Thanks so much for bringing this package to Python! Thanks especially for including all the distributions, it's a huge help.
One-column offset support for binomial models seems broken:
import numpy as np
from glmnet_python import glmnet
N = 100
p = 5
X = np.random.normal(size=(N, p))
y = (np.random.uniform(size=N) > 0.5).astype(float)
w = np.random.uniform(size=(N, 1))
offset = np.random.normal(size=(N, 1))
fit = glmnet(x=X, y=y, weights=w, family="binomial", offset=offset)
Throws:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-1-3390e77801ef> in <module>
12 offset = np.random.normal(size=(N, 1))
13
---> 14 fit = glmnet(x=X, y=y, weights=w, family="binomial", offset=offset)
~/git/glmnet_python/glmnet_python/glmnet.py in glmnet(x, y, family, **options)
451 elif (family == 'binomial') or (family == 'multinomial'):
452 # call lognet
--> 453 fit = lognet(x, is_sparse, irs, pcs, y, weights, offset, parm,
454 nobs, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam,
455 thresh, isd, intr, maxit, kopt, family)
~/git/glmnet_python/glmnet_python/lognet.py in lognet(x, is_sparse, irs, pcs, y, weights, offset, parm, nobs, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, isd, intr, maxit, kopt, family)
72 if nc == 1:
73 if do[1] == 1:
---> 74 offset = scipy.column_stack((offset, -offset), 1)
75 if do[1] > 2:
76 raise ValueError('offset should have 1 or 2 columns in binomial call to glmnet')
~/anaconda3/envs/football/lib/python3.8/site-packages/scipy/_lib/deprecation.py in call(*args, **kwargs)
18 warnings.warn(msg, category=DeprecationWarning,
19 stacklevel=stacklevel)
---> 20 return fun(*args, **kwargs)
21 call.__doc__ = msg
22 return call
<__array_function__ internals> in column_stack(*args, **kwargs)
TypeError: _column_stack_dispatcher() takes 1 positional argument but 2 were given
column_stack (since at least 2006?), doesn't seem to take a second argument, and the code works as expected if you take it out.
Thanks so much for bringing this package to Python! Thanks especially for including all the distributions, it's a huge help.
One-column offset support for binomial models seems broken:
Throws:
column_stack
(since at least 2006?), doesn't seem to take a second argument, and the code works as expected if you take it out.