R/helper_functions.R

In HostSwitch: Simulate the Extent of Host Switching by Consumers

#' Flatten a nested list
#' @param x A nested list
#' @details Flattens a nested list; https://stackoverflow.com/questions/8139677/how-to-flatten-a-list-to-a-list-without-coercion
#' @keywords internal

flatten2 <- function(x) {
  len <- sum(rapply(x, function(z) 1L))
  y <- vector('list', len)
  i <- 0L
  rapply(x, function(x) { i <<- i+1L; y[[i]] <<- x })
  y
}



#' Create input data of simulated jumped/survived individuals for plots
#' @param x A list of simulated jumped/survived parasite phenotypes for each generation
#' @details Converts list to dataframe and stack it
#' @keywords internal

createPlotInput_Ind_sim <- function(x){
  xx        = flatten2(x)
  parasites = utils::stack(setNames(xx,seq_along(xx)-1)) # need to start from generation 0!
  colnames(parasites)   = c("y","x")
  parasites$x           = as.numeric(as.character(parasites$x))
  return(parasites)
}


#' Echo personalized pattern and error message
#' @param x User input (string)
#' @details Checks if input is a string and either yes or no
#' @keywords internal

# assertPersonalizedPatternMsg <- function(x,name,pattern) {
#   res <- try(expr = checkmate::assert_character(x,pattern=pattern), silent = TRUE)
#   msg_attr=attr(x = res, which = "condition")$message
#   msg_gsub1 = gsub("[^[:alnum:][:blank:]+':|?&/\\-]","",msg_attr)
#   msg_gsub2 = gsub("\\|","' or '",msg_gsub1)
#   msg = gsub("'x'",paste("'",name,"'",sep=""),msg_gsub2)
#   if (inherits(x = res, what = "try-error")) {
#     stop(
#       call. = FALSE,
#       msg
#     )
#   }
# }

# Usage:assertPersonalizedPatternMsg(x=jump_back,name="jump_back",pattern="^no$|^yes$") # jump_back
# better option: assertChoice