Finalises interface changes #162
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…piNow2 into observation_model
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May 3, 2024
* setting up observation model * update documentation * scaling implemented * fully supporting scaling in estimate_infections * add support for simulate_infections * rebuild docs * check tests * bump dev version * review tests * fix missing sim data * CRAN check and protect lognormal pmg * spellings * fix obs example * add coverage config * drop model and method args * doc update * review local tests * updated news * review estimate_infections docs * update summary s3 methods * tests passing * update tests and aliasing * update readme * update Rt interface * update news * local cran check * add backcalc settings * compile * silence ggplot missing data warning * Update README.Rmd * Update README.md * Update estimate_infections.stan * Update README.Rmd
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This PR:
stan_args(dropping model and method).rtargument which accepts parameters that define the Rt process (i.eprior,use_breakpointsetc).rwpassed viart).backcalcargument for passing back calculation settings. As it stands this only containssmoothing_window.Hopefully this PR is the final large scale interface change with future updates being extensions that are largely hidden from normal users.