epiforecasts/epinowcast: Epinowcast 0.0.1

Summary

• Adds additional quality of life data processing so that the maximum number (max_confirm) of notifications is available in every row (for both cumulative and incidence notifications) and the cumulative and daily empirical proportion reported are calculated for the user during pre-processing (see #62 by @seabbs).
• The default approach to handling reported notifications beyond the maximum delay has been changed. In 0.0.6 and previous versions notifications beyond the maximum delay were silently dropped. In 0.0.7 this is now optional behaviour (set using max_delay_strat in [enw_preprocess_data()]) and the default is instead to add these notifications to the last included delay were present. This should produce more accurate long-term nowcasts when data is available but means that reported notifications for the maximum delay need to be interpreted with this in mind. See #62by @seabbs.
• Adds some basic testing and documentation for preprocessing functions. See #62by @seabbs.
• Stabilises calculation of expected observations by increasing the proportion of the calculation performed on the log scale. This results in reduced computation time with the majority of this coming from switching to using the neg_binomial_2_log family of functions (over their natural scale counterparts). See #65by @seabbs

• Checking IDate, Adding CmdStan Requirements, CmdStanR argument completion by @medewitt in https://github.com/epiforecasts/epinowcast/pull/26
• add michael dewitt as a contributor by @medewitt in https://github.com/epiforecasts/epinowcast/pull/28
• Add Adrian Lison as contributor by @adrian-lison in https://github.com/epiforecasts/epinowcast/pull/34
• Feature update docs by @seabbs in https://github.com/epiforecasts/epinowcast/pull/37
• Optional profiling by @adrian-lison in https://github.com/epiforecasts/epinowcast/pull/41
• Feature vectorise likelihood by @seabbs in https://github.com/epiforecasts/epinowcast/pull/40
• Update CmdStan version by @adrian-lison in https://github.com/epiforecasts/epinowcast/pull/45
• Bugfix optional profiling by @adrian-lison in https://github.com/epiforecasts/epinowcast/pull/46
• Fix bug causing pkgdown to fail by @seabbs in https://github.com/epiforecasts/epinowcast/pull/48
• Refactor functions/pmfs by @adrian-lison in https://github.com/epiforecasts/epinowcast/pull/42
• Refactor functions pmfs by @adrian-lison in https://github.com/epiforecasts/epinowcast/pull/50
• Feature vectorised truncated dists by @seabbs in https://github.com/epiforecasts/epinowcast/pull/51
• Update R-CMD-check.yaml to support current Rtools requirements by @seabbs in https://github.com/epiforecasts/epinowcast/pull/58
• Vectorise hazard_to_prob by @seabbs in https://github.com/epiforecasts/epinowcast/pull/53
• Feature optional profiling include paths by @adrian-lison in https://github.com/epiforecasts/epinowcast/pull/54
• Add inv_sqrt by @seabbs in https://github.com/epiforecasts/epinowcast/pull/60
• Bug: Fix proper scoring by @seabbs in https://github.com/epiforecasts/epinowcast/pull/61
• Feature: Add empirical reporting proportions and handle max confirmed by @seabbs in https://github.com/epiforecasts/epinowcast/pull/62
• Feature contributing by @seabbs in https://github.com/epiforecasts/epinowcast/pull/66
• Switch to using neg_binomial_2_log by @seabbs in https://github.com/epiforecasts/epinowcast/pull/65
• Fixed a few typos in README, vignettes and docstrings by @pitmonticone in https://github.com/epiforecasts/epinowcast/pull/63
• Rename cumulative_converse_hazard by @seabbs in https://github.com/epiforecasts/epinowcast/pull/69
• Add unstable dev instructions by @seabbs in https://github.com/epiforecasts/epinowcast/pull/67
• Feature: Prototype logo by @seabbs in https://github.com/epiforecasts/epinowcast/pull/70

• @medewitt made their first contribution in https://github.com/epiforecasts/epinowcast/pull/26

Full Changelog: https://github.com/epiforecasts/epinowcast/compare/v0.0.4...0.0.1