Phreg 1312 rebased #1825

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merged 38 commits into from Jul 11, 2014

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@josef-pkt
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rebased version of #1312

removed duplicate commits with interactive rebase dropping those commits

unit tests for test_phreg pass locally (py 2.7)

@coveralls

Coverage Status

Coverage increased (+0.35%) when pulling c12b56c on josef-pkt:phreg_1312_rebased into 1697f70 on statsmodels:master.

@coveralls

Coverage Status

Coverage increased (+0.35%) when pulling 22a6113 on josef-pkt:phreg_1312_rebased into 1697f70 on statsmodels:master.

kshedden and others added some commits Jan 10, 2014
@kshedden @josef-pkt kshedden phreg initial commit of working code
Added summary; other fixes; ready for PR
Added R results
3176300
@kshedden @josef-pkt kshedden Minor cleanup of phreg.py 5dcadc2
@kshedden @josef-pkt kshedden Changed test script to address python 3 issue with exe (exec no longe…
…r used)
1b8c21f
@kshedden @josef-pkt kshedden Renamed time to endog for clarity b61e1ff
@kshedden @josef-pkt kshedden Add missing data option to signature b16079c
@kshedden @josef-pkt kshedden Remove local test code e66ea2b
@kshedden @josef-pkt kshedden Need to explicitly convert extra arguments to ndarrays a5b818f
@kshedden @josef-pkt kshedden Add fields to summary 340ea45
@kshedden @josef-pkt kshedden Update compat import of ordereddict 67ec01a
@kshedden @josef-pkt kshedden Fix issues with 2.6 (set comprehension) and 3.3 (test import) b8e99fb
@kshedden @josef-pkt kshedden More 2.6, 3+ compatability fixes f8ebc83
@kshedden @josef-pkt kshedden Fix import for python 3 compatability ca625ea
@kshedden @josef-pkt kshedden Add HR's to table, change CI to apply to HR, not coeffs 09e8752
@kshedden @josef-pkt kshedden A few vectorizations to improve performance 2b4e27f
@kshedden @josef-pkt kshedden Minor fix to test script d6787fe
@kshedden @josef-pkt kshedden Adjusted setup.py to give access to sandbox.results 4e22670
@kshedden @josef-pkt kshedden Added score_obs; various cleanups. 2a0262d
@kshedden @josef-pkt kshedden Robust covariances 540d1fb
@kshedden @josef-pkt kshedden Added offset; cleaned up some indexing code a534552
@kshedden @josef-pkt kshedden Change behavior for selecting covariance type 7eeda2b
@kshedden @josef-pkt kshedden Added Schoenfeld residuals 2943ab1
@kshedden @josef-pkt kshedden Moved groups argument to fit cf59221
@kshedden @josef-pkt kshedden Remove uninformative cases fb10d5d
@kshedden @josef-pkt kshedden Use seed when generating data for tests 8dd6139
@kshedden @josef-pkt kshedden Minor changes 7e91353
@kshedden @josef-pkt kshedden Added predict method 6a1006b
@kshedden @josef-pkt kshedden Added get_distribution 0d3be97
@kshedden @josef-pkt kshedden Added fit_regularized 1f35e03
@kshedden @josef-pkt kshedden Improved algorithm for fit_regularized 08eb575
@kshedden @josef-pkt kshedden Added test vs. R for fit_regularized fe5363e
@josef-pkt josef-pkt REF: add `__init__.py` to tests/results 75294d7
@josef-pkt josef-pkt BUG py3 compat add `list` (`np.array(dict.values)` creates object array) 7e24f21
@josef-pkt josef-pkt REF: move phreg from sandbox to new statsmodels.duration d4402c8
@josef-pkt
Member

I squashed the first several commits that were still changing test data files, and two commits that had identical commit message to the preceding commits

moved to statsmodels.duration

renamed module to hazard_regression.py
renamed class to PHReg instead of PHreg (capitalize first R)
(forgot to rename to PHRegResults, same capitalized R)

not yet: add to api.py and rst docs

@kshedden is the module name ok? other changes ok?

(I'll try to find the time to merge tonight)

@kshedden
Contributor

Thanks, all looks good to me.

On Sat, Jul 12, 2014 at 3:43 AM, Josef Perktold notifications@github.com
wrote:

I squashed the first several commits that were still changing test data
files, and two commits that had identical commit message to the preceding
commits

moved to statsmodels.duration

renamed module to hazard_regression.py
renamed class to PHReg instead of PHreg (capitalize first R)
(forgot to rename to PHRegResults, same capitalized R)

not yet: add to api.py and rst docs

@kshedden https://github.com/kshedden is the module name ok? other
changes ok?

(I'll try to find the time to merge tonight)


Reply to this email directly or view it on GitHub
#1825 (comment)
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@coveralls

Coverage Status

Coverage remained the same when pulling d8e27f4 on josef-pkt:phreg_1312_rebased into 70a3921 on statsmodels:master.

josef-pkt added some commits Jul 11, 2014
@josef-pkt josef-pkt REF: rename module to hazard_regression, capitalization in PHReg(Resu…
…lts)
e9004c9
@josef-pkt josef-pkt DOC: add duration, PHReg to rst documentation (mostly stub page) 1b77997
@josef-pkt josef-pkt REF: rename PH_SurvivalTime - drop underline
690601e
@josef-pkt josef-pkt REF: add PHReg to api and formula.api, (only smoke test for import)
925358c
@coveralls

Coverage Status

Coverage remained the same when pulling 925358c on josef-pkt:phreg_1312_rebased into 70a3921 on statsmodels:master.

@josef-pkt josef-pkt BUG: forgot to commit `__init__.py` in duration
adf02bc
@josef-pkt
Member

all green, merging

needs some follow-up review

@josef-pkt josef-pkt merged commit 31e30a3 into statsmodels:master Jul 11, 2014

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@josef-pkt josef-pkt deleted the josef-pkt:phreg_1312_rebased branch Jul 11, 2014
@coveralls

Coverage Status

Coverage increased (+0.35%) when pulling adf02bc on josef-pkt:phreg_1312_rebased into 70a3921 on statsmodels:master.

@josef-pkt josef-pkt added the PR label Aug 11, 2014
@josef-pkt josef-pkt added this to the 0.6 milestone Aug 24, 2014
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