def test_GLM_both(self):
if (1==1):
csvFilenameList = [
('logreg', 'benign.csv', 'binomial', 3, 10),
# col is zero based
# FIX! what's wrong here? index error
## ('uis.dat', 'binomial', 8, 5, False),
## ('pros.dat', 'binomial', 1, 10, False),
## ('chdage.dat', 'binomial', 2, 5, True),
## ('icu.dat', 'binomial', 1, 10, False),
# how to ignore 6? '1,2,3,4,5', False),
## ('clslowbwt.dat', 'binomial', 7, 10, False),
# ('cgd.dat', 'gaussian', 12, 5, False),
# ('meexp.dat', 'gaussian', 3, 10, None),
]
else:
csvFilenameList = [
# leave out ID and birth weight
('logreg', 'benign.csv', 'gaussian', 3, 10),
(None, 'icu.dat', 'binomial', 1, 10),
# need to exclude col 0 (ID) and col 10 (bwt)
# but -x doesn't work..so do 2:9...range doesn't work? FIX!
(None, 'nhanes3.dat', 'binomial', 15, 10),
(None, 'lowbwt.dat', 'binomial', 1, 10),
(None, 'lowbwtm11.dat', 'binomial', 1, 10),
(None, 'meexp.dat', 'gaussian', 3, 10),
# FIX! does this one hang in R?
(None, 'nhanes3.dat', 'binomial', 15, 10),
(None, 'pbc.dat', 'gaussian', 1, 10),
(None, 'pharynx.dat', 'gaussian', 12, 10),
(None, 'uis.dat', 'binomial', 8, 10),
]
trial = 0
for (offset, csvFilename, family, y, timeoutSecs) in csvFilenameList:
# FIX! do something about this file munging
if offset:
csvPathname1 = offset + "/" + csvFilename
else:
csvPathname1 = 'logreg/umass_statdata/' + csvFilename
fullPathname = h2i.find_folder_and_filename('smalldata', csvPathname1, returnFullPath=True)
csvPathname2 = SYNDATASETS_DIR + '/' + csvFilename + '_2.csv'
h2o_util.file_clean_for_R(fullPathname, csvPathname2)
# we can inspect this to get the number of cols in the dataset (trust H2O here)
parseResult = h2i.import_parse(path=csvPathname2, schema='put', hex_key=csvFilename, timeoutSecs=10)
# we could specify key2 above but this is fine
destination_key = parseResult['destination_key']
inspect = h2o_cmd.runInspect(None, destination_key)
num_cols = inspect['numCols']
num_rows = inspect['numRows']
print "num_cols", num_cols, "num_rows", num_rows
## print h2o.dump_json(inspect)
# create formula and the x for H2O GLM
formula = "V" + str(y+1) + " ~ "
x = None
col_names = ""
for c in range(0,num_cols):
if csvFilename=='clslowbwt.dat' and c==6:
print "Not including col 6 for this dataset from x"
if csvFilename=='benign.csv' and (c==0 or c==1):
print "Not including col 0,1 for this dataset from x"
else:
# don't add the output col to the RHS of formula
if x is None:
col_names += "V" + str(c+1)
else:
col_names += ",V" + str(c+1)
if c!=y:
if x is None:
x = str(c)
formula += "V" + str(c+1)
else:
x += "," + str(c)
formula += "+V" + str(c+1)
