Need to replace some occurrences of parameters$... with values in arg list

[langfob]

Found this note lying around in a random text file. Not sure what code file it originally came from and not sure if it matters now, but don't want to throw it away yet:

#  2016 06 14 - BTL
#  Need to replace all occurrences in here of parameters$... with 
#  the actually value in the function arg lists so that you can run these 
#  with hard-coded values rather than passing in the parameters structure.
#  This matters because when you combine a bdp1 and bdp2 to get a combined 
#  biodiversity problem, there is currently no mechanism in the yaml file 
#  for specifying parameters for multiple problems.

# 25:    infile_name = parameters$Xu_problem_input_file_name
# 29:    parameters$given_correct_solution_cost) 
# 169:    if (PU_spp_pair_indices_sextet$num_spp > parameters$max_allowed_num_spp)
# 172:             parameters$max_allowed_num_spp, ").\n\n")
# 245:    if (parameters$read_Xu_problem_from_file)
# 258:#        max_allowed_num_spp = parameters$max_allowed_num_spp
# 266:    retVal$read_Xu_problem_from_file   = parameters$read_Xu_problem_from_file
# 814:    parameters$wrap_lognormal_around_Xu = TRUE    #  temp for testin only...
# 816:    if (parameters$wrap_lognormal_around_Xu & 
# 817:        parameters$read_Xu_problem_from_file)
# 834:         if (parameters$wrap_lognormal_around_Xu)
# 870:    parameters$gen_multi_bdproblem = TRUE
# 872:    if (parameters$gen_multi_bdproblem)