Pre-release cleanup (#649)

* deprecate adjust-functions * indicate check functions are stable * mark deprecated functions as internal * make more functions internal * move init_cumulative_fit to deprecated.R * move fit functions to fit.R * update lifecycle badges * remove explicit references to 2.0.0 * completely remove update_list * line spacing * update importFrom tags * remove prior_weight * hard deprecate old truncation options * make more get_ functions internal * categorise internal functions in pkgdown * order NEWS items * add news item * re-render documentation * remove package qualifier * add PR number * make sure all examples run * remove package qualifier on internal function * Apply suggestions from code review Co-authored-by: James Azam <[email protected]> * clarify wording in _pkgdown.yml Co-authored-by: James Azam <[email protected]> * simplify internal function listing in pkgdown Co-authored-by: James Azam <[email protected]> --------- Co-authored-by: James Azam <[email protected]>
epiforecasts · May 3, 2024 · 6a52995 · 6a52995
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diff --git a/NAMESPACE b/NAMESPACE
@@ -18,7 +18,6 @@ export(LogNormal)
 export(NonParametric)
 export(Normal)
 export(R_to_growth)
-export(add_day_of_week)
 export(adjust_infection_to_report)
 export(apply_tolerance)
 export(backcalc_opts)
@@ -29,20 +28,9 @@ export(calc_summary_measures)
 export(calc_summary_stats)
 export(clean_nowcasts)
 export(collapse)
-export(construct_output)
 export(convert_to_logmean)
 export(convert_to_logsd)
 export(convolve_and_scale)
-export(copy_results_to_latest)
-export(create_backcalc_data)
-export(create_clean_reported_cases)
-export(create_gp_data)
-export(create_initial_conditions)
-export(create_obs_model)
-export(create_rt_data)
-export(create_shifted_cases)
-export(create_stan_args)
-export(create_stan_data)
 export(delay_opts)
 export(discretise)
 export(discretize)
@@ -54,7 +42,6 @@ export(estimate_delay)
 export(estimate_infections)
 export(estimate_secondary)
 export(estimate_truncation)
-export(estimates_by_report_date)
 export(expose_stan_fns)
 export(extract_CrIs)
 export(extract_inits)
@@ -73,8 +60,6 @@ export(get_parameters)
 export(get_pmf)
 export(get_raw_result)
 export(get_regional_results)
-export(get_regions)
-export(get_regions_with_most_reports)
 export(gp_opts)
 export(growth_to_R)
 export(lognorm_dist_def)
@@ -96,27 +81,19 @@ export(rstan_sampling_opts)
 export(rstan_vb_opts)
 export(rt_opts)
 export(sample_approx_dist)
-export(save_estimate_infections)
-export(save_input)
 export(secondary_opts)
 export(set_dt_single_thread)
 export(setup_default_logging)
-export(setup_dt)
 export(setup_future)
 export(setup_logging)
-export(setup_target_folder)
 export(simulate_infections)
 export(simulate_secondary)
 export(stan_laplace_opts)
 export(stan_opts)
 export(stan_pathfinder_opts)
 export(stan_sampling_opts)
 export(stan_vb_opts)
-export(summarise_key_measures)
-export(summarise_results)
 export(trunc_opts)
-export(update_horizon)
-export(update_list)
 export(update_secondary_args)
 import(Rcpp)
 import(methods)

diff --git a/NEWS.md b/NEWS.md
@@ -3,12 +3,20 @@
 ## Major changes
 
 * Delay discretisation is now based on a two-day censoring window (with uniform probability in between), based on recommendations in [Park et al, medRxiv, 2024](https://doi.org/10.1101/2024.01.12.24301247). By @sbfnk in #518 and reviewed by @jamesmbaazam.
+* The interface to generating delay distributions has been completely overhauled. Instead of calling `dist_spec()` users now specify distributions using functions that represent the available distributions, i.e. `LogNormal()`, `Gamma()` and `Fixed()`. See `?EpiNow2::Distributions`. Uncertainty is specified using calls of the same nature, to `Normal()`. More information on the underlying design can be found in `inst/dev/design_dist.md` By @sbfnk in #504 and reviewed by @seabbs.
 