print 'formula:', formula
print 'col_names:', col_names
print 'x:', x
kwargs = {
'n_folds': 0,
'response': y,
# what about x?
'family': family,
'alpha': 0,
'lambda': 0,
'beta_epsilon': 1.0E-4,
'max_iter': 50 }
if csvFilename=='benign.csv':
kwargs['ignored_cols'] = '0,1'
if csvFilename=='clslowbwt.dat':
kwargs['ignored_cols'] = '6'
start = time.time()
glm = h2o_cmd.runGLM(parseResult=parseResult, timeoutSecs=timeoutSecs, **kwargs)
print "glm end (w/check) on ", csvPathname2, 'took', time.time()-start, 'seconds'
h2oResults = h2o_glm.simpleCheckGLM(self, glm, None, prettyPrint=True, **kwargs)
# now do it thru R and compare
(warningsR, cListR, interceptR) = glm_R_and_compare(self, csvPathname2, family, formula, y, h2oResults=h2oResults)
trial += 1
print "\nTrial #", trial
def test_GLM_both(self):
h2o.beta_features = True
if (1==1):
csvFilenameList = [
('logreg', 'benign.csv', 'binomial', 3, 10),
# col is zero based
# FIX! what's wrong here? index error
## ('uis.dat', 'binomial', 8, 5, False),
## ('pros.dat', 'binomial', 1, 10, False),
## ('chdage.dat', 'binomial', 2, 5, True),
## ('icu.dat', 'binomial', 1, 10, False),
# how to ignore 6? '1,2,3,4,5', False),
## ('clslowbwt.dat', 'binomial', 7, 10, False),
# ('cgd.dat', 'gaussian', 12, 5, False),
# ('meexp.dat', 'gaussian', 3, 10, None),
]
else:
csvFilenameList = [
# leave out ID and birth weight
('logreg', 'benign.csv', 'gaussian', 3, 10),
(None, 'icu.dat', 'binomial', 1, 10),
# need to exclude col 0 (ID) and col 10 (bwt)
# but -x doesn't work..so do 2:9...range doesn't work? FIX!
(None, 'nhanes3.dat', 'binomial', 15, 10),
(None, 'lowbwt.dat', 'binomial', 1, 10),
(None, 'lowbwtm11.dat', 'binomial', 1, 10),
(None, 'meexp.dat', 'gaussian', 3, 10),
# FIX! does this one hang in R?
(None, 'nhanes3.dat', 'binomial', 15, 10),
(None, 'pbc.dat', 'gaussian', 1, 10),
(None, 'pharynx.dat', 'gaussian', 12, 10),
(None, 'uis.dat', 'binomial', 8, 10),
]
trial = 0
for (offset, csvFilename, family, y, timeoutSecs) in csvFilenameList:
# FIX! do something about this file munging
if offset:
csvPathname1 = offset + "/" + csvFilename
else:
csvPathname1 = 'logreg/umass_statdata/' + csvFilename
fullPathname = h2i.find_folder_and_filename('smalldata', csvPathname1, returnFullPath=True)
csvPathname2 = SYNDATASETS_DIR + '/' + csvFilename + '_2.csv'
h2o_util.file_clean_for_R(fullPathname, csvPathname2)
# we can inspect this to get the number of cols in the dataset (trust H2O here)
parseResult = h2i.import_parse(path=csvPathname2, schema='put', hex_key=csvFilename, timeoutSecs=10)
# we could specify key2 above but this is fine
destination_key = parseResult['destination_key']
inspect = h2o_cmd.runInspect(None, destination_key)
if h2o.beta_features:
num_cols = inspect['numCols']
num_rows = inspect['numRows']
else:
num_cols = inspect['num_cols']
num_rows = inspect['num_rows']
print "num_cols", num_cols, "num_rows", num_rows
## print h2o.dump_json(inspect)
# create formula and the x for H2O GLM
formula = "V" + str(y+1) + " ~ "
x = None
col_names = ""
for c in range(0,num_cols):
if csvFilename=='clslowbwt.dat' and c==6:
print "Not including col 6 for this dataset from x"
if csvFilename=='benign.csv' and (c==0 or c==1):
print "Not including col 0,1 for this dataset from x"
else:
# don't add the output col to the RHS of formula
if x is None:
col_names += "V" + str(c+1)
else:
col_names += ",V" + str(c+1)
if c!=y:
if x is None:
x = str(c)
formula += "V" + str(c+1)
else:
x += "," + str(c)
formula += "+V" + str(c+1)
print 'formula:', formula
print 'col_names:', col_names
print 'x:', x
if h2o.beta_features:
