# Analog program run description file

# Blank lines are ignored.
# '#' and all chars to end of line are ignored.
# Leading whitespace is ignored
#
# Names can be in upper or lower case or a mixture, but UNIX file names
# must be given with the correct letter case, or the program won't find
# them.
#
# Items may be listed in any order, but the grouping described by braces
# must be maintained.  This keeps related information together.

# The input files are either basis files or sample files.  Basis files are
# the modern samples for which environmental data are available.  Sample
# files are the fossil samples whose environmental data we want to
# estimate.
#
# To specify a file, give its group (basis or sample), and begin a group
# that contains
#  1. the name of the file containing the data and (optionally) a
#     description of the file's format as "data <name>: <format>"
#     where the colon, if present, must be followed by whitespace, and the
#     name must not contain whitespace,
#  2. the name of the file containing the transformation rules.
#  3. The name and, optionally, the format of the file containing meta
#     data for the samples, as "meta <name>: <format>", like the data file.

basis {
	data specmap.071: specmap
	meta specmap.071: specmap
	}

basis {
	data specmap.072: specmap
	meta specmap.072: specmap
	}

basis {
	data file_name_2a: format_description
	transform file_name_2b
	meta file_name_2c: format_description
	}

sample {
	data file_name_3a: format_description
	transform file_name_3b
	meta file_name_3c: format_description
	}

sample{#This is a comment with the words data and transform and meta in it.
	data file_name_4a: format_description
	transform file_name_4b
# Here is a line with delimiters but no extra spaces and a closing brace at the end:
meta file_name_4c:format_description}

# "distance" may take the values
#     manhattan
#     euclidean
#     squared_euclidean
#     canberra
#     squared_chord
#     squared_chisquared
#     jaccard
#     dot_product
#     correlation

distance squared_chord

# "report" specifies what will be output.  In this section you can specify
# how many of the closest basis samples to report for each fossil sample,
# and which meta data variables from the modern samples to include in the
# description of the matches.
#
# "name" is optional (if omitted, results go to stdout); its syntax is the
# same as "data" and "meta" in input file specifications.
#
# "closest" should be followed by an integer; if "closest" is not followed
# by an integer, the number is assumed to be 1.
#
# "meta" should be followed by the name of a meta data variable, in which
# case the statement can be repeated, or "all" if you want all of them
# added to the output for each matching modern sample.  If the meta data
# variable's name contains any spaces, you must use underscores instead.

report {
	name file_name_5: format_description
	closest 10
	meta variable_name_1
	meta variable_name_2
	meta variable_name_n
	}

# "verbose", if present, causes the program to describe the input and
# report its progress.

verbose

# (end)