epinowcast · adrian-lison · Jan 29, 2022 · Jan 29, 2022 · Jan 29, 2022 · Apr 14, 2022
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,6 @@
 # epinowcast 0.1.0
 
-This is a major release and contains multiple breaking changes. If needing the old interface please install `0.0.7` from GitHub. A major focus of this release has been improving the user experience with an increase in modularity, development of a flexible and full featured formula interface, and hopefully future proofing as far as possible. For ease, we have stratified changes below into interface, package, and model changes.
+This is a major release and contains multiple breaking changes. If needing the old interface please install `0.0.7` from GitHub. A major focus of this release has been improving the user experience with an increase in modularity, development of a flexible and full featured formula interface, and hopefully future proofing as far as possible. For ease, we have stratified changes below into interface, package, documentation, and model changes.
 
 ## Interface
 
@@ -17,6 +17,10 @@ This is a major release and contains multiple breaking changes. If needing the o
 * Added support for parametric exponential delay distributions (note that this is comparable to an intercept-only non-parametric hazard model) and potentially no parametric delay (though this will currently throw an error due to the lack of appropriate non-parametric hazard). See [#84](https://github.com/epiforecasts/epinowcast/pull/84) by [@seabbs](https://github.com/seabbs).
 * Update the expectation random walk model to use a more efficient `cumulative_sum` implementation suggested by [@adrian-lison](https://github.com/adrian-lison) in [#98](https://github.com/epiforecasts/epinowcast/issues/98)]. See [#103](https://github.com/epiforecasts/epinowcast/pull/103/) by [@seabbs](https://github.com/seabbs).
 
+## Documentation
+
+* The model descriptipn has been updated to reflect the currently implemented model and to improve readability. The use use of reference and report date nomenclature has also been standardised across the package. See [#71](https://github.com/epiforecasts/epinowcast/pull/71) by [@sbfnk](https://github.com/sbfnk) and [@seabbs](https://github.com/seabbs).
+
 ## Internals
 
 * Array declarations in the stan model have been updated. To maintain compatibility with [expose_stan_fns()] (which itself depends on `rstan`), additional functionality has been added to parse stan code in this function. See [#74](https://github.com/epiforecasts/epinowcast/issues/74), [#85](https://github.com/epiforecasts/epinowcast/pull/85#issuecomment-1172010003), and [#93](https://github.com/epiforecasts/epinowcast/pull/93) by [@sbfnk](https://github.com/sbfnk) and [@seabbs](https://github.com/seabbs).