kwargs = {
'n_folds': 0,
'response': y,
# what about x?
'family': family,
'alpha': 0,
'lambda': 0,
'beta_epsilon': 1.0E-4,
'max_iter': 50 }
else:
kwargs = {
'n_folds': 0,
'y': y,
'x': x,
'family': family,
'alpha': 0,
'lambda': 1e-4,
'beta_epsilon': 1.0E-4,
'max_iter': 50 }
if csvFilename=='benign.csv':
kwargs['ignored_cols'] = '0,1'
if csvFilename=='clslowbwt.dat':
kwargs['ignored_cols'] = '6'
start = time.time()
glm = h2o_cmd.runGLM(parseResult=parseResult, timeoutSecs=timeoutSecs, **kwargs)
print "glm end (w/check) on ", csvPathname2, 'took', time.time()-start, 'seconds'
h2oResults = h2o_glm.simpleCheckGLM(self, glm, None, prettyPrint=True, **kwargs)
# now do it thru R and compare
(warningsR, cListR, interceptR) = glm_R_and_compare(self, csvPathname2, family, formula, y, h2oResults=h2oResults)
trial += 1
print "\nTrial #", trial
def test_GLM_umass(self):
if 1 == 1:
csvFilenameList = [
# col is zero based
# FIX! what's wrong here? index error
("uis.dat", "binomial", 8, 5, False),
# ('cgd.dat', 'gaussian', 12, 5, False),
# ('meexp.dat', 'gaussian', 3, 10, None),
("pros.dat", "binomial", 1, 10, False),
("chdage.dat", "binomial", 2, 5, True),
("icu.dat", "binomial", 1, 10, False),
# how to ignore 6? '1,2,3,4,5', False),
("clslowbwt.dat", "binomial", 7, 10, False),
]
else:
csvFilenameList = [
# leave out ID and birth weight
("icu.dat", "binomial", 1, 10, None),
# need to exclude col 0 (ID) and col 10 (bwt)
# but -x doesn't work..so do 2:9...range doesn't work? FIX!
("nhanes3.dat", "binomial", 15, 10),
("lowbwt.dat", "binomial", 1, 10, "2,3,4,5,6,7,8,9"),
("lowbwtm11.dat", "binomial", 1, 10, None),
("meexp.dat", "gaussian", 3, 10, None),
# FIX! does this one hang in R?
("nhanes3.dat", "binomial", 15, 10, None),
("pbc.dat", "gaussian", 1, 10, None),
("pharynx.dat", "gaussian", 12, 10, None),
("uis.dat", "binomial", 8, 10, None),
]
trial = 0
for (csvFilename, family, y, timeoutSecs, header) in csvFilenameList:
# FIX! do something about this file munging
csvPathname1 = h2o.find_file("smalldata/logreg/umass_statdata/" + csvFilename)
csvPathname2 = SYNDATASETS_DIR + "/" + csvFilename + "_2.csv"
h2o_util.file_clean_for_R(csvPathname1, csvPathname2)
# we can inspect this to get the number of cols in the dataset (trust H2O here)
parseKey = h2o_cmd.parseFile(None, csvPathname2, key=csvFilename, timeoutSecs=10)
# we could specify key2 above but this is fine
destination_key = parseKey["destination_key"]
inspect = h2o_cmd.runInspect(None, destination_key)
num_cols = inspect["num_cols"]
num_rows = inspect["num_rows"]
print "num_cols", num_cols, "num_rows", num_rows
## print h2o.dump_json(inspect)
# create formula and the x for H2O GLM
formula = "V" + str(y + 1) + " ~ "
x = None
col_names = ""
for c in range(0, num_cols):
# don't add the output col to the RHS of formula
if x is None:
col_names += "V" + str(c + 1)
else:
col_names += ",V" + str(c + 1)
if c != y:
if x is None:
x = str(c)
formula += "V" + str(c + 1)
else:
x += "," + str(c)
formula += "+V" + str(c + 1)
print "formula:", formula
print "col_names:", col_names
print "x:", x
kwargs = {
"n_folds": 0,
"y": y,
"x": x,
"family": family,
"link": "familyDefault",
"alpha": 0,
