def fit(results, components):
"""Basic OLS model to predict test results."""
X = np.zeros((len(results),26+len(components)*2))
Y = np.zeros((len(results),1))
for i,result in enumerate(results):
Y[i] = result.correct
x = np.zeros(len(components))
test_components = result.test.double.components+result.test.single.components
for component in test_components:
try:
index = components.index(component)
except ValueError:
print "Couldn't find %s" % component
sys.exit(0)
else:
x[index] += 1
for j in range(len(components)):
X[i,26+2*j] = x[j]==1
X[i,26+2*j+1] = x[j]==2
X[i,result.subject_id] = 1
from scikits.statsmodels.api import OLS
from sklearn import linear_model as lm
clf = lm.Lasso(0.001)#alpha = alpha)
results = clf.fit(X,Y)
for i,beta in enumerate(results.coef_):
result = round(1000*beta)
if abs(result) > 0.1:
print i,result
print Y.shape,X.shape
model = OLS(Y,X)
results = model.fit()
print results.summary()
return Y,X
def typeIII(response, ancova, recarray):
"""
Produce an ANCOVA table
with type III sum of squares
from a given ANCOVA formula.
Inputs
------
response: str
field name of response in recarray
ancova: ANCOVA
specifies the model to be fit
recarray: np.ndarray
should contain all field names in the terms of ancova
as well as response
"""
X = ancova.formula.design(recarray, return_float=True)
Y = recarray[response]
model = OLS(Y, X)
results = model.fit()
SSE_F = np.sum(results.resid**2)
df_F = results.df_resid
names = []
fs = []
dfs = []
sss = []
pvals = []
for contrast in ancova.contrast_names:
r = results.f_test(ancova.contrast_matrices[contrast])
names.append(contrast)
fs.append(r.fvalue)
dfs.append(r.df_num)
pvals.append(r.pvalue)
sss.append(r.fvalue * results.scale * r.df_num)
# Add in the "residual row"
sss.append(SSE_F)
dfs.append(df_F)
pvals.append(np.nan)
fs.append(np.nan)
names.append('Residuals')
result = np.array(
names, np.dtype([('contrast', 'S%d' % max([len(n) for n in names]))]))
result = ML.rec_append_fields(
result, ['SS', 'df', 'MS', 'F', 'p_value'],
[sss, dfs, np.array(sss) / np.array(dfs), fs, pvals])
return result
def typeIII(response, ancova, recarray):
"""
Produce an ANCOVA table
with type III sum of squares
from a given ANCOVA formula.
Inputs
------
response: str
field name of response in recarray
ancova: ANCOVA
specifies the model to be fit
recarray: np.ndarray
should contain all field names in the terms of ancova
as well as response
"""
X = ancova.formula.design(recarray, return_float=True)
Y = recarray[response]
model = OLS(Y, X)
results = model.fit()
SSE_F = np.sum(results.resid**2)
df_F = results.df_resid
names = []
fs = []
dfs = []
sss = []
pvals = []
for contrast in ancova.contrast_names:
r = results.f_test(ancova.contrast_matrices[contrast])
names.append(contrast)
fs.append(r.fvalue)
dfs.append(r.df_num)
pvals.append(r.pvalue)
sss.append(r.fvalue * results.scale * r.df_num)
# Add in the "residual row"
sss.append(SSE_F)
dfs.append(df_F)
pvals.append(np.nan)
fs.append(np.nan)
names.append('Residuals')
result = np.array(names, np.dtype([('contrast','S%d' % max([len(n) for n in names]))]))
result = ML.rec_append_fields(result, ['SS', 'df', 'MS', 'F', 'p_value'], [sss, dfs, np.array(sss) / np.array(dfs), fs, pvals])
return result
def typeII(response, ancova, recarray):
"""
Produce an ANCOVA table
from a given ANCOVA formula
with type II sums of squares.
