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v0.1.2.6 #79

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merged 79 commits into from
Jan 10, 2019
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7b9f5f4
adding Surv & Id stateful transforms
jburos Feb 24, 2017
d715db7
work in progress on surv-related tests
jburos Feb 24, 2017
5455d8f
fix test code
jburos Feb 24, 2017
5fbbf44
add SurvivalModelDesc class; fix unique_timepoints error
jburos Feb 24, 2017
1085f00
fix test cases through surv
jburos Feb 24, 2017
6b4d0bf
ignore swp files
jburos Feb 24, 2017
3d23a8c
add test cases for SurvivalFactor & SurvivalModelDesc
jburos Feb 24, 2017
d9d0fe8
import re
jburos Feb 24, 2017
b9bd4eb
remove whitespace
jburos Feb 24, 2017
1d3b323
pseudocode for parts of SurvivalStanData using formula
jburos Feb 24, 2017
0336f40
add formulas to test suite
jburos Feb 24, 2017
ebd15b1
add test for group-id spec
jburos Feb 26, 2017
cd77f8e
fix bug in group-id spec
jburos Feb 26, 2017
4a15869
first attempts to support formulas in fit_stan_survival_model
jburos Feb 27, 2017
8b0be20
fix bug in formula with bool event; add test cases
jburos Feb 27, 2017
15e4ab1
fix key-incl assertion
jburos Feb 27, 2017
a5ad14a
add M param to stan_data
jburos Feb 27, 2017
675c1d5
fix sample_col bug in SurvivalStanData
jburos Feb 27, 2017
2a61f9e
first set of SurvivalStanData tests
jburos Feb 27, 2017
303e3c0
quick hack to put id col names in SSDATA object
jburos Feb 27, 2017
e056725
py2.7 compat
jburos Feb 27, 2017
49ee61f
better fix to py2.7 compat
jburos Feb 27, 2017
a37cc69
another py2 compat fix
jburos Feb 27, 2017
ce26706
address pylint errors
jburos Feb 27, 2017
82de8a6
yet another pylint error
jburos Feb 27, 2017
447d63c
rename y -> event in long data; update tests
jburos Feb 27, 2017
9de7f2c
remove whitespace
jburos Feb 27, 2017
b69d1d5
clean up some SurvivalStanData helpoer functions
jburos Feb 27, 2017
a83bc24
remove some whitespace
jburos Feb 27, 2017
54d5769
fix error caused by decode_df including NaN values
jburos Feb 27, 2017
4309bd8
use left-join in case decode includes bad values
jburos Feb 27, 2017
684670f
remove NaN values from subject ids in case they leak through
jburos Feb 27, 2017
3e18808
save code args for use by SurvivalStanData
jburos Feb 27, 2017
68bbf6e
add & use column names from survival formula
jburos Feb 27, 2017
51b6450
rename generated id vars for safety against user-provided values
jburos Feb 27, 2017
cb97df6
update functions to handle custom parameter names
jburos Feb 27, 2017
f63b1bc
remove hard-setting of index - fix error joining dfs
jburos Feb 27, 2017
10811e5
check for NaN values more aggressively; make sure merge events are clean
jburos Feb 27, 2017
2058302
add test case for get_group_names
jburos Feb 27, 2017
3193432
add `by` param to plot_coefs
jburos Feb 27, 2017
50571ba
update some tests to use formula syntax
jburos Feb 28, 2017
1946c51
fix pylint errors
jburos Feb 28, 2017
f14ad33
make separate WideSurvData inheriting from SurvData; docstring for ge…
Mar 3, 2017
63274fb
update test_formulas to reflect new inheritance
Mar 3, 2017
e5101c3
move formula-related functions to formulas.py
Mar 3, 2017
43b7b86
update comment about formulas [ci skip]
Mar 3, 2017
55d55ee
add `iter` column to time-betas
jburos Apr 13, 2017
b90d8e0
test case for _get_args
jburos Sep 5, 2018
2dee964
refactor _prep_wide & _prep_long
jburos Sep 5, 2018
67fb4a5
fix pep8 errors
jburos Jan 3, 2019
5bc20e9
fix #76 - merge error on plot_pp_survival
jburos Jan 8, 2019
5675693
re-render notebooks
jburos Jan 8, 2019
7c593cc
remove deprecated example notebook
jburos Jan 8, 2019
8ece2fb
fix log_t_dur bug - #71
jburos Jan 8, 2019
88c553b
remove print statements
jburos Jan 8, 2019
88db9ee
Merge branch 'dev' into v2.0
jburos Jan 8, 2019
c193e86
Merge branch 'v2.0' of github.com:hammerlab/survivalstan into v2.0
jburos Jan 8, 2019
c1e1417
Merge pull request #73 from hammerlab/add-iter-time-betas
jburos Jan 8, 2019
996f007
Merge branch 'dev' into v2.0
jburos Jan 8, 2019
efc01a6
Merge branch 'v2.0' of github.com:hammerlab/survivalstan into v2.0
jburos Jan 8, 2019
6db4ed1
fix _get_arg test failure; ignore UserWarning
jburos Jan 8, 2019
43e6b9e
update tests to be consistent with surv result
jburos Jan 8, 2019
9092aaa
re-render notebooks for model updates
jburos Jan 8, 2019
13d210d
update code for mpl backend on tests; constrain param in exp model
jburos Jan 8, 2019
bd24fe9
update notebook
jburos Jan 8, 2019
5c8bf3e
fix FutureWarning
jburos Jan 9, 2019
d4376df
fix other pd.merge issue - #76
jburos Jan 9, 2019
5a4d3c5
re-render notebook
jburos Jan 9, 2019
888ccc0
restore loading of survivalstan
jburos Jan 9, 2019
6a2682e
fix #78
jburos Jan 9, 2019
630b3ea
set backend
jburos Jan 9, 2019
759473b
code formatting / pep8 rules
jburos Jan 9, 2019
abd67e7
ignore pylint error
jburos Jan 9, 2019
7308214
only run lint once
jburos Jan 9, 2019
bc53279
remove print lines from byo-stan code
jburos Jan 9, 2019
93f3515
remove py3.7 testing
jburos Jan 9, 2019
d3f8c1a
update long-surv data structure to alphabetize columns
jburos Jan 9, 2019
037cb47
Merge pull request #77 from hammerlab/v2.0
jburos Jan 10, 2019
41f6502
update notebooks [skip ci]
jburos Jan 10, 2019
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3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@