"lambda": 0,
"case_mode": "=",
"case": 1,
"beta_eps": 1.0e-4,
"max_iter": 50,
}
start = time.time()
glm = h2o_cmd.runGLMOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
print "glm end (w/check) on ", csvPathname2, "took", time.time() - start, "seconds"
h2oResults = h2o_glm.simpleCheckGLM(self, glm, None, prettyPrint=True, **kwargs)
# now do it thru R and compare
(warningsR, cListR, interceptR) = glm_R_and_compare(
self, csvPathname2, family, formula, y, header=header, h2oResults=h2oResults
)
trial += 1
print "\nTrial #", trial
def test_GLM_umass(self):
if (1==1):
csvFilenameList = [
# col is zero based
# FIX! what's wrong here? index error
('uis.dat', 'binomial', 8, 5, False),
# ('cgd.dat', 'gaussian', 12, 5, False),
# ('meexp.dat', 'gaussian', 3, 10, None),
('pros.dat', 'binomial', 1, 10, False),
('chdage.dat', 'binomial', 2, 5, True),
('icu.dat', 'binomial', 1, 10, False),
# how to ignore 6? '1,2,3,4,5', False),
('clslowbwt.dat', 'binomial', 7, 10, False),
]
else:
csvFilenameList = [
# leave out ID and birth weight
('icu.dat', 'binomial', 1, 10, None),
# need to exclude col 0 (ID) and col 10 (bwt)
# but -x doesn't work..so do 2:9...range doesn't work? FIX!
('nhanes3.dat', 'binomial', 15, 10),
('lowbwt.dat', 'binomial', 1, 10, '2,3,4,5,6,7,8,9'),
('lowbwtm11.dat', 'binomial', 1, 10, None),
('meexp.dat', 'gaussian', 3, 10, None),
# FIX! does this one hang in R?
('nhanes3.dat', 'binomial', 15, 10, None),
('pbc.dat', 'gaussian', 1, 10, None),
('pharynx.dat', 'gaussian', 12, 10, None),
('uis.dat', 'binomial', 8, 10, None),
]
trial = 0
for (csvFilename, family, y, timeoutSecs, header) in csvFilenameList:
# FIX! do something about this file munging
csvPathname1 = h2o.find_file("smalldata/logreg/umass_statdata/" + csvFilename)
csvPathname2 = SYNDATASETS_DIR + '/' + csvFilename + '_2.csv'
h2o_util.file_clean_for_R(csvPathname1, csvPathname2)
# we can inspect this to get the number of cols in the dataset (trust H2O here)
parseKey = h2o_cmd.parseFile(None, csvPathname2, key=csvFilename, timeoutSecs=10)
# we could specify key2 above but this is fine
destination_key = parseKey['destination_key']
inspect = h2o_cmd.runInspect(None, destination_key)
num_cols = inspect['num_cols']
num_rows = inspect['num_rows']
print "num_cols", num_cols, "num_rows", num_rows
## print h2o.dump_json(inspect)
# create formula and the x for H2O GLM
formula = "V" + str(y+1) + " ~ "
x = None
col_names = ""
for c in range(0,num_cols):
if csvFilename=='clslowbwt.dat' and c==6:
print "Not including col 6 for this dataset from x"
else:
# don't add the output col to the RHS of formula
if x is None:
col_names += "V" + str(c+1)
else:
col_names += ",V" + str(c+1)
if c!=y:
if x is None:
x = str(c)
formula += "V" + str(c+1)
else:
x += "," + str(c)
formula += "+V" + str(c+1)
print 'formula:', formula
print 'col_names:', col_names
print 'x:', x
kwargs = { 'n_folds': 0, 'y': y, 'x': x,
'family': family, 'link': 'familyDefault',
'alpha': 0, 'lambda': 0, 'case_mode': '=', 'case': 1,
'beta_epsilon': 1.0E-4, 'max_iter': 50 }
start = time.time()
glm = h2o_cmd.runGLMOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
print "glm end (w/check) on ", csvPathname2, 'took', time.time()-start, 'seconds'