Inputs
------
response: str
field name of response in recarray
ancova: ANCOVA
specifies the model to be fit
recarray: np.ndarray
should contain all field names in the terms of ancova
as well as response
"""
Y = recarray[response]
X = ancova.formula.design(recarray, return_float=True)
model = OLS(Y, X)
results = model.fit()
SSE_F = np.sum(results.resid**2)
df_F = results.df_resid
names = []
sss = []
fs = []
dfs = []
pvals = []
for name, expr_factors in zip(ancova.contrast_names, ancova.sequence()):
expr, factors = expr_factors
F = ancova.all_but_above(expr, factors)
C = ancova.contrasts[name]
XF, contrast_matrices = F.formula.design(recarray, contrasts={'C': C})
modelF = OLS(Y, XF)
resultsF = modelF.fit()
SSEF = np.sum(resultsF.resid**2)
dfF = resultsF.df_resid
ftest = resultsF.f_test(contrast_matrices['C'])
SSER = SSEF + ftest.fvalue * ftest.df_num * (SSEF / dfF)
dfR = dfF + ftest.df_num
sss.append(SSER - SSEF)
dfs.append(ftest.df_num)
fs.append(((SSER - SSEF) / (dfR - dfF)) / (SSE_F / df_F))
pvals.append(f_dbn.sf(fs[-1], dfR - dfF, df_F))
names.append(name)
# Add in the "residual row"
sss.append(SSE_F)
dfs.append(df_F)
pvals.append(np.nan)
fs.append(np.nan)
names.append('Residuals')
result = np.array(
names, np.dtype([('contrast', 'S%d' % max([len(n) for n in names]))]))
result = ML.rec_append_fields(
result, ['SS', 'df', 'MS', 'F', 'p_value'],
[sss, dfs, np.array(sss) / np.array(dfs), fs, pvals])
return result
def typeI(response, ancova, recarray):
"""
Produce an ANCOVA table
from a given ANCOVA formula
with type I sums of squares
where the order is based on the order of terms
in the contrast_names of ancova.
Inputs
------
response: str
field name of response in recarray
ancova: ANCOVA
specifies the model to be fit
recarray: np.ndarray
should contain all field names in the terms of ancova
as well as response
"""
Y = recarray[response]
X = ancova.formula.design(recarray, return_float=True)
model = OLS(Y, X)
results = model.fit()
SSE_F = np.sum(results.resid**2)
df_F = results.df_resid
model = OLS(Y, ancova.formulae[0].design(recarray, return_float=True))
results = model.fit()
SSE_old = np.sum(results.resid**2)
df_old = results.df_resid
names = []
sss = []
fs = []
dfs = []
pvals = []
names.append(ancova.contrast_names[0])
fs.append(
((np.sum(Y**2) - SSE_old) / (Y.shape[0] - df_old)) / (SSE_F / df_F))
sss.append((np.sum(Y**2) - SSE_old))
dfs.append(Y.shape[0] - df_old)
pvals.append(f_dbn.sf(fs[-1], Y.shape[0] - df_old, df_F))
for d in range(1, len(ancova.formulae)):
terms = []
for f in ancova.formulae[:(d + 1)]:
terms += list(f.terms)
# JT: this is not numerically efficient
# could be done by updating some factorization of the full X
X = Formula(terms).design(recarray, return_float=True)
model = OLS(Y, X)
results = model.fit()
SSE_new = np.sum(results.resid**2)
df_new = results.df_resid
sss.append(SSE_old - SSE_new)
dfs.append(df_old - df_new)
fs.append(((SSE_old - SSE_new) / (df_old - df_new)) / (SSE_F / df_F))
pvals.append(f_dbn.sf(fs[-1], df_old - df_new, df_new))
names.append(ancova.contrast_names[d])
SSE_old = SSE_new
df_old = df_new
# Add in the "residual row"
sss.append(SSE_new)
dfs.append(df_new)
pvals.append(np.nan)
fs.append(np.nan)
names.append('Residuals')
result = np.array(
names, np.dtype([('contrast', 'S%d' % max([len(n) for n in names]))]))
result = ML.rec_append_fields(
result, ['SS', 'df', 'MS', 'F', 'p_value'],
[sss, dfs, np.array(sss) / np.array(dfs), fs, pvals])
return result
def typeII(response, ancova, recarray):
"""
Produce an ANCOVA table
from a given ANCOVA formula
with type II sums of squares.
