design {biometryassist}

Create a complete experimental design with graph of design layout and skeletal ANOVA table

Description

Create a complete experimental design with graph of design layout and skeletal ANOVA table

Usage

design(
  type,
  treatments,
  reps,
  nrows,
  ncols,
  brows = NA,
  bcols = NA,
  byrow = TRUE,
  sub_treatments = NULL,
  fac.names = NULL,
  fac.sep = c("", " "),
  plot = TRUE,
  rotation = 0,
  size = 4,
  margin = FALSE,
  save = FALSE,
  savename = paste0(type, "_design"),
  plottype = "pdf",
  seed = TRUE,
  quiet = FALSE,
  ...
)

Arguments

type

The type of design. Supported design types are crd, rcbd, lsd, ⁠crossed:<type>⁠ where ⁠<type>⁠ is one of the previous types, and split. See Details for more information.

treatments

A vector containing the treatment names or labels.

reps

The number of replicates. Ignored for Latin Square Designs.

nrows

The number of rows in the design.

ncols

The number of columns in the design.

brows

For RCBD and Split Plot designs. The number of rows in a block.

bcols

For RCBD and Split Plot designs. The number of columns in a block.

byrow

For split-plot only. Logical (default TRUE). Provides a way to arrange plots within whole-plots when there are multiple possible arrangements.

sub_treatments

A vector of treatments for sub-plots in a split plot design.

fac.names

Allows renaming of the A level of factorial designs (i.e. those using agricolae::design.ab()) by passing (optionally named) vectors of new labels to be applied to the factors within a list. See examples and details for more information.

fac.sep

The separator used by fac.names. Used to combine factorial design levels. If a vector of 2 levels is supplied, the first separates factor levels and label, and the second separates the different factors.

plot

Logical (default TRUE). If TRUE, display a plot of the generated design. A plot can always be produced later using autoplot().

rotation

Rotate the text output as Treatments within the plot. Allows for easier reading of long treatment labels. Takes positive and negative values being number of degrees of rotation from horizontal.

size

Increase or decrease the text size within the plot for treatment labels. Numeric with default value of 4.

margin

Logical (default FALSE). Expand the plot to the edges of the plotting area i.e. remove white space between plot and axes.

save

One of FALSE (default)/"none", TRUE/"both", "plot" or "workbook". Specifies which output to save.

savename

A file name for the design to be saved to. Default is the type of the design combined with "_design".

plottype

The type of file to save the plot as. Usually one of "pdf", "png", or "jpg". See ggplot2::ggsave() for all possible options.

seed

Logical (default TRUE). If TRUE, return the seed used to generate the design. If a numeric value, use that value as the seed for the design.

quiet

Logical (default FALSE). Hide the output.

...

Additional parameters passed to ggplot2::ggsave() for saving the plot.

Details

The designs currently supported by type are Completely Randomised designs (crd), Randomised Complete Block designs (rcbd), Latin Square Designs (lsd), Factorial with crossed structure (use ⁠crossed:<type>⁠ where ⁠<type>⁠ is one of the previous types e.g. crossed:crd) and Split Plot designs (split). Nested factorial designs are supported through manual setup, see Examples.

If save = TRUE (or "both"), both the plot and the workbook will be saved to the current working directory, with filename given by savename. If one of either "plot" or "workbook" is specified, only that output is saved. If save = FALSE (the default, or equivalently "none"), nothing will be output.

fac.names can be supplied to provide more intuitive names for factors and their levels in factorial and split plot designs. They can be specified in a list format, for example fac.names = list(A_names = c("a", "b", "c"), B_names = c("x", "y", "z")). This will result a design output with a column named A_names with levels ⁠a, b, c⁠ and another named B_names with levels ⁠x, y, z⁠. Labels can also be supplied as a character vector (e.g. c("A", "B")) which will result in only the treatment column names being renamed. Only the first two elements of the list will be used, except in the case of a 3-way factorial design.

... allows extra arguments to be passed to ggsave() for output of the plot. The details of possible arguments can be found in ggplot2::ggsave().

Value

A list containing a data frame with the complete design (⁠$design⁠), a ggplot object with plot layout (⁠$plot.des⁠), the seed (⁠$seed⁠, if return.seed = TRUE), and the satab object (⁠$satab⁠), allowing repeat output of the satab table via cat(output$satab).

Examples

# Completely Randomised Design
des.out <- design(type = "crd", treatments = c(1, 5, 10, 20),
                  reps = 5, nrows = 4, ncols = 5, seed = 42)

# Randomised Complete Block Design
des.out <- design("rcbd", treatments = LETTERS[1:11], reps = 4,
                  nrows = 11, ncols = 4, brows = 11, bcols = 1, seed = 42)

# Latin Square Design
# Doesn't require reps argument
des.out <- design(type = "lsd", c("S1", "S2", "S3", "S4"),
                  nrows = 4, ncols = 4, seed = 42)

# Factorial Design (Crossed, Completely Randomised)
des.out <- design(type = "crossed:crd", treatments = c(3, 2),
                  reps = 3, nrows = 6, ncols = 3, seed = 42)

# Factorial Design (Crossed, Completely Randomised), renaming factors
des.out <- design(type = "crossed:crd", treatments = c(3, 2),
                  reps = 3, nrows = 6, ncols = 3, seed = 42,
                  fac.names = list(N = c(50, 100, 150),
                                   Water = c("Irrigated", "Rain-fed")))

# Factorial Design (Crossed, Randomised Complete Block Design),
# changing separation between factors
des.out <- design(type = "crossed:rcbd", treatments = c(3, 2),
                  reps = 3, nrows = 6, ncols = 3,
                  brows = 6, bcols = 1,
                  seed = 42, fac.sep = c(":", "_"))

# Factorial Design (Nested, Latin Square)
trt <- c("A1", "A2", "A3", "A4", "B1", "B2", "B3")
des.out <- design(type = "lsd", treatments = trt,
                  nrows = 7, ncols = 7, seed = 42)

# Split plot design
des.out <- design(type = "split", treatments = c("A", "B"), sub_treatments = 1:4,
                  reps = 4, nrows = 8, ncols = 4, brows = 4, bcols = 2, seed = 42)

# Alternative arrangement of the same design as above
des.out <- design(type = "split", treatments = c("A", "B"), sub_treatments = 1:4,
                  reps = 4, nrows = 8, ncols = 4, brows = 4, bcols = 2,
                  byrow = FALSE, seed = 42)