h2oResults = h2o_glm.simpleCheckGLM(self, glm, None, prettyPrint=True, **kwargs)
# now do it thru R and compare
(warningsR, cListR, interceptR) = glm_R_and_compare(self, csvPathname2, family, formula, y,
header=header, h2oResults=h2oResults)
trial += 1
print "\nTrial #", trial
def test_GLM_umass(self):
if (1==1):
csvFilenameList = [
# col is zero based
# FIX! what's wrong here? index error
('uis.dat', 'binomial', 8, 5, False),
# ('cgd.dat', 'gaussian', 12, 5, False),
# ('meexp.dat', 'gaussian', 3, 10, None),
('pros.dat', 'binomial', 1, 10, False),
('chdage.dat', 'binomial', 2, 5, True),
('icu.dat', 'binomial', 1, 10, False),
# how to ignore 6? '1,2,3,4,5', False),
('clslowbwt.dat', 'binomial', 7, 10, False),
]
else:
csvFilenameList = [
# leave out ID and birth weight
('icu.dat', 'binomial', 1, 10, None),
# need to exclude col 0 (ID) and col 10 (bwt)
# but -x doesn't work..so do 2:9...range doesn't work? FIX!
('nhanes3.dat', 'binomial', 15, 10),
('lowbwt.dat', 'binomial', 1, 10, '2,3,4,5,6,7,8,9'),
('lowbwtm11.dat', 'binomial', 1, 10, None),
('meexp.dat', 'gaussian', 3, 10, None),
# FIX! does this one hang in R?
('nhanes3.dat', 'binomial', 15, 10, None),
('pbc.dat', 'gaussian', 1, 10, None),
('pharynx.dat', 'gaussian', 12, 10, None),
('uis.dat', 'binomial', 8, 10, None),
]
trial = 0
for (csvFilename, family, y, timeoutSecs, header) in csvFilenameList:
# FIX! do something about this file munging
csvPathname1 = h2o.find_file("smalldata/logreg/umass_statdata/" + csvFilename)
csvPathname2 = SYNDATASETS_DIR + '/' + csvFilename + '_2.csv'
h2o_util.file_clean_for_R(csvPathname1, csvPathname2)
# we can inspect this to get the number of cols in the dataset (trust H2O here)
parseKey = h2o_cmd.parseFile(None, csvPathname2, key=csvFilename, timeoutSecs=10)
# we could specify key2 above but this is fine
destination_key = parseKey['destination_key']
inspect = h2o_cmd.runInspect(None, destination_key)
num_cols = inspect['num_cols']
num_rows = inspect['num_rows']
print "num_cols", num_cols, "num_rows", num_rows
## print h2o.dump_json(inspect)
# create formula and the x for H2O GLM
formula = "V" + str(y+1) + " ~ "
x = None
col_names = ""
for c in range(0,num_cols):
# don't add the output col to the RHS of formula
if x is None:
col_names += "V" + str(c+1)
else:
col_names += ",V" + str(c+1)
if c!=y:
if x is None:
x = str(c)
formula += "V" + str(c+1)
else:
x += "," + str(c)
formula += "+V" + str(c+1)
print 'formula:', formula
print 'col_names:', col_names
print 'x:', x
kwargs = { 'num_cross_validation_folds': 0, 'y': y, 'x': x,
'family': family, 'link': 'familyDefault',
'alpha': 0, 'lambda': 0, 'case_mode': '=', 'case': 1,
'beta_epsilon': 1.0E-4, 'max_iter': 50 }
start = time.time()
glm = h2o_cmd.runGLMOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
print "glm end (w/check) on ", csvPathname2, 'took', time.time()-start, 'seconds'
h2oResults = h2o_glm.simpleCheckGLM(self, glm, None, prettyPrint=True, **kwargs)
# now do it thru R and compare
(warningsR, cListR, interceptR) = glm_R_and_compare(csvPathname2, family, formula, y,
header=header, h2oResults=h2oResults)
trial += 1
print "\nTrial #", trial
