# This is a parameter file for ADZE.
# The entire line after a '#' will be ignored.

###----Main Parameters----###
MAX_G 8               #Max standardized sample size

DATA_LINES 22          #Number of lines of data

LOCI 5                #Number of loci

NON_DATA_ROWS 1       #Number of rows preceeding data
                     #including at least the locus names

NON_DATA_COLS 5       #Number of classifier columns
                     #at the beginning of each data line

GROUP_BY_COL 5        #The column number by which to
                     #group the data

DATA_FILE small_data.stru       #Name of the datafile

R_OUT small_r           #Name of the allelic richness output file

P_OUT small_p           #Name of the private allelic richness
                     #output file

###----Combination Parameters----###
COMB 1               #Calculate private allelic richness for
                     #combinations of groupings?

K_RANGE 2             #A listing of combinations to calculate

C_OUT small_c           #Name of the private allelic richness of
                     #combinations output file

###----Advanced Options----###
MISSING -9           #Missing data representation

TOLERANCE 1          #Filter loci with a grouping having more
                     #than this fraction of missing data

FULL_R 1             #Output allelic richness results for
                     #all loci?

FULL_P 1             #Output private allelic richness results
                     #for all loci?

FULL_C 1             #Output private allelic richness for
                     #combinations results for all loci?

PRINT_PROGRESS 1     #Track calculation progress on screen?

###----Command line arguments----###
# -g MAX_G
# -d DATA_LINES
# -l LOCI
# -nr NON_DATA_ROWS
# -nc NON_DATA_COLS
# -s GROUP_BY_COL
# -f DATA_FILE
# -r R_OUT
# -p P_OUT
# -c COMB
# -k K_RANGE
# -o COUT
# -m MISSING
# -t TOLERANCE
# -tnocalc
# -fr FULL_R
# -fp FULL_P
# -fc FULL_C
# -pp PRINT_PROGRESS
###----End of file----###
