---
title: "Speed"
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{Speed}
  %\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

Version 1.0.0 computes every analysis from closed forms on the table of cell means and one block analysis of the plot
data, instead of refitting models branch by branch. This vignette reports the timings against version 0.6.0.

# Timings

Median time and memory over 20 runs (`tools/bench.R` in the source repository), on the shipped data and on simulated
diallels of 12 and 20 parents with 3 replicates:

```{r bench}
b <- data.table::fread(file = system.file("extdata", "bench.csv", package = "DiallelAnalysisR"))
w <- data.table::dcast(data = b, formula = case ~ version, value.var = "median_ms")
data.table::setnames(x = w, old = c("0.6.0", "1.0.0"), new = c("ms_0.6.0", "ms_1.0.0"))
w[, speedup := round(x = ms_0.6.0 / ms_1.0.0, digits = 1)]
knitr::kable(x = w, digits = 2)
```

# Where the time goes

Version 0.6.0 fitted `aov()` and built several tables with `tapply()` in each branch, and its cost grew quickly with
the number of parents. Version 1.0.0 builds the table of cell means in one grouped sum, computes the error mean
square in closed form for complete blocks, and evaluates the sums of squares, effects, standard errors and expected
mean squares as matrix expressions; its time hardly changes between 8 and 20 parents.

# Summary

The modernised package is faster for every analysis and many times faster for larger diallels, with less memory.