design.rcbd: Generate a randomized complete block design

Description Usage Arguments Details References Examples

View source: R/design.rcbd_function_vFldTrial.R

Description

Randomized complete block designs (RCBD) are exceedingly common experimental designs in many field, including agricultural reserach. Details on RCBDs can easily be found in basic experimental design textbooks or an internet search; briefly, a set of experimental entries along with check lines, if desired, comprise a single block. This block is then replicated in its entirety at least once (i.e. two blocks) and up to any number of times.

Usage

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design.rcbd(enviro = format(Sys.Date(), "%x"), exp.name = NULL,
  nBlks = 2, entries = NULL, nEntries = NULL, chks = NULL, nChks = 0,
  nChkReps = 1, nFieldRows = NULL, nFieldCols = NULL, plot.start = 1001,
  fillWithEntry = T, fillWithChk = F, dup.list = NULL,
  plot_id.template = NULL)

Arguments

enviro

Optional character string describing the environment which the field trial will be grown in. Default is the current date and time.

exp.name

Required character string identifying name for the experiment.

nBlks

Optional Integer indicating the number of complete blocks desired. Default is 2. If a single replication is desired to grow across multiple environments (aka locations, see Details for further information) then set nBlks to 1.

entries

A character vector of experimental (i.e. not check) entries. User must either provide this OR nEntries (see next).

nEntries

Integer argument indicating how many experimental entries are to be included in the trial. If nEntries = m, then m generic entry names will be generated and included in the output. User must either provide this OR entries.. nEntries will be superceded if entries is provided.

chks

A character vector including the set of check lines to be included. User must either provide this OR nChks (see next).

nChks

Integer argument indicating how many check lines (see Details) are to be included in the trial. DUser must either provide this OR chks.

nChkReps

Optional Integer argument indicating how many times each check line should be replicated per block. Default is 1 meaning that each check line will appear in each block twice (i.e. replicated once).

nFieldRows

Optional, but must be provided if nFieldCols is not. Integer argument indicating the number of field rows (dimension 'a' in Figure 1).This value can be calculated internally by passing only nFieldCols.

nFieldCols

Optional, but must be provided if nFieldRows is not integer argument indicating the number of field columns (dimension 'b',Figure 1). This value can be calculated internally by passing only nFieldRows.

plot.start

Optional integer indicating the identification number of the first plot. design.aibd places the first plot in the "bottom-left" corner of the field and numbering then serpentines, starting to the right (Figure 1). Default is 1001.

fillWithEntry

Optional Logical. Default is TRUE, meaning fill plots (i.e. plots remaining after the defined sets of experimental entries and check lines are assigned) will be replaced by randomly-selected experimental entries. A "D" will appear in the output next to these replicated entries.

fillWithChk

Optional Logical. If TRUE this will supercede fillWithEntry and any fill plots will be replaced by a balanced set of check lines. Default is FALSE.

dup.list

Optional character vector containing the candidates that could be replicated if fillWithEntry = TRUE. This is useful if there is a low amount of source seed for some experimental entries; those, for example, would be excluded from dup.list. Default is NULL, meaning that all entries are candidates for duplication.

plot_id.template

Optional character vector of length two. The first character is a string that will preceed the plot number in the plot_id field of the output, and the second character is the character to delimit the provided string and the plot number. For example, c("EnvA_TrialA", "_") will result in "EnvA_TrialA_1001", etc.

Details

Figure 1 presents a simplified version of an RCBD with two replications within an environment where each block is a rectangle and there are no fill plots. In reality a block may end and the next start in the middle of a row; this is done to minimize the size of the experiment while meeting all requirements.

rcbd_Fig1.jpg RCBD may not be well-suited for all circumstances; in these cases consider using other design functions included in FldTrial: design.aibd or design.mad.

@return A list containing:

References

Bernardo, Rex. 2010. Breeding for Quantitative Traits in Plants. Stemma Press. Woodbury, MN.

Examples

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## Not run: 
## Example 1 - Generic layout with 2 reps
rcbd.ex1 <- design.rcbd(exp.name = "ex1", nBlks = 2,
               nEntries = 80, nChks = 3, nChkReps = 3,
               nFieldRows = 8)

## Example 2 - Layout with defined lines and checks
rcbd.ex2 <- design.rcbd(exp.name = "ex2", nBlks = 2,
               entries = paste("Line", 1:75, sep="."),
               chks = c("Larry", "Curly", "Moe"),
               nChkReps = 4, nFieldCols = 20)

## End(Not run)

austinjcase/BreedR documentation built on May 16, 2019, 6:45 p.m.