[glu-genetics] push by bioinformed@gmail.com - Fix GLM to work with newer versions of SciPy. on 2012-03-21 17:47 GMT

[glu-ge...@googlecode.com]

Revision: 1de5b876249b
Author: Kevin B. Jacobs <jac...@bioinformed.com>
Date: Wed Mar 21 10:46:20 2012
Log: Fix GLM to work with newer versions of SciPy.
http://code.google.com/p/glu-genetics/source/detail?r=1de5b876249b

Modified:
/glu/lib/glm/glm.py

=======================================
--- /glu/lib/glm/glm.py Sat Aug 20 11:22:40 2011
+++ /glu/lib/glm/glm.py Wed Mar 21 10:46:20 2012
@@ -291,9 +291,17 @@
b1 = b2

if gelss.module_name.startswith('flapack'):
- lwork = calc_lwork.gelss(gelss.prefix,m,n,nrhs)[1]
- v,x,s,rank,info = gelss(a1, b1, cond=cond, lwork=lwork,
- overwrite_a=0, overwrite_b=0)
+ try:
+ work = gelss(a1, b1, lwork=-1)[4]
+ lwork = work[0].real.astype(np.int)
+ v,x,s,rank,work,info = gelss(a1, b1, cond=cond, lwork=lwork,
+ overwrite_a=0, overwrite_b=0)
+
+ # There has to be a better way to do this...
+ except Exception, e:
+ lwork = calc_lwork.gelss(gelss.prefix,m,n,nrhs)[1]
+ v,x,s,rank,info = gelss(a1, b1, cond=cond, lwork=lwork,
+ overwrite_a=0, overwrite_b=0)
else:
raise NotImplementedError('gelss not available from %s' %
gelss.module_name)

@@ -1125,7 +1133,7 @@
>>> print 'lr test=%.6f df=%d' % g.lr_test().test()
lr test=18.218406 df=6
'''
- def __init__(self, y, X, ref=None, vars=None, add_mean=False,
max_iterations=50):
+ def __init__(self, y, X, ref=None, vars=None, add_mean=False,
max_iterations=100):
y = np.asarray(y,dtype=int)
X = np.asarray(X,dtype=float)