Doxygen warnings

[eloch216]

I noticed some Doxygen warnings about un-documented parameters. These aren't high priority but it would be nice to fix them at some point:

C:/Users/eloch/Documents/GitHub/biocro/src/framework/R_helper_functions.cpp:302: warning: argument 'm_ptr' of command @param is not found in the argument list of finalize_module_creator(SEXP mw_ptr)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/R_helper_functions.cpp:311: warning: The following parameters of finalize_module_creator(SEXP mw_ptr) are not documented:
  parameter 'mw_ptr'

C:/Users/eloch/Documents/GitHub/biocro/src/framework/utils/module_dependency_utilities.cpp:255: warning: argument 'module_names' of command @param is not found in the argument list of order_ok(mc_vector mcs)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/utils/module_dependency_utilities.cpp:266: warning: The following parameters of order_ok(mc_vector mcs) are not documented:
  parameter 'mcs'

C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'in' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'out' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'in' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'out' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:635: warning: The following parameters of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates) are not documented:
  parameter 'target_vector'
  parameter 'duplicates'

C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:43: warning: The following parameters of validate_dynamical_system_inputs(std::string &message, state_map initial_values, state_map params, state_vector_map drivers, mc_vector const &direct_mcs, mc_vector const &differential_mcs) are not documented:
  parameter 'initial_values'
  parameter 'params'
  parameter 'drivers'
  parameter 'direct_mcs'
  parameter 'differential_mcs'

C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.h:156: warning: The following parameters of create_message(std::string message_if_empty, std::string message_at_beginning, std::string message_at_end, string_list_type string_list, std::string success_indicator="", std::string failure_indicator="") are not documented:
  parameter 'success_indicator'
  parameter 'failure_indicator'

C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'in' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'out' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'in' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.cpp:621: warning: argument 'out' of command @param is not found in the argument list of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates)
C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.h:71: warning: The following parameters of insert_quantity_name_if_new(std::string quantity_name, string_vector &target_vector, string_vector &duplicates) are not documented:
  parameter 'target_vector'
  parameter 'duplicates'

C:/Users/eloch/Documents/GitHub/biocro/src/framework/validate_dynamical_system.h:15: warning: The following parameters of validate_dynamical_system_inputs(std::string &message, state_map initial_values, state_map params, state_vector_map drivers, mc_vector const &direct_mcs, mc_vector const &differential_mcs) are not documented:
  parameter 'initial_values'
  parameter 'params'
  parameter 'drivers'
  parameter 'direct_mcs'
  parameter 'differential_mcs'