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Generates an Spatial Un-replicated Optimized Arrangement Design

Source: R/fct_optimized_arrangement.R
optimized_arrangement.Rd

Randomly generates a spatial un-replicated optimized arrangement design, where the distance between checks is maximized in such a way that each row and column have control plots. Note that design generation needs the dimension of the field (number of rows and columns).

Usage

optimized_arrangement(
  nrows = NULL,
  ncols = NULL,
  lines = NULL,
  amountChecks = NULL,
  checks = NULL,
  planter = "serpentine",
  l = 1,
  plotNumber = 101,
  seed = NULL,
  exptName = NULL,
  locationNames = NULL,
  spread_reps = TRUE,
  data = NULL,
  year = NULL,
  rep_checks = NULL
)

Arguments

nrows

Number of rows in the field.

ncols

Number of columns in the field.

lines

Number of genotypes, experimental lines or treatments.

amountChecks

Deprecated alias for rep_checks.

checks

Number of genotypes as checks.

planter

Option for serpentine or cartesian arrangement. By default planter = 'serpentine'.

l

Number of locations. By default l = 1.

plotNumber

Numeric vector with the starting plot number for each location. By default plotNumber = 101.

seed

(optional) Real number that specifies the starting seed to obtain reproducible designs.

exptName

(optional) Name of the experiment.

locationNames

(optional) Name for each location.

spread_reps

A logical value indicating whether to maximize the spatial distance between replicated treatments in the field. Default is TRUE.

data

(optional) Data frame with 3 columns: ENTRY | NAME | REPS.

year

(optional) Year recorded in the YEAR column of the field book. By default the current year.

rep_checks

Integer with the total amount of checks, or a numeric vector with the replicates of each check label.

Value

A list with five elements.

  • infoDesign is a list with information on the design parameters.

  • layoutRandom is a matrix with the randomization layout.

  • plotNumber is a matrix with the layout plot number.

  • dataEntry is a data frame with the data input.

  • genEntries is a list with the entries for replicated and no replicated part.

  • fieldBook is a data frame with field book design. This includes the index (Row, Column).

Reproducibility

The result records effective inputs and the resolved seed in metadata$parameters. Under the same package versions and RNG settings, rebuild a result x with do.call(optimized_arrangement, x$metadata$parameters).

References

Clarke, G. P. Y., & Stefanova, K. T. (2011). Optimal design for early-generation plant breeding trials with unreplicated or partially replicated test lines. Australian & New Zealand Journal of Statistics, 53(4), 461–480.

Author

Didier Murillo [aut], Salvador Gezan [aut], Ana Heilman [ctb], Thomas Walk [ctb], Johan Aparicio [ctb], Richard Horsley [ctb]

Examples

# Example 1: Generates a spatial unreplicated optimized arrangement design in one location
# with 120 genotypes + 20 check plots (4 checks) for a field with dimension 14 rows x 10 cols.
if (FALSE) { # \dontrun{
optim_unrep1 <- optimized_arrangement(
  nrows = 14, 
  ncols = 10, 
  lines = 120,
  rep_checks = 20,
  checks = 1:4,
  planter = "cartesian", 
  plotNumber = 101,
  exptName = "20RW1",
  locationNames = "CASSELTON",
  seed = 14124
)
optim_unrep1$infoDesign
optim_unrep1$layoutRandom
optim_unrep1$plotNumber
head(optim_unrep1$fieldBook, 12)
} # }
                  
# Example 2: Generates a spatial unreplicated optimized arrangement design in one location
# with 200 genotypes + 20 check plots (4 checks) for a field with dimension 10 rows x 22 cols.
# As example, we set up the data option with the entries list.
if (FALSE) { # \dontrun{
checks <- 4
list_checks <- paste("CH", 1:checks, sep = "")
treatments <- paste("G", 5:204, sep = "")
REPS <- c(5, 5, 5, 5, rep(1, 200))
treatment_list <- data.frame(list(ENTRY = 1:204, NAME = c(list_checks, treatments), REPS = REPS))
head(treatment_list, 12) 
tail(treatment_list, 12)
optim_unrep2 <- optimized_arrangement(
  nrows = 10, 
  ncols = 22, 
  planter = "serpentine", 
  plotNumber = 101,
  seed = 120,
  exptName = "20YWA2",
  locationNames = "MINOT",
  data = treatment_list
)
optim_unrep2$infoDesign
optim_unrep2$layoutRandom
optim_unrep2$plotNumber
head(optim_unrep2$fieldBook,12)
} # }