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Some failing CoxPH tests #89

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merged 42 commits into from
Nov 27, 2014
Merged

Some failing CoxPH tests #89

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49622e5
Predicting with CoxPH could raise an error
spacecowboy Nov 22, 2014
72e0d92
Add tests for CoxPH which are currently failing
spacecowboy Nov 22, 2014
99e1cb1
fixing inequality bug, and adding noise to tests
CamDavidsonPilon Nov 22, 2014
812315d
fix typo
CamDavidsonPilon Nov 22, 2014
d34d259
adding predict method to fitters, and cleaning up some tests + adding…
CamDavidsonPilon Nov 23, 2014
dec7e4e
fixing coxph prediction values
CamDavidsonPilon Nov 23, 2014
737d6ad
fixing a few tets
CamDavidsonPilon Nov 23, 2014
538556f
Change to gaussian noise, increase limits
spacecowboy Nov 24, 2014
241d285
reverting the keyword argument for birth_col, I found a better way
CamDavidsonPilon Nov 24, 2014
9bd3947
getting baseline survival for CoxPH correct! Adding new baseline piec…
CamDavidsonPilon Nov 24, 2014
84148ae
adding new CoxPH test for p-values and se
CamDavidsonPilon Nov 24, 2014
69bacde
make test more liberal
CamDavidsonPilon Nov 24, 2014
abd58ab
in order to allow for weighted values, and to keep thing non-boolean,…
CamDavidsonPilon Nov 24, 2014
f369d07
Make CoxPHs summary print more details, like in R
spacecowboy Nov 24, 2014
eeeb05a
Set scientific format
spacecowboy Nov 24, 2014
cc49f27
Set format on concordance in summary print
spacecowboy Nov 24, 2014
0e817a8
Fix errors with singular matrix in CoxPH
spacecowboy Nov 24, 2014
ca8a112
Correct numerical errors in Newton-Raphson
spacecowboy Nov 24, 2014
5b5d3bb
adding normalizer (default True) to coxPH model - this helps with avo…
CamDavidsonPilon Nov 25, 2014
23ef126
adding new test for normalizing time variable: why does this improve …
CamDavidsonPilon Nov 25, 2014
6b3b277
Adding test for shifting inputs to c-index
CamDavidsonPilon Nov 25, 2014
3241721
Renamed test method for consistency
spacecowboy Nov 25, 2014
2faf932
Repeat tests for statistics and lower limit somewhat
spacecowboy Nov 25, 2014
cd07bb1
Adding some more samples to help inference a c-index
CamDavidsonPilon Nov 26, 2014
1f2d61c
Add similar test for AAf
CamDavidsonPilon Nov 26, 2014
ac52561
there appears to be a divergence in python 3+ in this test
CamDavidsonPilon Nov 26, 2014
880381d
removing unused lstsq and fixing output of tset
CamDavidsonPilon Nov 26, 2014
a9b807d
Found a problem with data sorting
spacecowboy Nov 26, 2014
19fb043
Apply normalization to future data
spacecowboy Nov 26, 2014
ae46f1c
Add test to compare concordance between methods
spacecowboy Nov 26, 2014
d928978
Mistakenly added a new file
spacecowboy Nov 26, 2014
046f155
Allow (n,1) or (1,n) arrays in C-index
spacecowboy Nov 26, 2014
9e10813
Make predict_partial_hazard output a DataFrame
spacecowboy Nov 26, 2014
12635b7
Have crossval tests use predict_partial_hazard
spacecowboy Nov 26, 2014
907882a
Expect failure on predict test
spacecowboy Nov 26, 2014
38e118d
no more abiguity - DataFrame are always returned
CamDavidsonPilon Nov 27, 2014
a7b6c9f
update a sorting test to now compare np vs dataframes
CamDavidsonPilon Nov 27, 2014
f67a8f0
Update this test to use new dataframe outputs
CamDavidsonPilon Nov 27, 2014
7a89a21
adding in respecful indexing, refactoring the logic around that, addi…
CamDavidsonPilon Nov 27, 2014
acb1e83
fixing cv for cox survival functions, cleaning test code
CamDavidsonPilon Nov 27, 2014
5650dff
Update comments
spacecowboy Nov 27, 2014
c838831
Making sure behavior is consistent wrt Py2/Py3
spacecowboy Nov 27, 2014
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