Generate Spatially Efficient Experimental Designs • speed

Overview
Installation
Features
Example
Citation
License

Overview

The speed package optimises spatial experimental designs by rearranging treatments to improve statistical efficiency while maintaining statistical validity. It uses simulated annealing to:

Minimise treatment adjacency (reducing neighbour effects)
Maintain spatial balance across rows and columns
Respect blocking constraints if specified
Provide visualisation tools for design evaluation

Installation

You can install the development version of speed from GitHub with:

# install.packages("pak")
pak::pak("biometryhub/speed")

Features

Flexible optimisation of experimental designs
Support for blocked designs
Customisable optimisation parameters
Built-in visualisation functions
Progress tracking during optimisation
Early stopping when convergence is reached

See the package documentation for more detailed examples and options.

Example

Basic

A simple example optimising a 4×3 completely randomised design with 4 treatments:

library(speed)

# Create a simple design with 3 replicates of 4 treatments
df <- data.frame(
  row = rep(1:4, each = 3),
  col = rep(1:3, times = 4),
  treatment = rep(LETTERS[1:4], each = 3)
)

# Optimise the design with seed for reproducibility
result <- speed(df, "treatment", seed = 42)
#> row and col are used as row and column, respectively.
#> Iteration: 1000 Score: 1 Best: 1 Since Improvement: 475 
#> Iteration: 2000 Score: 1 Best: 1 Since Improvement: 1475 
#> Early stopping at iteration 2525

# Plot the optimised design
autoplot(result)


# View optimisation progress
plot_progress(result)

Blocked design

You can also optimise designs within blocks:

# Create a design with blocks
df <- data.frame(
  row = rep(1:6, each = 4),
  col = rep(1:4, times = 6),
  treatment = rep(LETTERS[1:8], 3),
  block = rep(1:3, each = 8)
)

# Optimise while respecting blocks
result <- speed(df,
  "treatment",
  swap_within = "block",
  iterations = 5000,
  seed = 42
)
#> row and col are used as row and column, respectively.
#> Iteration: 1000 Score: 2.571429 Best: 2.571429 Since Improvement: 543 
#> Iteration: 2000 Score: 2.571429 Best: 2.571429 Since Improvement: 1543 
#> Early stopping at iteration 2457

# Plot the design with block boundaries
autoplot(result)

More Examples

For more detailed examples, visit here.

Citation

If you use speed in your research, please cite:

Warning in citation("speed"): could not determine year for 'speed' from package
DESCRIPTION file
To cite package 'speed' in publications use:

  Rogers S, Taylor J, Edson R, Pipattungsakul W (????). _speed:
  Generate Spatially Efficient Experimental Designs_. R package version
  0.0.1, <https://biometryhub.github.io/speed/>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {speed: Generate Spatially Efficient Experimental Designs},
    author = {Sam Rogers and Julian Taylor and Russell Edson and Wasin Pipattungsakul},
    note = {R package version 0.0.1},
    url = {https://biometryhub.github.io/speed/},
  }

License

This project is licensed under the MIT License - see the LICENSE file for details.

speed - Spatially Efficient Experimental Designs

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