R/config.r

In AndySouth/resistanceGame: prototyping an insecticide resistance management computer game

#' configure control plan
#'
#' allows start & stop of controls to be set, depends on controls available in config file
#'
#' @param l_config list of config parameters
#' @param t_strt vector of start times
#' @param t_stop vector of stop times
#' @param control_id vector of control_ids for the times
#' @param add whether to add the new controls to exisiting ones, default FALSE to replace
#' @examples
#' l_config <- read_config()
#' l_config2 <- config_plan(l_config, t_strt=1, t_stop=15, control_id='irs_pyr')
#' l_config2 <- config_plan(l_config, t_strt=c(1,15), t_stop=c(10,20), control_id='irs_pyr')
#' l_config2 <- config_plan(l_config, t_strt=c(1,11), t_stop=c(10,20), control_id=c('irs_pyr','irs_ops'))
#' l_config2 <- config_plan(l_config, t_strt=c(1,11), t_stop=c(10,20), control_id=c('irs_pyr','irs_ddt'))
#' plot_sim( run_sim(l_config=l_config2))
#' #to create a blank config_plan
#' #l_config$control_plan <- l_config$control_plan[0,]
#' @return list with modified control_plan
#' @export
config_plan <- function( l_config,
                         t_strt,
                         t_stop,
                         control_id,
                         add = FALSE) 
{
  
  #todo add checks that times are within those specified
  #todo add check that control_ids are present  
  bad_indices <- which(!control_id %in% l_config$controls[['control_id']])
  if (length(bad_indices)>0)
  {
    warning("these control_ids are not in your controls config file and will cause problems :",control_id[bad_indices])
  }
  
  #put passed data into a dataframe ready to put into list
  dF <- data.frame(t_strt=t_strt, t_stop=t_stop, control_id=control_id, stringsAsFactors = FALSE)
  
  
  if (add)
  {
    l_config$control_plan <- rbind(l_config$control_plan, dF) 
  } else
  {
    l_config$control_plan <- dF    
  }
  
  
  return(l_config)
  
}


#' configure controls available
#'
#' modifies the input from config files
#'
#' @param l_config list of config parameters
#' @param control_id vector of control_ids
#' @param control_name vector of control_names (optional)
#' @param control_desc vector of control descriptions (optional)
#' @param vector_id vector of vector_ids
#' @param control_kill_rate vector of control_kill_rates
#' @param add whether to add, default FALSE to replace
#' @examples
#' l_config <- read_config()
#' l_config2 <- config_controls(l_config, control_id=c('irs_pyr','irs_ops'), vector_id='an_gamb', control_kill_rate=c(0.3,0.4))
#' plot_sim( run_sim(l_config=l_config2))
#' @return list with modified controls
#' @export
config_controls <- function( l_config,
                             control_id,
                             control_name=NA,
                             control_desc=NA,
                             vector_id,
                             control_kill_rate,
                             add = FALSE) 
{
  

  #check that control_ids are present  
#   bad_indices <- which(!control_id %in% l_config$controls[['control_id']])
#   if (length(bad_indices)>0)
#   {
#     warning("these control_ids are not in your controls config file and will cause problems :",control_id[bad_indices])
#   }
  
  #put passed data into a dataframe ready to put into list
  dF <- data.frame(control_id=control_id, 
                   control_name=control_name,
                   control_desc=control_desc,
                   vector_id=vector_id, 
                   control_kill_rate=control_kill_rate, stringsAsFactors = FALSE)
  
  
  if (add)
  {
    l_config$controls <- rbind(l_config$controls, dF) 
  } else
  {
    l_config$controls <- dF    
  }
  
  return(l_config)
}

#' configure resistances
#'
#' modifies the input from config files
#'
#' @param l_config list of config parameters
#' @param resistance_id vector of resistance_ids
#' @param resistance_name vector of resistance_names (optional)
# @param resistance_desc vector of resistance descriptions (optional)
#' @param control_id vector of control_ids that each resistance works on
#' @param resistance_strength vector of resistance_strengths
#' @param resistance_incr vector of resistance increase params
#' @param resistance_decr vector of resistance decrease params
#' @param add whether to add, default FALSE to replace
#' @examples
#' l_config <- read_config()
#' l_config2 <- config_resistances(l_config, resistance_id="target_site", control_id=c('irs_ops'), resistance_strength=c(0.8), resistance_incr=c(0.2), resistance_decr=c(0.1))
#' plot_sim_oldcc( run_sim_oldcc(l_config=l_config2))
#' @return list with modified controls
#' @export
config_resistances <- function( l_config,
                             resistance_id,
                             resistance_name=NA,
                             control_id,
                             resistance_strength,
                             resistance_incr,
                             resistance_decr,
                             add = FALSE) 
{
  
  
  #check that control_ids are present  
  bad_indices <- which(!control_id %in% l_config$controls[['control_id']])
  if (length(bad_indices)>0)
  {
    warning("these control_ids are not in your controls config file and will cause problems :",control_id[bad_indices])
  }
  
  #put passed data into a dataframe ready to put into list
  dF <- data.frame(resistance_id=resistance_id, 
                   resistance_name=resistance_name,
                   control_id=control_id, 
                   resistance_strength=resistance_strength,
                   resistance_incr=resistance_incr,
                   resistance_decr=resistance_decr,
                   stringsAsFactors = FALSE)
  
  
  if (add)
  {
    l_config$resistances <- rbind(l_config$resistances, dF) 
  } else
  {
    l_config$resistances <- dF    
  }
  
  return(l_config)
}