R/raf_get.r

In ian-hastings/rotations: Simulating the Evolution of Insecticide Resistance under Rotations

#' get selected Resistance Allele Frequencies from array
#' 
#' @param RAF array of resistance allele frequencies, either [insecticide, sex, site, gen] or without generationd dimension
#' @param insecticide which insecticide, by number, default to all (TRUE), vector e.g. c(1,2)
#' @param sex 'm' or 'f', default to all (TRUE)
#' @param site 'intervention' or 'refugia', default to all (TRUE)
#' @param gen which generation, single or vector e.g. c(1:10), default to all (TRUE)
#' @param asdf to return as dataframe instead of array default FALSE
#' 
#' @examples
#' #frequencies different for each insecticide
#' RAF <- set_start_freqs(max_gen = 2, freqs=c(0.1,0.01,0.001))
#' 
#' raf_get(RAF, sex='f')
#' raf_get(RAF, site='intervention')
#' raf_get(RAF, gen=1, asdf=TRUE)
#' 
#' 
#' @return array or dataframe of resistance frequencies
#' @export
#' 
raf_get <- function( RAF,
                     insecticide = TRUE,
                     sex = TRUE,
                     site = TRUE,
                     gen = TRUE,
                     asdf = FALSE )
{
  

  # to allow selection from array with or without generations dimension  
  if (length(dim(RAF)) == 4)
  {
    toreturn <- RAF[insecticide, sex, site, gen] 
    
  } else if (length(dim(RAF)) == 3)
  {
    toreturn <- RAF[insecticide, sex, site]  
    
  } else
  {
    #TODO improve checking that the array has correct dimnames
    stop("array of resistance allele frequencies with 3 or 4 dimensions required")
  }

  
  if (asdf) toreturn <- as.data.frame(toreturn)
  
  return(toreturn)  
}