R/ablandscape_control.R

In acorg/ablandscapes: Making Antibody landscapes Using R

#' Get defaults for antibody landscape fitting
#'
#' This function returns all the options that can be set for fitting of antibody
#' landscapes and the default values for them.
#'
#' @return Returns a list of default fitting options for making antibody
#'   landscapes.
#' 
#' @export
#' 
ablandscape.control <- function(
  max.titer.possible   = 10,
  min.titer.possible   = -4,
  max.slope            = Inf,
  error.sd             = 1.1,
  confint.stepsize     = 0.1,
  optimise.cone.coords = TRUE,
  optimise.cone.slope  = TRUE,
  start.cone.coords    = NULL,
  start.cone.slope     = NULL,
  model.fn             = NULL
) {
  
  
  list(
    max.titer.possible   = max.titer.possible,
    min.titer.possible   = min.titer.possible,
    max.slope            = max.slope,
    error.sd             = error.sd,
    confint.stepsize     = confint.stepsize,
    optimise.cone.coords = optimise.cone.coords,
    optimise.cone.slope  = optimise.cone.slope,
    start.cone.coords    = start.cone.coords,
    start.cone.slope     = start.cone.slope,
    model.fn             = model.fn
  )
  
}