Factorial Design with speed

Factorial Design

Overview

Factorial designs are experimental designs used to study the effects of two or more factors simultaneously. They allow estimation of main effects and interactions between factors, making them efficient and informative.

library(speed)
library(patchwork)

When to Use

Studying multiple factors at the same time
Detecting interactions between factors
Efficient use of experimental units

Setting Up Factorial Design with speed

Now we can create a data frame representing a factorial design. Note that the treatment column we are creating is the interaction (or combination) of the individual treatments.

treatment_a <- paste0("A", 1:8)
treatment_b <- paste0("B", 1:3)
treatments <- with(expand.grid(treatment_a, treatment_b), paste(Var1, Var2, sep = "-"))
factorial_design <- initialise_design_df(treatments, 24, 3, 8, 3)

head(factorial_design)

##   row col treatment row_block col_block block
## 1   1   1     A1-B1         1         1     1
## 2   2   1     A2-B1         1         1     1
## 3   3   1     A3-B1         1         1     1
## 4   4   1     A4-B1         1         1     1
## 5   5   1     A5-B1         1         1     1
## 6   6   1     A6-B1         1         1     1

Plotting these factors shows the initial layout of the interaction and main effects.

Performing the Optimisation

For factorial designs, speed provides a customised objective function objective_function_factorial which allows us to pass interaction_weight and main_weight arguments to control the spatial balance of those effects. The optimise_params argument is also used in this case to adjust the optimisation strategy due to the difficulty of optimising such designs.

Make sure factorial_separator matches how you constructed the interaction treatment (here we used "-"). If your treatments use a different separator (e.g. "A1:B2"), pass factorial_separator = ":".

optimise_params <- optim_params(
  swap_count = 3,
  random_initialisation = 10,
  adaptive_swaps = TRUE,
  swap_all_blocks = TRUE,
  cooling_rate = 0.999
)

factorial_result <- speed(
  data = factorial_design,
  swap = "treatment",
  swap_within = "block",
  spatial_factors = ~ row + col,
  obj_function = objective_function_factorial,
  optimise_params = optimise_params,
  early_stop_iterations = 10000,
  iterations = 200000,
  interaction_weight = 10,
  seed = 112
)

## row and col are used as row and column, respectively.

## Optimising level: single treatment within block
## Level: single treatment within block Iteration: 1000 Score: 158.118 Best: 105.3975 Since Improvement: 174
## Level: single treatment within block Iteration: 2000 Score: 123.3043 Best: 105.3975 Since Improvement: 1174
## Level: single treatment within block Iteration: 3000 Score: 121.795 Best: 100.6957 Since Improvement: 261
## Level: single treatment within block Iteration: 4000 Score: 104.8199 Best: 93.92547 Since Improvement: 202
## Level: single treatment within block Iteration: 5000 Score: 65.14907 Best: 58.38509 Since Improvement: 140
## Level: single treatment within block Iteration: 6000 Score: 51.15528 Best: 51.15528 Since Improvement: 89
## Level: single treatment within block Iteration: 7000 Score: 42.10559 Best: 42.10559 Since Improvement: 381
## Level: single treatment within block Iteration: 8000 Score: 40.81988 Best: 40.81988 Since Improvement: 501
## Level: single treatment within block Iteration: 9000 Score: 39.81988 Best: 39.81988 Since Improvement: 742
## Level: single treatment within block Iteration: 10000 Score: 36.81988 Best: 36.81988 Since Improvement: 537
## Level: single treatment within block Iteration: 11000 Score: 36.81988 Best: 36.81988 Since Improvement: 1537
## Level: single treatment within block Iteration: 12000 Score: 36.81988 Best: 36.81988 Since Improvement: 2537
## Level: single treatment within block Iteration: 13000 Score: 36.81988 Best: 36.81988 Since Improvement: 3537
## Level: single treatment within block Iteration: 14000 Score: 36.81988 Best: 36.81988 Since Improvement: 4537
## Level: single treatment within block Iteration: 15000 Score: 36.81988 Best: 36.81988 Since Improvement: 5537
## Level: single treatment within block Iteration: 16000 Score: 36.81988 Best: 36.81988 Since Improvement: 6537
## Level: single treatment within block Iteration: 17000 Score: 36.81988 Best: 36.81988 Since Improvement: 7537
## Level: single treatment within block Iteration: 18000 Score: 36.81988 Best: 36.81988 Since Improvement: 8537
## Level: single treatment within block Iteration: 19000 Score: 36.81988 Best: 36.81988 Since Improvement: 9537
## Early stopping at iteration 19463 for level single treatment within block

factorial_result

## Optimised Experimental Design
## ----------------------------
## Score: 36.81988
## Iterations Run: 19464
## Stopped Early: TRUE
## Treatments: A1-B1, A1-B2, A1-B3, A2-B1, A2-B2, A2-B3, A3-B1, A3-B2, A3-B3, A4-B1, A4-B2, A4-B3, A5-B1, A5-B2, A5-B3, A6-B1, A6-B2, A6-B3, A7-B1, A7-B2, A7-B3, A8-B1, A8-B2, A8-B3
## Seed: 112

Output of the Optimisation

The output summarises the optimisation of the factorial interaction treatment (e.g. "A1-B2") across the spatial layout. The reported score is for the whole design after optimisation, and the returned design_df contains the updated treatment allocation.

