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Feature/survival#323

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sambrilleman wants to merge 250 commits intomasterstan-dev/rstanarm:masterfrom feature/survivalstan-dev/rstanarm:feature/survivalCopy head branch name to clipboard

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Commits on Oct 26, 2018

• Add surv.stan with Stan hazard functions

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• Add stan_surv function

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• Add roxygen template for stan_surv model objects

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• Add stansurv function for returning models of class stansurv

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• Add stan_surv for package documentation of modelling functions

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• misc.R: add helper functions for stan_surv and stan_jm

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• Add plot method for stansurv objects

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• Add stop to posterior_linpred for stansurv objects

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• Add stop to posterior_predict for stansurv objects

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• Move offsets to bottom of pp_data.R

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• pp_data.R: add more obvious subheadings to help organise file

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• Add pp_data for stansurv objects

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• Get print.stanreg working for stansurv objects

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• Get summary.stanreg working for stansurv objects

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• Add stansurv objects to prior_summary

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• Add stansurv objects to ps_check

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• Add some tests for stan_surv

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• surv.stan: add += in places and avoid integer division

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• stan_surv.R: add some missing helper functions

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• Fix typo in plot.stansurv

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• log_lik.R: add evaluators for log baseline hazard or survival

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• Add splines2 to Imports

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• Fix typo in plot.stansurv

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• Add stansurv objects to stanreg methods

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• print & summary: add more info about censoring type for stansurv objects

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• Allow NA in unstandardise_qpts and unstandardise_qwts functions

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• Add log_lik method for stansurv objects

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• Add loo for stansurv models with quadrature

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• Handle stansurv objects in is_discrete function

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• Updated NAMESPACE

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Commits on Oct 28, 2018

• stan_surv.R: make sure data argument is a data frame

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• Add reloo and kfold for stansurv objects

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Commits on Oct 29, 2018

• Rename some of the testthat helper functions

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• Update NAMESPACE

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• Rename get_extrapolation_control function

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• Add WAIC for stansurv objects

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• Add tests for stansurv models with time-dependent effects

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• Stop ps_check for stansurv models with delayed entry

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• Generate a workaround for stansurv pp_data when all times are NA

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• Add posterior_survfit for stansurv models

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• Fix small typo

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• Small bit of reformatting

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• Add mice lung tumor data to example datasets

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• Update stan_surv documentation

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• Add additional models to tests for stan_surv

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• Fix small bug in stan_surv design matrix

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• Fix small bug in surv.stan with interval censoring and quadrature combined

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• Add dummy = in a bunch of places to get around Stan parser messages

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• Add simsurv to DESCRIPTION Suggests

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Commits on Oct 30, 2018

• Add the breast cancer survival dataset

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• Update stan_surv help documentation

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• log_lik.R: fix small bug in baseline survival evaluator for Gompertz

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• Update aliases for rstanarm datasets documentation

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• Drop response from model frame when building x in pp_data_surv

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• Add vignette for stan_surv

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• Small changes to stan_surv vignette

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Commits on Oct 31, 2018

• Add a couple more useful error messages to stan_surv

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• Add more tests for stan_surv

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• Don't check_constant_vars for Surv objects

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• stan_surv tests: use PBC data for interval censoring test

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• Add stan_surv test for interval censoring

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• stan_surv: disallow event or censoring times equal to zero

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• Add more stan_surv tests

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• Improve generalisability of the subset_ids function

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• Clean up plot.survfit function

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• Remove icenReg from Suggests

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• Fix up plot.survfit

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• Comment out stan_surv tests to avoid adding packages to Suggests

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Commits on Nov 1, 2018

• Update rename_e_aux function

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• Tidy up priors documentation for stan_surv

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• Update mice dataset using negative infinity for left censoring

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• Shorten stan_surv examples

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• Fixes to solve R CMD Check warnings

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• Fix failing mvmer test

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• Fix small bug in dummy_matrix function

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• Change default df for M-splines to 6

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• Don't attach testthat in test_stan_surv

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Commits on Nov 19, 2018

• Remove intercept from spline basis

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• Add explicit intercept parameter to baseline hazard and survival for spline models

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• Center predictor matrix, and center intercept using log crude event rate

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• Center intercept, center predictor matrix, and use contrained coefficients for M-splines