Inputs
------
response: str
field name of response in recarray
ancova: ANCOVA
specifies the model to be fit
recarray: np.ndarray
should contain all field names in the terms of ancova
as well as response
"""
Y = recarray[response]
X = ancova.formula.design(recarray, return_float=True)
model = OLS(Y, X)
results = model.fit()
SSE_F = np.sum(results.resid**2)
df_F = results.df_resid
names = []
sss = []
fs = []
dfs = []
pvals = []
for name, expr_factors in zip(ancova.contrast_names,
ancova.sequence()):
expr, factors = expr_factors
F = ancova.all_but_above(expr, factors)
C = ancova.contrasts[name]
XF, contrast_matrices = F.formula.design(recarray, contrasts={'C':C})
modelF = OLS(Y, XF)
resultsF = modelF.fit()
SSEF = np.sum(resultsF.resid**2)
dfF = resultsF.df_resid
ftest = resultsF.f_test(contrast_matrices['C'])
SSER = SSEF + ftest.fvalue * ftest.df_num * (SSEF / dfF)
dfR = dfF + ftest.df_num
sss.append(SSER - SSEF)
dfs.append(ftest.df_num)
fs.append(((SSER - SSEF) / (dfR - dfF)) / (SSE_F / df_F))
pvals.append(f_dbn.sf(fs[-1], dfR-dfF, df_F))
names.append(name)
# Add in the "residual row"
sss.append(SSE_F)
dfs.append(df_F)
pvals.append(np.nan)
fs.append(np.nan)
names.append('Residuals')
result = np.array(names, np.dtype([('contrast','S%d' % max([len(n) for n in names]))]))
result = ML.rec_append_fields(result, ['SS', 'df', 'MS', 'F', 'p_value'], [sss, dfs, np.array(sss) / np.array(dfs), fs, pvals])
return result
def typeI(response, ancova, recarray):
"""
Produce an ANCOVA table
from a given ANCOVA formula
with type I sums of squares
where the order is based on the order of terms
in the contrast_names of ancova.
Inputs
------
response: str
field name of response in recarray
ancova: ANCOVA
specifies the model to be fit
recarray: np.ndarray
should contain all field names in the terms of ancova
as well as response
"""
Y = recarray[response]
X = ancova.formula.design(recarray, return_float=True)
model = OLS(Y, X)
results = model.fit()
SSE_F = np.sum(results.resid**2)
df_F = results.df_resid
model = OLS(Y, ancova.formulae[0].design(recarray, return_float=True))
results = model.fit()
SSE_old = np.sum(results.resid**2)
df_old = results.df_resid
names = []
sss = []
fs = []
dfs = []
pvals = []
names.append(ancova.contrast_names[0])
fs.append(((np.sum(Y**2) - SSE_old) / (Y.shape[0] - df_old)) / (SSE_F / df_F))
sss.append((np.sum(Y**2) - SSE_old))
dfs.append(Y.shape[0] - df_old)
pvals.append(f_dbn.sf(fs[-1], Y.shape[0]-df_old, df_F))
for d in range(1,len(ancova.formulae)):
terms = []
for f in ancova.formulae[:(d+1)]:
terms += list(f.terms)
# JT: this is not numerically efficient
# could be done by updating some factorization of the full X
X = Formula(terms).design(recarray, return_float=True)
model = OLS(Y, X)
results = model.fit()
SSE_new = np.sum(results.resid**2)
df_new = results.df_resid
sss.append(SSE_old - SSE_new)
dfs.append(df_old - df_new)
fs.append(((SSE_old-SSE_new) / (df_old - df_new)) / (SSE_F / df_F))
pvals.append(f_dbn.sf(fs[-1], df_old-df_new, df_new))
names.append(ancova.contrast_names[d])
SSE_old = SSE_new
df_old = df_new
# Add in the "residual row"
sss.append(SSE_new)
dfs.append(df_new)
pvals.append(np.nan)
fs.append(np.nan)
names.append('Residuals')
result = np.array(names, np.dtype([('contrast','S%d' % max([len(n) for n in names]))]))
result = ML.rec_append_fields(result, ['SS', 'df', 'MS', 'F', 'p_value'], [sss, dfs, np.array(sss) / np.array(dfs), fs, pvals])
return result