diff --git a/README.Rmd b/README.Rmd
@@ -197,6 +197,10 @@ sum_across_last_7_days <- enw_summarise_samples(samples)
 enw_plot_nowcast_quantiles(sum_across_last_7_days, latest_germany_hosp_7day)
 ```
 
+## Learning more
+
+The package has extensive documentation as well as vignettes describing the underlying methodology, and several case studies. Please see [the package site](https://epiforecasts.io/epinowcast) for details. Note that the development version of the package also has supporting documentation which are available [here](https://epiforecasts.io/epinowcast/dev).
+
 ## Citation
 
 If using `epinowcast` in your work please consider citing it using the following,
@@ -207,13 +211,13 @@ citation("epinowcast")
 
 ## How to make a bug report or feature request
 
-Please briefly describe your problem and what output you expect in an [issue](https://github.com/epiforecasts/epinowcast/issues). If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epiforecasts/epinowcast/discussions/categories/q-a).
+Please briefly describe your problem and what output you expect in an [issue](https://github.com/epiforecasts/epinowcast/issues). If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epiforecasts/epinowcast/discussions/categories/q-a). See our [contributing guide](https://github.com/epiforecasts/epinowcast/blob/main/CONTRIBUTING.md) for more information.
 
 ## Contributing
 
 We welcome contributions and new contributors! We particularly appreciate help on priority problems in the [issues](https://github.com/epiforecasts/epinowcast/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epiforecasts/epinowcast/pulls). See our [contributing guide](https://github.com/epiforecasts/epinowcast/blob/main/CONTRIBUTING.md) for more information.
 
-If interested in expanding the functionality of the underlying model note that `epinowcast` allows users to pass in their own models meaning that alternative parameterisations, for example altering the forecast model used for inferring expected observations, may be easily tested within the package infrastructure. Once this testing has been done alterations that increase the flexibility of the package model and improves its defaults are very welcome via pull request or other communication with the package authors.
+If interested in expanding the functionality of the underlying model note that `epinowcast` allows users to pass in their own models meaning that alternative parameterisations, for example altering the forecast model used for inferring expected observations, may be easily tested within the package infrastructure. Once this testing has been done alterations that increase the flexibility of the package model and improves its defaults are very welcome via pull request or other communication with the package authors. Even if not wanting to add your updated model to the package please do reach out as we would love to hear about your use case.
 
 ## Code of Conduct
 

diff --git a/README.md b/README.md
@@ -354,6 +354,10 @@ enw_plot_nowcast_quantiles(sum_across_last_7_days, latest_germany_hosp_7day)
 
 <img src="man/figures/README-week_nowcast-1.png" width="100%" />
 
+## Learning more
+
+The package has extensive documentation as well as vignettes describing the underlying methodology, and several case studies. Please see [the package site](https://epiforecasts.io/epinowcast) for details. Note that the development version of the package also has supporting documentation which are available [here](https://epiforecasts.io/epinowcast/dev).
+
 ## Citation
 
 If using `epinowcast` in your work please consider citing it using the
@@ -377,34 +381,15 @@ following,
 
 ## How to make a bug report or feature request
 
-Please briefly describe your problem and what output you expect in an
-[issue](https://github.com/epiforecasts/epinowcast/issues). If you have
-a question, please don’t open an issue. Instead, ask on our [Q and A
-page](https://github.com/epiforecasts/epinowcast/discussions/categories/q-a).
+Please briefly describe your problem and what output you expect in an [issue](https://github.com/epiforecasts/epinowcast/issues). If you have a question, please don't open an issue. Instead, ask on our [Q and A page](https://github.com/epiforecasts/epinowcast/discussions/categories/q-a). See our [contributing guide](https://github.com/epiforecasts/epinowcast/blob/main/CONTRIBUTING.md) for more information.
 
 ## Contributing
 
-We welcome contributions and new contributors\! We particularly
-appreciate help on priority problems in the
-[issues](https://github.com/epiforecasts/epinowcast/issues). Please
-check and add to the issues, and/or add a [pull
-request](https://github.com/epiforecasts/epinowcast/pulls). See our
-[contributing
-guide](https://github.com/epiforecasts/epinowcast/blob/main/CONTRIBUTING.md)
-for more information.
-
-If interested in expanding the functionality of the underlying model
-note that `epinowcast` allows users to pass in their own models meaning
-that alternative parameterisations, for example altering the forecast
-model used for inferring expected observations, may be easily tested
-within the package infrastructure. Once this testing has been done
-alterations that increase the flexibility of the package model and
-improves its defaults are very welcome via pull request or other
-communication with the package authors.
+We welcome contributions and new contributors! We particularly appreciate help on priority problems in the [issues](https://github.com/epiforecasts/epinowcast/issues). Please check and add to the issues, and/or add a [pull request](https://github.com/epiforecasts/epinowcast/pulls). See our [contributing guide](https://github.com/epiforecasts/epinowcast/blob/main/CONTRIBUTING.md) for more information.
+
+If interested in expanding the functionality of the underlying model note that `epinowcast` allows users to pass in their own models meaning that alternative parameterisations, for example altering the forecast model used for inferring expected observations, may be easily tested within the package infrastructure. Once this testing has been done alterations that increase the flexibility of the package model and improves its defaults are very welcome via pull request or other communication with the package authors. Even if not wanting to add your updated model to the package please do reach out as we would love to hear about your use case.
 
 ## Code of Conduct
+
+Please note that the `epinowcast` project is released with a [Contributor Code of Conduct](https://epiforecasts.io/epinowcast/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
 
-Please note that the `epinowcast` project is released with a
-[Contributor Code of
-Conduct](https://epiforecasts.io/epinowcast/CODE_OF_CONDUCT.html). By
-contributing to this project, you agree to abide by its terms.
diff --git a/vignettes/germany-age-stratified-nowcasting.Rmd b/vignettes/germany-age-stratified-nowcasting.Rmd
@@ -362,7 +362,7 @@ plot(age_week_nowcast, latest_obs = latest_nat_germany) +
 
 ## Independent models  for each age group.
 
-The obvious question to ask at this stage is if using a model that jointly fits to all age groups at once is actually beneficial. Here we explore this by fitting the same model as previously (a day of week effect for report date and a random walk on the week of the occurrence date stratified by age) to each age group independently.
+The obvious question to ask at this stage is if using a model that jointly fits to all age groups at once is actually beneficial. Here we explore this by fitting the same model as previously (a day of week effect for report date and a random walk on the week of the reference date stratified by age) to each age group independently.
 
 We could define this model with a single call to `epinowcast` but fitting each dataset independently but in a joint setting would likely lead to long fit times for no real benefit. Instead here we write a small helper function to preprocess our input data, define report and reference date models and then run a nowcast.
 

diff --git a/vignettes/germany-age-stratified-nowcasting.Rmd.orig b/vignettes/germany-age-stratified-nowcasting.Rmd.orig
@@ -266,7 +266,7 @@ plot(age_week_nowcast, latest_obs = latest_nat_germany) +
 
 ## Independent models  for each age group.
 
-The obvious question to ask at this stage is if using a model that jointly fits to all age groups at once is actually beneficial. Here we explore this by fitting the same model as previously (a day of week effect for report date and a random walk on the week of the occurrence date stratified by age) to each age group independently.
+The obvious question to ask at this stage is if using a model that jointly fits to all age groups at once is actually beneficial. Here we explore this by fitting the same model as previously (a day of week effect for report date and a random walk on the week of the reference date stratified by age) to each age group independently.
 
 We could define this model with a single call to `epinowcast` but fitting each dataset independently but in a joint setting would likely lead to long fit times for no real benefit. Instead here we write a small helper function to preprocess our input data, define report and reference date models and then run a nowcast.