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Commits on Nov 20, 2018

• Use array for constrained spline coefficients

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Commits on Nov 21, 2018

• Use dirichlet prior directly on constrained M-spline coefficients

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Commits on Nov 22, 2018

• Add dirichlet prior to handle_glm_prior function

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• Add prior_concentration (for dirichlet) to summarize_jm_prior

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• Use dirichlet prior for M-spline coefficients

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• Add exponential rate to summarize_jm_prior function

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• prior_summary: handle exponential and dirichlet distributions for stan_surv prior_aux

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• Update stan_surv documentation and vignette

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Commits on Nov 23, 2018

• Update vignette to align with an intercept being included in the spline baseline hazards

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• Fix type in stan_surv vignette

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• Add AFT models to stan_surv

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Commits on Nov 26, 2018

• Update stan_surv documentation

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Commits on Nov 29, 2018

• Add AFT models to vignette

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• Add tests for AFT models

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• Add AFT models to surv.stan

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• Add AFT models to hazard_functions.stan

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• Add AFT models to stan_surv documentation, and add a few standata items

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• Add plots of time-varying acceleration factor to plot.stansurv

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• Add AFT models to doc on rstanarm modelling functions

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• Add Eren Elci as contributor in DESCRIPTION

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• Merge pull request #326 from stan-dev/feature/aft-models

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Commits on Dec 4, 2018

• surv.stan: remove use of cpts

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• stan_surv: remove remaining cpts code

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Commits on Dec 5, 2018

• surv.stan: fix small typo

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Commits on Dec 6, 2018

• stan_surv.R: tidy up use of cpts

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• plots for stan_surv: fix extraction of tde basis

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• Clean up some of stan_surv helper functions

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• Use make_x instead of make_s for pp_data.stansurv

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• Tidy up stan_surv's parse_formula function

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Commits on Feb 5, 2019

• Update roxygen version

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• Remove preclean

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• stan_surv.R: start adding prior_covariance and Stan data for random effects structure

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Commits on Feb 8, 2019

• stan_surv.R: handle group-specific terms

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Commits on Feb 11, 2019

• surv.stan: start adding random effects structure

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• surv.stan: add common functions

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• jm_data_block.R: fix small typo

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• surv.stan: fix typo in data declaration

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• Merge branch 'master' into feature/frailty-models

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• surv.stan: get frailty models working

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• stansurv.R: add some missing elements to returned model object

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• Fix bug in handle_cov_prior

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Commits on Feb 12, 2019

• stan_surv.R: fix reported number of levels for grouping factors

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Commits on Feb 19, 2019

• Merge branch 'feature/frailty-models' into revise-priors-for-stansurv

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• stan_surv.R: fix stuff related to merging in dirichlet prior

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• stan_surv.R: add quotes to a switch call

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• stan_surv.R: add default prior_aux for AFT models

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• Merge pull request #335 from stan-dev/revise-priors-for-stansurv

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Commits on Feb 20, 2019

• stan_surv.R: fix intercept shift for AFT models

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• prior_summary: fix auxiliary paramters for AFT survival models

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• Merge pull request #336 from stan-dev/revise-priors-for-stansurv

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Commits on Feb 28, 2019

• Add an example dataset for frailty models

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• Start adding some tests for frailty models

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Commits on Mar 19, 2019

• Add formula and terms methods for stansurv objects

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• Handle predvars in make_model_frame for stansurv

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• pp_data.R: start dealing with random effects for stansurv objects

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Commits on May 8, 2019

• Allow tde() to be piecewise constant or a B-spline function

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Commits on May 9, 2019

• Add some tests for piecewise tde()

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• Fix small bug in stansurv pp_data

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Commits on May 10, 2019

• Create make_s function

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• Deal with NAs in stansurv pp_data

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• Get stansurv loo test passing

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• Add a couple of tests for prior_aux in stansurv models

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• Fix x_bar for stan_surv when there is just one predictor

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• Merge pull request #358 from stan-dev/bugfix/tde-wrapper-for-factors

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• stan_surv: add an exported tde function with help file

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• stan_surv: small change to tde documentation

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Commits on May 14, 2019

• Rename tde() as tve()

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• Update stan_surv documentation for tve()

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• Rename tde() to tve() in NAMESPACE

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Commits on May 15, 2019

• Add another stan_surv tve() example

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• Updates to stan_surv vignette

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• More additions to stan_surv vigenette (technical details)

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• More changes to stan_surv vignette

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• Update examples in stan_surv vignette