*.sublime-*

# swp files
*.swp

# C extensions
*.so

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17 changes: 12 additions & 5 deletions .travis.yml
Original file line number Diff line number Diff line change
@@ -1,13 +1,15 @@
sudo: false # Use container-based infrastructure
language: python
cache:
cache:
pip: true
directories:
directories:
- $HOME/.cached_models
python:
- "2.7"
- "3.4"
- "3.6"
env:
- TEST=lint
- TEST=test/test_exp_survival_model.py
- TEST=test/test_exp_survival_model_sim.py
- TEST=test/test_pem_survival_model.py
Expand All @@ -21,6 +23,8 @@ env:
- TEST=test/test_byo-gamma_survival_model.py
- TEST=test/test_byo-gamma_survival_model_sim.py
- TEST=test/test_jointmodel_datasets.py
- TEST=test/test_formulas.py
- TEST=test/test_SurvivalStanData.py
before_install:
# Commands below copied from: http://conda.pydata.org/docs/travis.html
# We do this conditionally because it saves us some downloading if the
Expand All @@ -38,7 +42,7 @@ before_install:
- conda update -q conda
# Useful for debugging any issues with conda
- conda info -a
# borrow following from http://github.com/stan-dev/rstan
# borrow following from http://github.com/stan-dev/rstan
- echo -e "#\x21/bin/bash\n\$@ > wait4.out 2>&1 3>&1 &\nPROCESS=\"\$!\"\nfunction finish {\ncat wait4.out\n}\ntrap finish EXIT\nwhile :\ndo\n RESULT=\`ps -p \${PROCESS} -o comm=\`" > wait4.sh
- echo -e " if [ -z \"\${RESULT}\" ]; then\n wait \${PROCESS}; exit \$?\n else\n echo \"-\"; sleep 10\n fi\ndone\nexit \$?" >> wait4.sh
- more wait4.sh
Expand All @@ -57,8 +61,11 @@ install:
- pip install .
- pip install coveralls
script:
- ./lint.sh
- ./wait4.sh nosetests $TEST --with-coverage --cover-package=survivalstan
- if [[ "$TEST" == "lint" ]]; then
./lint.sh;
else
./wait4.sh nosetests $TEST --with-coverage --cover-package=survivalstan;
fi
after_success:
coveralls
deploy:
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481 changes: 288 additions & 193 deletions example-notebooks/Test new_gamma_survival_model with simulated data.ipynb

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1,633 changes: 461 additions & 1,172 deletions example-notebooks/Test pem_survival_model with simulated data.ipynb

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