Because the treatment column encodes multiple factors, it can be helpful to split it back into its component factors (e.g. treatment_a and treatment_b) when inspecting the result. This lets you check whether the optimisation improved not only the interaction layout, but also the balance/adjacency patterns of the main effects.

str(factorial_result)

## List of 9
##  $ design_df     :Classes 'design' and 'data.frame': 72 obs. of  8 variables:
##   ..$ row        : int [1:72] 1 1 1 2 2 2 3 3 3 4 ...
##   ..$ col        : int [1:72] 1 2 3 1 2 3 1 2 3 1 ...
##   ..$ treatment  : chr [1:72] "A7-B1" "A8-B2" "A6-B3" "A6-B2" ...
##   ..$ row_block  : num [1:72] 1 1 1 1 1 1 1 1 1 1 ...
##   ..$ col_block  : num [1:72] 1 1 1 1 1 1 1 1 1 1 ...
##   ..$ block      : num [1:72] 1 1 1 1 1 1 1 1 1 1 ...
##   ..$ treatment_a: chr [1:72] "A1" "A1" "A1" "A2" ...
##   ..$ treatment_b: chr [1:72] "B1" "B2" "B3" "B1" ...
##   ..- attr(*, "out.attrs")=List of 2
##   .. ..$ dim     : Named int [1:2] 24 3
##   .. .. ..- attr(*, "names")= chr [1:2] "row" "col"
##   .. ..$ dimnames:List of 2
##   .. .. ..$ row: chr [1:24] "row= 1" "row= 2" "row= 3" "row= 4" ...
##   .. .. ..$ col: chr [1:3] "col=1" "col=2" "col=3"
##  $ score         : num 36.8
##  $ scores        : num [1:19464] 131 141 139 141 153 ...
##  $ temperatures  : num [1:19464] 100 99.9 99.8 99.7 99.6 ...
##  $ iterations_run: num 19464
##  $ stopped_early : logi TRUE
##  $ treatments    : chr [1:24] "A1-B1" "A1-B2" "A1-B3" "A2-B1" ...
##  $ seed          : num 112
##  $ metadata      :List of 6
##   ..$ levels    : chr "single treatment within block"
##   ..$ row_column: chr "row"
##   ..$ col_column: chr "col"
##   ..$ grid_by   : NULL
##   ..$ per_level :List of 1
##   .. ..$ single treatment within block:List of 13
##   .. .. ..$ swap            : chr "treatment"
##   .. .. ..$ spatial_factors :Class 'formula'  language ~row + col
##   .. .. .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
##   .. .. ..$ spatial_cols    : chr [1:2] "row" "col"
##   .. .. ..$ adj_weight      : num 1
##   .. .. ..$ bal_weight      : num 1
##   .. .. ..$ iterations      : num 2e+05
##   .. .. ..$ start_temp      : num 100
##   .. .. ..$ cooling_rate    : num 0.999
##   .. .. ..$ obj_function    :function (layout_df, swap, spatial_cols, interaction_weight = 1, main_weight = 1,
##     factorial_separator = "-", ...)
##   .. .. .. ..- attr(*, "srcref")= 'srcref' int [1:8] 109 33 159 1 33 1 109 159
##   .. .. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x000002b0cae73a50>
##   .. .. ..$ final_score     : num 36.8
##   .. .. ..$ final_components: Named num [1:2] 9.43 27.39
##   .. .. .. ..- attr(*, "names")= chr [1:2] "main" "interaction"
##   .. .. ..$ optimal_score   : num NA
##   .. .. ..$ stop_reason     : chr "no_improvement"
##   ..$ call      : language speed(data = factorial_design, swap = "treatment", swap_within = "block",      spatial_factors = ~row + col, iter| __truncated__ ...
##  - attr(*, "class")= chr [1:2] "design" "list"

Visualise the Output

treatments <- strsplit(as.character(factorial_result$design_df$treatment), "-") |>
  unlist() |>
  matrix(ncol = 2, byrow = TRUE)
factorial_result$design_df[c("treatment_a", "treatment_b")] <- treatments

pa <- autoplot(factorial_result, treatments = "treatment_a")
pb <- autoplot(factorial_result, treatments = "treatment_b")
p <- autoplot(factorial_result)
p + pa + pb + plot_layout(ncol = 3)

This design has now been optimised for both main and interaction effects.

Spatial Design Considerations

Field Shape and Orientation

Neighbour Effects

Using `speed` Effectively

Set appropriate parameters: Balance optimisation time with improvement
Visualise designs: Always plot layouts before implementation
Compare alternatives: Test multiple blocking strategies
Validate results: Check constraint satisfaction and efficiency factors