comment = "", fig.width = 7, fig.height = 4.2,
                      dev = if (knitr::is_latex_output()) "cairo_pdf" else
                        if (requireNamespace("svglite", quietly = TRUE)) "svglite" else "png")
if (requireNamespace("DiallelAnalysisR", quietly = TRUE)) library(DiallelAnalysisR) else
  pkgload::load_all(export_all = FALSE, helpers = FALSE, quiet = TRUE)
```

# Abstract

Results of every analysis can be written as tables for a paper, in Word, LaTeX, HTML, Markdown or CSV, with
`da_export()`; `da_tables()` gives the same tables as data frames. `DiallelApp()` runs the analyses in a web browser
without writing code. This vignette shows both.

# The tables of an analysis

```{r tables}
fit <-
  Griffing(
      y          = Yield
    , Rep        = Rep
    , Cross1     = Cross1
    , Cross2     = Cross2
    , data       = GriffingData2
    , Method     = 2
    , Model      = 1
    , Reciprocal = c("combined", "split")[1]
    )
tb <-
  da_tables(
      x      = fit
    , digits = 3
    )
names(tb)
tb[["Analysis of variance"]]
```

Each analysis has its own set: Hayman's analysis gives the analysis of variance, the $W_r$-$V_r$ table and the
genetic parameters; the line $\times$ tester analysis the analysis of variance, the proportional contributions, the
effects and the components; and so on.

# Export to Word, LaTeX, HTML, Markdown or CSV

`da_export()` writes the tables, all or a chosen few, with a set number of decimal places. A LaTeX file uses the
`booktabs` rules and can be included in a paper with `\input{}`:

```{r latex}
tex <- tempfile(fileext = ".tex")
da_export(
    x      = fit
  , file   = tex
  , format = c("docx", "latex", "html", "markdown", "csv")[2]
  , tables = "Analysis of variance"
  , digits = 2
  , title  = "Combining-ability analysis of variance"
  )
cat(readLines(con = tex), sep = "\n")
```

A Word file (with the suggested packages officer and flextable) has one formatted table per result, each with its
title, ready to paste into a manuscript:

```{r docx, eval = requireNamespace("officer", quietly = TRUE) && requireNamespace("flextable", quietly = TRUE)}
docx <- tempfile(fileext = ".docx")
da_export(
    x      = fit
  , file   = docx
  , format = c("docx", "latex", "html", "markdown", "csv")[1]
  , tables = NULL
  , digits = 3
  , title  = NULL
  )
file.exists(docx)
```

Markdown tables suit Quarto and R Markdown documents; CSV writes one file per table for a spreadsheet.

# The interactive application

```{r app, eval = FALSE}
DiallelApp(
    launch.browser = TRUE
  )
```

The application (packages shiny and bslib) has four tabs:

1. **Data**: an example data set of the package or a CSV file with one row per plot.
2. **Results**: the printed analysis and its tables. The sidebar sets the analysis (Griffing, Griffing over
   environments, heterosis, Hayman, Gardner and Eberhart, partial diallel, line $\times$ tester, North Carolina
   designs), the columns of the response, replicates and parents, and the options of the analysis.
3. **Plots**: every plot of the analysis.
4. **Export**: the tables in Word, LaTeX, HTML or Markdown, and the R code that repeats the analysis in a script, in
   the style of the examples of this package.

![The application with Griffing's Method 2 analysis of `GriffingData2`.](DiallelAnalysisR-app.png){width=100%}

# Summary

`da_tables()` and `da_export()` turn any result into tables for a report; `DiallelApp()` gives the same analyses
and tables without code, and shows the code for later use.