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Also add tests to make sure it works, and a couple of additional test files.   I think this will keep code coverage from going down.\r\n\r\n* update construct_survival and tabular_input to work with mixed specifications (defined distributions and fits).\r\n(May remove construct_survival from namespace later.)\r\n\r\n* update vignette and related files\r\n\r\n* update survival fitting to automatically include the Kaplan-Meier curve in the fit, with distribution \"km\".\r\n\r\n* update a test for survival_fits (to catch the Kaplan-Meier curve appended to the end of the fits with distributions), because I forgot last time\r\n\r\n* improve construct_survival in a variety of ways\r\n\r\n* add convenience functions used in models\r\n\r\n* small improvements to the vignette\r\n\r\n* updating from survival-from-files;\r\nrename eval_surv_.lazy and eval_surv_.character to eval_surv.lazy and eval_surv.character to keep up with a change made elsewhere so that vignette m-survfiles.Rmd knits again.\r\n\r\n* add convenience functions for dose pricing\r\n\r\n* a faster version of compute_values\r\n\r\n* improve some convenience functions\r\n\r\n* allow multiple subsets to be fit at once\r\n\r\n* update the vignette to work with fits on subsets, and include some documentation I forgot to include last commit.\r\n\r\n* merging in the change to strategy_eval (makes it faster; recently merged into devel).\r\n\r\n* example in new format\r\n\r\n* first set of changes for two things:\r\n  1.  using a new file format; and\r\n  2.  replacing the fit matrices with tibbles that hold the fits.\r\nCurrently works when defined distributions are provided - not yet using fits.\r\n\r\n* further adjustments - fit matrices replaced with tibbles, file options broadened, with subsets.\r\n\r\n* fixing some things to make the vignette m-survfiles.Rmd work, particularly in construct_survival, to allow for mixing fits and directly defined distributions.   Defined a new function to extract fit metrics like AIC and BIC, since we can't use sapply_matrix anymore because they are no longer used.  And got rid of outdated code related to the old fix matrices, now replaced with tibbles.\r\n\r\n* rename construct_survival as construct_part_surv_tib, and move the code from its own file to part_surv.R.\r\n\r\n* remove obsolete files (used in eliminated tests), and add some tests for new functions.\r\n\r\n* move make_part_surv_from_small_tibble from survival_fit.R to part_surv.R, and add tests for part_surv.R.\r\n\r\n* remove a file accidentally put there\r\n\r\n* additional tests for survival_fit.R, particularly making sure that fitting with subsets defined works - and a change to survival_fit so it does.\r\nAlso for part_surv.R, in particular making sure we catch situations in which no fit matches a specification.\r\n\r\n* additional tests for survival_fits.R and part_surv.R, and moving one function from survival_fits.R to part_surv.R.\r\n\r\n* merging changes from suvival-from-files-with-fits, and then clearing out convenience functions and code related to survival fits.\r\n\r\n* add a test of reporting errors in parameter evaluation","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/4a651b2f5dee7b9b5ddb4240f298446270dc2b80"},{"sha":"32f2634d29888457614bf6134d66d30827cafd84","author":{"name":"Antoine Filipovic-Pierucci","email":"742318a0214939608072a59ef9c1e7bae8cbb49c@gmail.com"},"message":":package:faster CHECK","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/32f2634d29888457614bf6134d66d30827cafd84"},{"sha":"72292bb1c67e10388c6abba40ceebafaa2db31b1","author":{"name":"Antoine