# This is the file that sets the parameters for the program CLUMPP, version 1.1

# Everything after "#" will be ignored by the program. Parameters are:
# K, C, R, M, W, GREEDY_OPTION, REPEATS, PERMUTATIONFILE, PRINT_PERMUTED_DATA,
# PERMUTED_DATAFILE, PRINT_EVERY_PERM and EVERY_PERMFILE. 
# All parameter names shall be followed by at least one blank space and then
# the parameter-value.



# --------------- Main parameters ---------------------------------------------

DATATYPE 1				# The type of data to be read in.
					# 0 = individual data in the file
					# specified by INDFILE, 1 = population
					# data in the file specified by
					# POPFILE.

INDFILE arabid.indfile   		# The name of the individual datafile.
					# Required if DATATYPE = 0.

POPFILE arabid.popfile			# The name of the population datafile.
					# Required if DATATYPE = 1.

OUTFILE arabid.outfile     		# The average cluster membership 
					# coefficients across the permuted runs
					# are printed here.

MISCFILE arabid.miscfile		# The parameters used and a summary of
					# the results are printed here. 

K 3      				# Number of clusters.

C 95				      	# Number of individuals or populations.

R 9			            	# Number of runs.

M 1					# Method to be used (1 = FullSearch,
					# 2 = Greedy, 3 = LargeKGreedy).

W 1					# Weight by the number of individuals
					# in each population as specified in 
					# the datafile (1 if yes, 0 if no).

S 2                                     # Pairwise matrix similarity statistic 
                                        # to be used. 1 = G, 2 = G'. 


# - Additional options for the Greedy and LargeKGreedy algorithm (M = 2 or 3) -

GREEDY_OPTION 2				# 1 = All possible input orders,
					# 2 = random input orders,
					# 3 = pre-specified input orders.

REPEATS 1000				# If GREEDY_OPTION = 2, then REPEATS
					# determines the number of random input
					# orders to be tested. If GREEDY_OPTION
					# = 3, then REPEATS is the number of 
					# input orders in PERMUTATIONFILE.  

PERMUTATIONFILE arabid.permutationfile 	# The permutations of the runs in 
					# PERMUTATIONFILE will be used, if 
					# GREEDY_OPTION = 3.


# --------------- Optional outputs --------------------------------------------

PRINT_PERMUTED_DATA 1			# Print the permuted data (clusters) in
					# INDFILE or POPFILE to 
					# PERMUTED_DATAFILE (0 = don't print,
					# 1 = print into one file, 2 = print 
					# into separate files for each run).

PERMUTED_DATAFILE arabid.perm_datafile	# The permuted data (clusters) will be 
					# printed to this file (if 
					# PRINT_PERMUTED_DATA = 2, several 
					# files with the extensions "_1" to 
					# "_R" will be created).

PRINT_EVERY_PERM 0			# Print every tested permutation of the
					# runs and the corresponding value of 
					# SSC to a file specified by 
					# EVERY_PERMFILE (0 = don't print, 
					# 1 = print). 
					# Note that printing may result in a 
					# very large file.

EVERY_PERMFILE arabid.every_permfile	# Every tested permutation of the runs
					# and the corresponding SSC will be
					# printed here. 

PRINT_RANDOM_INPUTORDER 0               # Print random input orders of runs to
                                        # RANDOM_INPUTORDER (0 = don't print,
                                        # 1 = print). This option is only 
                                        # available if GREEDY_OPTION = 2.

RANDOM_INPUTORDERFILE arabid.random_inputorderfile # Every random input order 
                                        # of the runs (generated by CLUMPP if 
                                        # GREEDY_OPTION = 2) will be printed
                                        # here. 


# --------------- Advanced options --------------------------------------------

OVERRIDE_WARNINGS 0			# This option allows the user to 
					# override non-crucial warnings from 
					# the program (0 allow warnings, 1 do 
					# not issue non-crucial warnings).

ORDER_BY_RUN 1				# Permute the clusters of the output 
					# files by the specified run. (0 to 
					# not specify a run, 1 to R specifies
					# a run in the INDFILE or POPFILE).   


# --------------- Additional comments -----------------------------------------

# The term ''permutation'' is used in two different contexts, permutations of 
# membership coefficients, or clusters, and permutations of runs.

# For example, if the datafile has has data A B C D E (each letter indicates a 
# column corresponding to a cluster), then permutation 3 2 5 1 4 of the
# clusters means C B E A D.

# Permutation 4 1 2 3 of runs 1-4 would mean start with run 4, then run 1, then
# run 2, and then run 3.


# --------------- Command line arguments --------------------------------------

# -i INDFILE
# -p POPFILE
# -o OUTFILE
# -j MISCFILE
# -k K
# -c C
# -r R
# -m M
# -w W
# -s S
# -----------------------------------------------------------------------------