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Commits on May 16, 2019

• Fix up capitalisation for pbcLong dataset documentation

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• pp_data.R & log_lik.R: add stan_surv frailty models

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Commits on May 17, 2019

• posterior_survfit: handle fraily models & don't condition by default

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• stan_surv.R: remove unnecessary code from parse_formula

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• Tidy up stan_surv tests

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Commits on Jun 4, 2019

• plot.stansurv: allow user to specify number of points at which to interpolate function

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• posterior_survfit: tidy print method

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• plot.stansurv: don't use geom_smooth

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• posterior_survfit: fix up last_time when not conditioning

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• stan_surv: allow user to specify degree for MS and BS baseline hazards

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• stan_surv: fix bug in M-spline baseline hazard

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Commits on Jun 6, 2019

• plot.stansurv: add more documentation for param n

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• use bSpline function instead of bs

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• Fix small bug in handle_basehaz

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• stan_surv: add example for frailty models

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• Fix typo

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• stan_surv: update documentation for M-splines

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• Merge pull request #368 from stan-dev/frailty-models-update-with-master

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• Fix typo

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• stan_surv vignette: fix small typo

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• posterior_survfit: add return_matrix argument

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• posterior_survfit: document return_matrix argument

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• Allow marginalised survival predictions for stan_jm

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• Avoid error when using exponential distribution with prior_PD = TRUE

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• Change default scale for prior_aux with Gompertz models

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• Fix up default df for M-splines & allow degree = 0 for tve function

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• Fix up renaming of tve coefs

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• Add some simulation tests for stan_surv with piecewise constant hazard ratios

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• Use 200 interpolation points for ps_check

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• psoterior_traj and posterior_survfit: use 100 points by default for interpolation and extrapolation

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• ps_check and posterior_survfit: reduce default number of draws to 400

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• Use hexNumeric for deparsing bSpline call

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• Remove type="pw" option for tve function

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• Merge pull request #381 from stan-dev/feature/frailty-models

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• Merge branch 'master' into feature/survival-update-with-master

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• stan_surv.R: allow any number of grouping factors

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• surv.stan: change dimension of redundant simplex

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• Merge pull request #388 from stan-dev/feature/survival

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• stan_surv.R: fix up get_iknots function

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• test_stan_surv.R: only use simulations that converged (based on Rhat)

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• Merge pull request #391 from stan-dev/feature/survival-update-with-master

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• posterior_survfit.R: fix up validate_newdata

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• stan_surv vignette: some small fixes

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• Merge pull request #392 from stan-dev/update-survival-vignette

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• stan_surv vignette: updates to vignette

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• Merge branch 'master' into feature/survival

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• Don't run stan_surv examples on 32 bit

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• change return type from void to real

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• Fix docstring when returning target

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• Remove redundant assignments in hazard_functions.stan

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• Catch some undesirable inputs that were being absorbed in dots (i.e. extra args)

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• Include stansurv objects in is.mer function

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• Merge pull request #526 from stan-dev/bugfix-survival

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• Reverse order of tests to address #535

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• update terms as well

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• reverse order of checks per #535

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• Add some more checks for is.surv

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• Merge pull request #536 from jburos/bugfix/stansurv-formula

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• Merge branch 'master' into survival_2_21_3

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• Fix up the overlapping test helper functions

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• Remove reference to csr_matrix_times_vector2

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• Merge branch 'master' into feature/survival

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• csr_matrix_times_vector2 -> csr_matrix_times_vector

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• Use | instead of || for or condition

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• Merge pull request #594 from stan-dev/bug_fix_for_or_condition

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• Merge branch 'master' into survival_2_26_1

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• Fix remaining reference to target in stan functions

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• Fix doc reference for S3 plot method on stansurv objects

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• Fix undefined global reference to xlevs ... how did this not break the code up until now?? :explodinghead:

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• Try deal with the xlevs stuff

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• Remove if condition from step that uploads artifacts

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• Fix inherits - broken due to breaking change in splines2 0.5

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• Don't offset sparse parts by -1L

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• Merge branch 'master' into survival_2_26_1

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• Merge pull request #607 from stan-dev/survival_2_26_1

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• Fix mispelling of context() in test_stan_surv.R

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• Don't explicitly set knots at boundary

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• Remove use of || in log_lik.R for stan_surv models

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• Just try using larger sample sizes for the failing tests

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• Merge branch 'master' into feature/survival

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• Try deal with reserved naming issue

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• Update deprecated array syntac

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