Filipovic-Pierucci","email":"742318a0214939608072a59ef9c1e7bae8cbb49c@gmail.com"},"message":":sparkles:better error message in eval_par()","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/72292bb1c67e10388c6abba40ceebafaa2db31b1"},{"sha":"3a6c8d44663c6f78b0fe859e7eef5b5d9daf20d7","author":{"name":"Antoine Filipovic-Pierucci","email":"742318a0214939608072a59ef9c1e7bae8cbb49c@gmail.com"},"message":":soon:finish PR #268","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/3a6c8d44663c6f78b0fe859e7eef5b5d9daf20d7"},{"sha":"8ca0641ca5a6e3aaa9371fe2e41af7126d5dec63","author":{"name":"Antoine Filipovic-Pierucci","email":"742318a0214939608072a59ef9c1e7bae8cbb49c@gmail.com"},"message":":package:dev version number","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/8ca0641ca5a6e3aaa9371fe2e41af7126d5dec63"},{"sha":"c83b39b8509f5e99fab4f9f1cb0448d42a6ac81c","author":{"name":"Antoine Filipovic-Pierucci","email":"742318a0214939608072a59ef9c1e7bae8cbb49c@gmail.com"},"message":":beetle:fix bug in run_dsa() with state expansion","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/c83b39b8509f5e99fab4f9f1cb0448d42a6ac81c"},{"sha":"203e79cf2420bdba58661d4d1e5b1cb6c6400e72","author":{"name":"Antoine Filipovic-Pierucci","email":"742318a0214939608072a59ef9c1e7bae8cbb49c@gmail.com"},"message":":white_check_mark:remove GHO test because of WHO problems","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/203e79cf2420bdba58661d4d1e5b1cb6c6400e72"},{"sha":"f3f0640f48ea64efc9a6d965d470acb4a53c7980","author":{"name":"Antoine Filipovic-Pierucci","email":"742318a0214939608072a59ef9c1e7bae8cbb49c@gmail.com"},"message":":sparkles:relative NMB, closes # 269","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/f3f0640f48ea64efc9a6d965d470acb4a53c7980"},{"sha":"8081f0081d2028e2dc7675d631634475aeeb8e90","author":{"name":"MattWiener","email":"2e11aaeaa890622b1025902817e89c92eb0dcd44@gmail.com"},"message":"Merge pull request #4 from pierucci/devel\n\nmerging latest Pierucci devel","distinct":false,"url":"https://api.github.com/repos/MattWiener/heemod/commits/8081f0081d2028e2dc7675d631634475aeeb8e90"},{"sha":"4757ba16491c55ae008bf5e1d9b4f309b3bb9538","author":{"name":"Wiener, Matthew","email":"afa47e1d894d7e47468f347edb83169c9944661d@merck.com"},"message":"Merge branch 'devel' into survival-from-files-with-fits\n(Merging most of what was done; removed some incomplete changes, which will come back in later commits.)\n\n# Conflicts:\n#\tNAMESPACE\n#\tR/tabular_input.R\n#\tman/construct_part_surv_tib.Rd\n#\tman/part_survs_from_surv_inputs.Rd\n#\ttests/testthat/test_parameters.R\n#\ttests/testthat/test_part_surv.R","distinct":true,"url":"https://api.github.com/repos/MattWiener/heemod/commits/4757ba16491c55ae008bf5e1d9b4f309b3bb9538"},{"sha":"3175262ea7016ef394b1c854b27e45561631cdd3","author":{"name":"Wiener, Matthew","email":"afa47e1d894d7e47468f347edb83169c9944661d@merck.com"},"message":"switch vial use optimization to lpSolve","distinct":true,"url":"https://api.github.com/repos/MattWiener/heemod/commits/3175262ea7016ef394b1c854b27e45561631cdd3"},{"sha":"caf451324ba364b3d36fb34557d7ce1ed8ca1206","author":{"name":"Wiener, Matthew","email":"afa47e1d894d7e47468f347edb83169c9944661d@merck.com"},"message":"steps toward fitting shifted distributions (for example, starting at a particular time > 0).  Includes:\n- putting a time_subtract column in the subset definition file\n- defining surv_shift objects with constructors (apply_shift) and eval_surv_ methods.\n- one line new test for very basic - but probably not enough yet.","distinct":true,"url":"https://api.github.com/repos/MattWiener/heemod/commits/caf451324ba364b3d36fb34557d7ce1ed8ca1206"}]}
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