nelder_biculture_optim: Create a composition-density-conformity-optimized Biculture...

In kevinwolz/sysdesign: An R Toolbox for Creating & Analyzing Systematic Experimental Designs in Biology

Description

Creates a competition-conformity-optimized Biculture Nelder Fan experimental design.

Usage

nelder_biculture_optim(
  data,
  save.path = ".",
  init.pop = NULL,
  MU = 100,
  LAMBDA = MU,
  MAX.GEN = 150,
  P.RECOMB = 1,
  RECOMB = 0.1,
  P.MUT = 1,
  MUT = 0.05
)

Arguments

data	An object of class nelder-biculture.
save.path	A character string of the path for where to save data after each generation.
init.pop	If NULL, the default, then the initial population will be generated via MU calls to nelder. Otherwise, a character string of the path to the file containing the data from which to generate the initial population. This file should be the "data" output file that was saved by this function on a previous call. The iniital population will be taken as the final population in this file.
MU	The population size.
LAMBDA	The number of offspring to produce in each generation.
MAX.GEN	The number of generations to run the evolutionary algorithm.
P.RECOMB	The probability of two parents to perform crossover.
RECOMB	The crossover probability for each gene.
P.MUT	The probability to apply mutation to a child.
MUT	The mutation probability for each gene.

Details

While nelder_biculture creates Biculture Nelder Fan designs that follow a composition-conformity criterion across spokes, this function creates designs that are optimized to also conform to a composition-density-conformity criterion for species composition environments across arcs using an evolutionary algorithm. Function parameters other than data, save.path, and, init.pop are all controls on the evolutionary algorithm. The ecr package is used for the evolutionary algorithm. In addition to the data returned in the environment, the "stats" and "data" data frames are written as csv files to save.path.

Value

An list containing:

• "layout" - A data frame (tibble) containing the base nelder design.

• "stats" - A data frame (tibble) containing statistics on each generation in the evolutionary algorithm.

• "data" - A data frame (tibble) containing the actual data (designs) of each Biculture Nelder Fan in eac generation.

Author(s)

Kevin J Wolz, [e-mail]

See Also

Other definition functions: goelz_add_border(), goelz_corners(), goelz_guides(), goelz_mirror(), goelz_optim(), goelz_starts(), goelz(), nelder_biculture_competition(), nelder_biculture(), nelder_decision(), nelder_interspoke_distance(), nelder(), select_optimal_goelz(), select_optimal_nelder_biculture()

Examples

dat <- nelder()
dat.bi <- nelder_biculture(data = dat)
dat.bi.optim <- nelder_biculture_optim(data = dat.bi)

kevinwolz/sysdesign documentation built on June 13, 2020, 1:35 a.m.