Cmdstanr option #537
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Cmdstanr option #537
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This was referenced Feb 2, 2024
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All checks now passing except windows one which looks unrelated. |
Agree, I see this in multiple places including the |
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This reverts commit e57ae76.
Co-authored-by: Sam Abbott <[email protected]>
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* add cmdstan backend * add cmdstanr model * generalise extract functions * create general fit_model function * initial values for cmdstanr * move stan model creation to create func * make dist_fit cmdstanr ready * make estimate_infections cmdstanr ready * make estimate_secondary cmdstanr ready * make estimate_truncation cmdstanr ready * make simulate_infections cmdstanr ready * gitignore for binaries * add cmdstanr as suggest * make forecast_secondary cmdstanr ready * update stanargs test * make simulations work with updated options * add globals * tests for cmdstanr backend * update actions * updates in response to lintr * don't use future_lapply for cmdstanr * backend-specific success criteria * use epinowcast action for installing cmdstan * improve .gitignore for compiled stan files * deactivate testing on windows for now * Revert "use epinowcast action for installing cmdstan" This reverts commit e57ae76. * Apply suggestions from code review Co-authored-by: Sam Abbott <[email protected]> * match arguments in `stan_model` * don't match args$method but explictly stop instead * put choices in argument --------- Co-authored-by: Sam Abbott <[email protected]>
sbfnk
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* add cmdstan backend * add cmdstanr model * generalise extract functions * create general fit_model function * initial values for cmdstanr * move stan model creation to create func * make dist_fit cmdstanr ready * make estimate_infections cmdstanr ready * make estimate_secondary cmdstanr ready * make estimate_truncation cmdstanr ready * make simulate_infections cmdstanr ready * gitignore for binaries * add cmdstanr as suggest * make forecast_secondary cmdstanr ready * update stanargs test * make simulations work with updated options * add globals * tests for cmdstanr backend * update actions * updates in response to lintr * don't use future_lapply for cmdstanr * backend-specific success criteria * use epinowcast action for installing cmdstan * improve .gitignore for compiled stan files * deactivate testing on windows for now * Revert "use epinowcast action for installing cmdstan" This reverts commit e57ae76. * Apply suggestions from code review Co-authored-by: Sam Abbott <[email protected]> * match arguments in `stan_model` * don't match args$method but explictly stop instead * put choices in argument --------- Co-authored-by: Sam Abbott <[email protected]>
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Closes #48 by implementing a
backend = "cmdstanr"option.This contains everything in #472 except the profiling bits (which don't seem supported by
rstan).This necessitated some (ultimately probably positive) streamlining of how the stan arguments are constructed for the different models.