# 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
# -----------------------------------------------------------------------------