-## OTher breaking changes
+## Deprecations
 
-* The functions `get_dist`, `get_generation_time`, `get_incubation_period` have been deprecated and replaced with examples. By @sbfnk in #481 and reviewed by @seabbs.
+* The functions `sample_approx_dist()`, `report_cases()`, and `adjust_infection_reports()` have been deprecated as the functionality they provide can now be achieved with `simulate_secondary()`. See #597 by @jamesmbaazam and reviewed by @sbfnk.
 * The utility function `update_list()` has been deprecated in favour of `utils::modifyList()` because it comes with an installation of R. By @jamesmbaazam in #491 and reviewed by @seabbs.
 * The `fixed` argument to `dist_spec` has been deprecated and replaced by a `fix_dist()` function. By @sbfnk in #503 and reviewed by @seabbs.
+* The functions `get_dist()`, `get_generation_time()`, `get_incubation_period()` have been deprecated and replaced with examples. By @sbfnk in #481 and reviewed by @seabbs.
+* The function `init_cumulative_fit()` has been deprecated. By @jamesmbaazam in #541 and reviewed by @sbfnk.
+* The model-specific `weigh_delay_priors` argument has been deprecated in favour of delay-specific prior weighting using `weight_priors`. See `generation_time_opts()`, `delay_opts()`, and `trunc_opts()`. By @sbfnk in #630 and reviewed by @jamesmbaazam.
+* All functions now use a `data` argument to pass data. The existing `reported_cases`, `reports`, and `obs` arguments are deprecated and will be removed in v2.0.0. By @jamesmbaazam in #638 and reviewed by @sbfnk.
+
+## Other breaking changes
+
 * Updated `estimate_infections()` so that rather than imputing missing data, it now skips these data points in the likelihood. This is a breaking change as it alters the behaviour of the model when dates are missing from a time series but are known to be zero. We recommend that users check their results when updating to this version but expect this to in most cases improve performance. By @seabbs in #528 and reviewed by @sbfnk.
 * `simulate_infections` has been renamed to `forecast_infections` in line with `simulate_secondary` and `forecast_secondary`. The terminology is: a forecast is done from a fit to existing data, a simulation from first principles. By @sbfnk in #544 and reviewed by @seabbs.
 * A new `simulate_infections` function has been added that can be used to simulate from the model from given initial conditions and parameters. By @sbfnk in #557 and reviewed by @jamesmbaazam.
@@ -23,9 +31,10 @@
 * Removed references to the no longer existing `forecast_infections` function. By @sbfnk in #460 and reviewed by @seabbs.
 * The contribution guide has been improved to include more detail on ways to contribute new features/enhancements, report bugs, and improve or suggest vignettes. By @jamesmbaazam in #464 and reviewed by @seabbs.
 * Updated the code in `inst/CITATION` and added a GitHub Actions workflow to auto-generate `citation.cff` so that the two citation files are always in sync with `DESCRIPTION`. By @jamesmbazam in #467, with contributions from @Bisaloo, and reviewed by @seabbs and @sbfnk.
-* Updated the documentation of the `reported_cases` argument in `estimate_infections()` and `confirm` column in the `obs` argument of `estimate_truncation()` to allow `numeric` types, not just `integer`. See #594, by @jamesmbaazam, and reviewed by @sbfnk.
+* Updated the documentation of the `data` argument in `estimate_infections()` and `confirm` column in the `obs` argument of `estimate_truncation()` to allow `numeric` types, not just `integer`. See #594, by @jamesmbaazam, and reviewed by @sbfnk.
 * Removed the reporting templates that were previously provided. See #604 by @jamesmbaazam, and reviewed by @sbfnk.
 * Clarified how estimated or specified uncertainty around data truncation can be passed to `epinow()`, `regional_epinow()`, and `estimate_infections()` using the `truncation` argument. By @jamesmbaazam in #644 and reviewed by @sbnfk.
+* Internal functions have been removed from the pkgdown index. By @sbfnk in #735.
 
 ## Package
 
@@ -43,9 +52,7 @@
 * Replaced descriptions and plot labels to be more general and clearer. By @sbfnk in #621 and reviewed by @jamesmbaazam.
 * Argument choices have been moved into default arguments. By @sbfnk in #622 and reviewed by @seabbs.
 * `simulate_infections()` gained the argument `seeding_time` to change the seeding time. Additionally, the documentation was improved. By @sbfnk in #627 and reviewed by @jamesmbaazam.
-* The model-specific `weigh_delay_priors` argument has been deprecated in favour of delay-specific prior weighting using `weight_priors`. See `generation_time_opts()`, `delay_opts()`, and `trunc_opts()`. By @sbfnk in #630 and reviewed by @jamesmbaazam.
 * A `cmdstanr` backend has been added. By @sbfnk in #537 and #642 and reviewed by @seabbs.
-* All functions now use a `data` argument to pass data. The existing `reported_cases`, `reports`, and `obs` arguments are deprecated and will be removed in v2.0.0. By @jamesmbaazam in #638 and reviewed by @sbfnk.
 
 ## Model changes
 

diff --git a/R/EpiNow2-package.R b/R/EpiNow2-package.R
@@ -10,5 +10,7 @@
 # roxygen namespace tags. Modify with care!
 ## usethis namespace: start
 #' @importFrom lifecycle deprecate_soft
+#' @importFrom lifecycle deprecate_warn
+#' @importFrom lifecycle deprecate_stop
 ## usethis namespace: end
 NULL