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v0.1.2.6#79

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jburos merged 79 commits intomasterhammerlab/survivalstan:masterfrom devhammerlab/survivalstan:devCopy head branch name to clipboardJan 10, 2019

+3,177-3,652

Commits

Commits on Feb 24, 2017

• adding Surv & Id stateful transforms

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• work in progress on surv-related tests

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• fix test code

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• add SurvivalModelDesc class; fix unique_timepoints error

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• fix test cases through surv

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• ignore swp files

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• add test cases for SurvivalFactor & SurvivalModelDesc

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• import re

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• remove whitespace

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• pseudocode for parts of SurvivalStanData using formula

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• add formulas to test suite

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Commits on Feb 26, 2017

• add test for group-id spec

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• fix bug in group-id spec

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Commits on Feb 27, 2017

• first attempts to support formulas in fit_stan_survival_model

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• fix bug in formula with bool event; add test cases

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• fix key-incl assertion

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• add M param to stan_data

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• fix sample_col bug in SurvivalStanData

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• first set of SurvivalStanData tests

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• quick hack to put id col names in SSDATA object

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• py2.7 compat

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• better fix to py2.7 compat

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• another py2 compat fix

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• address pylint errors

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• yet another pylint error

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• rename y -> event in long data; update tests

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• remove whitespace

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• clean up some SurvivalStanData helpoer functions

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• remove some whitespace

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• fix error caused by decode_df including NaN values

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• use left-join in case decode includes bad values

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• remove NaN values from subject ids in case they leak through

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• save code args for use by SurvivalStanData

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• add & use column names from survival formula

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• rename generated id vars for safety against user-provided values

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• update functions to handle custom parameter names

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• remove hard-setting of index - fix error joining dfs

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• check for NaN values more aggressively; make sure merge events are clean

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• add test case for get_group_names

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• add by param to plot_coefs

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Commits on Feb 28, 2017

• update some tests to use formula syntax

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• fix pylint errors

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Commits on Mar 3, 2017

• make separate WideSurvData inheriting from SurvData; docstring for get_args

  

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• update test_formulas to reflect new inheritance

  

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• move formula-related functions to formulas.py

  

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• update comment about formulas [ci skip]

  

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Commits on Apr 13, 2017

• add iter column to time-betas

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Commits on Sep 5, 2018

• test case for _get_args

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• refactor _prep_wide & _prep_long

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Commits on Jan 4, 2019

• fix pep8 errors

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Commits on Jan 8, 2019

• fix #76 - merge error on plot_pp_survival

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• re-render notebooks

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• remove deprecated example notebook

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• fix log_t_dur bug - #71

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• remove print statements

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• Merge branch 'dev' into v2.0

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• Merge branch 'v2.0' of github.com:hammerlab/survivalstan into v2.0

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• Merge pull request #73 from hammerlab/add-iter-time-betas

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• Merge branch 'dev' into v2.0

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• Merge branch 'v2.0' of github.com:hammerlab/survivalstan into v2.0

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• fix _get_arg test failure; ignore UserWarning

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• update tests to be consistent with surv result

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• re-render notebooks for model updates

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• update code for mpl backend on tests; constrain param in exp model

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• update notebook

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Commits on Jan 9, 2019

• fix FutureWarning

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• fix other pd.merge issue - #76

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• re-render notebook

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• restore loading of survivalstan

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• fix #78

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• set backend

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• code formatting / pep8 rules

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• ignore pylint error

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• only run lint once

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• remove print lines from byo-stan code

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• remove py3.7 testing

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• update long-surv data structure to alphabetize columns

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Commits on Jan 10, 2019

• Merge pull request #77 from hammerlab/v2.0

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• update notebooks [skip ci]

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