def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: r_test.py 2782 2009-09-10 11:40:29Z andreas $")
parser.add_option("-m",
"--method",
dest="method",
type="choice",
help="method to use [t-test=t-test,wilcox=wilcox]",
choices=("t-test", "wilcox"))
parser.add_option("-1",
"--infile",
dest="filename_input",
type="string",
help="input filename with vector of values.")
parser.add_option("-2",
"--infile2",
dest="filename_input2",
type="string",
help="input filename with vector of values.")
parser.add_option("--header",
dest="header",
type="string",
help="""header of value column [default=%default].""")
parser.set_defaults(
method="t-test",
filename_input=None,
header="value",
)
(options, args) = E.Start(parser, add_pipe_options=True)
if options.filename_input:
infile = open(options.filename_input, "r")
else:
infile = sys.stdin
values, errors = IOTools.ReadList(infile, map_function=float)
if options.filename_input:
infile.close()
if errors:
E.warn("errors in input: %s" % ";".join(map(str, errors)))
kwargs = {}
xargs = []
for arg in args:
if "=" in arg:
key, value = arg.split("=")
kwargs[key] = value
else:
xargs.append(arg)
if options.filename_input2:
infile = open(options.filename_input2, "r")
values2, errors2 = IOTools.ReadList(infile, map_function=float)
infile.close()
else:
values2 = None
stat = Stats.Summary(values)
power, diff_at_power95 = None, None
if options.method == "t-test":
if values2:
result = R.t_test(values, values2, *xargs, **kwargs)
else:
result = R.t_test(values, *xargs, **kwargs)
# compute power of test
power = R.power_t_test(n=len(values),
delta=abs(stat["mean"]),
sd=stat["stddev"],
sig_level=0.05)['power']
diff_at_power95 = R.power_t_test(n=len(values),
power=0.95,
sd=stat["stddev"],
sig_level=0.05)['delta']
if options.method == "wilcox":
result = R.wilcox_test(values, *xargs, **kwargs)
options.stdout.write("%s\t%s\n" % ("key", options.header))
for key, value in sorted(result.items()):
if key == "data.name":
continue
if key == "p.value":
options.stdout.write("%s\t%5.2e\n" % (str(key), value))
else:
options.stdout.write("%s\t%s\n" % (str(key), str(value)))
for key, value in stat.items():
options.stdout.write("%s\t%s\n" % (str(key), str(value)))
if power:
options.stdout.write("1-power\t%5.2e\n" % (1.0 - power))
options.stdout.write("diff_at_power95\t%f\n" % diff_at_power95)
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id: r_test.py 2782 2009-09-10 11:40:29Z andreas $")
parser.add_option("-m", "--method", dest="method", type="choice",
help="method to use [t-test=t-test,wilcox=wilcox]",
choices=("t-test", "wilcox"))
parser.add_option("-1", "--infile", dest="filename_input", type="string",
help="input filename with vector of values.")
parser.add_option("-2", "--infile2", dest="filename_input2", type="string",
help="input filename with vector of values.")
parser.add_option("--header", dest="header", type="string",
help="""header of value column [default=%default].""")
parser.set_defaults(
method="t-test",
filename_input=None,
header="value",
)
(options, args) = E.Start(parser,
add_pipe_options=True)
if options.filename_input:
infile = open(options.filename_input, "r")
else:
infile = sys.stdin
values, errors = IOTools.ReadList(infile,
map_function=float)
if options.filename_input:
infile.close()
if errors:
E.warn("errors in input: %s" % ";".join(map(str, errors)))
kwargs = {}
xargs = []
for arg in args:
if "=" in arg:
key, value = arg.split("=")
kwargs[key] = value
else:
xargs.append(arg)
if options.filename_input2:
infile = open(options.filename_input2, "r")
values2, errors2 = IOTools.ReadList(infile,
map_function=float)
infile.close()
else:
values2 = None
stat = Stats.Summary(values)
power, diff_at_power95 = None, None
if options.method == "t-test":
if values2:
result = R.t_test(values, values2, *xargs, **kwargs)
else:
result = R.t_test(values, *xargs, **kwargs)
# compute power of test
power = R.power_t_test(n=len(values),
delta=abs(stat["mean"]),
sd=stat["stddev"],
sig_level=0.05)['power']
diff_at_power95 = R.power_t_test(n=len(values),
power=0.95,
sd=stat["stddev"],
sig_level=0.05)['delta']
if options.method == "wilcox":
result = R.wilcox_test(values, *xargs, **kwargs)
options.stdout.write("%s\t%s\n" % ("key", options.header))
for key, value in sorted(result.items()):
if key == "data.name":
continue
if key == "p.value":
options.stdout.write("%s\t%5.2e\n" % (str(key), value))
else:
options.stdout.write("%s\t%s\n" % (str(key), str(value)))
for key, value in stat.items():
options.stdout.write("%s\t%s\n" % (str(key), str(value)))
if power:
options.stdout.write("1-power\t%5.2e\n" % (1.0 - power))
options.stdout.write("diff_at_power95\t%f\n" % diff_at_power95)
E.Stop()
map_function=float )
infile.close()
else:
values2 = None
stat = Stats.Summary(values)
power, diff_at_power95 = None, None
if options.method == "t-test":
if values2:
result = R.t_test( values, values2, *xargs, **kwargs )
else:
result = R.t_test( values, *xargs, **kwargs )
## compute power of test
power = R.power_t_test(n=len(values),
delta=abs(stat["mean"]),
sd=stat["stddev"],
sig_level=0.05 )['power']
diff_at_power95= R.power_t_test(n=len(values),
power=0.95,
sd=stat["stddev"],
sig_level=0.05 )['delta']
if options.method == "wilcox":
result = R.wilcox_test( values, *xargs, **kwargs )
options.stdout.write( "%s\t%s\n" % ("key", options.header) )
for key, value in sorted(result.items()):
if key == "data.name": continue
if key == "p.value":