1.6.0 release (#794)

* polish NEWS

* fix typos/links

NEWS.md

@@ -1,4 +1,6 @@
-# EpiNow2 (development version)
+# EpiNow2 1.6.0
+
+A release that introduces model improvements to the Gaussian Process models, alongside a number of other improvements and bug fixes.
 
 ## Documentation
 
@@ -9,8 +11,6 @@
 
 ## Model changes
 
-- All functions now use the `{cli}` R package to signal errors, warnings, and messages. By @jamesmbaazam in #762 and reviewed by @seabbs.
-- `epinow()` now returns the "timing" output in a "time difference"" format that is easier to understand and work with. By @jamesmbaazam in #688 and reviewed by @sbfnk.
 - The interface for defining delay distributions has been generalised to also cater for continuous distributions
 - When defining probability distributions these can now be truncated using the `tolerance` argument
 - Ornstein-Uhlenbeck and 5 / 2 Matérn kernels have been added. By @sbfnk in #741 and reviewed by @seabbs.
@@ -19,7 +19,7 @@
 - The default stan control options have been updated from `list(adapt_delta = 0.95, max_treedepth = 15)` to `list(adapt_delta = 0.9, max_treedepth = 12)` due to improved performance and to reduce the runtime of the default parameterisations. By @seabbs in #742 and reviewed by @jamesmbaazam.
 - Initialisation has been simplified by sampling directly from the priors, where possible, rather than from a constrained space. By @seabbs in #742 and reviewed by @jamesmbaazam.
 - Unnecessary normalisation of delay priors has been removed. By @seabbs in #742 and reviewed by @jamesmbaazam.
-- Ornstein-Uhlenbeck and 5 / 2 Matérn kernels have been added. By @sbfnk in # and reviewed by @.
+- Ornstein-Uhlenbeck and 5 / 2 Matérn kernels have been added. By @sbfnk in #741 and reviewed by @seabbs.
 - Switch to broadcasting from random walks and added unit tests. By @seabbs in #747 and reviewed by @jamesmbaazam.
 - Optimised convolution code to take into account the relative length of the vectors being convolved. See #745 by @seabbs and reviewed by @jamesmbaazam.
 - Switch to broadcasting the day of the week effect. By @seabbs in #746 and reviewed by @jamesmbaazam.
@@ -28,6 +28,8 @@
 
 ## Package changes
 
+- `epinow()` now returns the "timing" output in a "time difference"" format that is easier to understand and work with. By @jamesmbaazam in #688 and reviewed by @sbfnk.
+- All functions now use the `{cli}` R package to signal errors, warnings, and messages. By @jamesmbaazam in #762 and reviewed by @seabbs.
 - `fix_dist()` has been renamed to `fix_parameters()` because it removes the uncertainty in a distribution's parameters. By @sbfnk in #733 and reviewed by @jamesmbaazam.
 - `plot.dist_spec` now uses color instead of line types to display pmfs vs cmfs. By @jamesmbaazam in #788 and reviewed by @sbfnk.
 

R/dist_spec.R

@@ -20,10 +20,10 @@
 #' Charniga, K., et al. “Best practices for estimating and reporting
 #'   epidemiological delay distributions of infectious diseases using public
 #'   health surveillance and healthcare data”, *arXiv e-prints*, 2024.
-#'   <https://doi.org/10.48550/arXiv.2405.08841>
+#'   \doi{10.48550/arXiv.2405.08841}
 #' Park,  S. W.,  et al.,  "Estimating epidemiological delay distributions for
 #'   infectious diseases", *medRxiv*, 2024.
-#'   <https://doi.org/10.1101/2024.01.12.24301247>
+#'   \doi{<https://doi.org/10.1101/2024.01.12.24301247}
 #'
 #' @param distribution A character string representing the distribution to be
 #'   used (one of "exp", "gamma", "lognormal", "normal" or "fixed")

R/opts.R

@@ -571,7 +571,7 @@ gp_opts <- function(basis_prop = 0.2,
 #'   `familiy` is "negbin". Can be supplied either as a single numeric value
 #'   (fixed overdispersion) or a list with numeric elements mean (`mean`) and
 #'   standard deviation (`sd`) defining a normally distributed prior.
-#'   Internally parametersed such that the overedispersion is one over the
+#'   Internally parameterised such that the overdispersion is one over the
 #'   square of this prior overdispersion. Defaults to a list with elements
 #'   `mean = 0` and `sd = 0.25`.
 #' @param weight Numeric, defaults to 1. Weight to give the observed data in the

README.Rmd

@@ -15,7 +15,7 @@ knitr::opts_chunk$set(
 
 [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing) [![R-CMD-check](https://github.com/epiforecasts/EpiNow2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiforecasts/EpiNow2/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/epiforecasts/EpiNow2/branch/main/graph/badge.svg?token=FZWwEMdpq6)](https://app.codecov.io/gh/epiforecasts/EpiNow2) [![metacran downloads](http://cranlogs.r-pkg.org/badges/grand-total/EpiNow2?color=ff69b4)](https://cran.r-project.org/package=EpiNow2)
 
-[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epiforecasts/EpiNow2/blob/main/LICENSE.md/)   [![GitHub contributors](https://img.shields.io/github/contributors/epiforecasts/EpiNow2)](https://github.com/epiforecasts/EpiNow2/graphs/contributors)  [![universe](https://epiforecasts.r-universe.dev/badges/EpiNow2)](http://epiforecasts.r-universe.dev/ui/#package:EpiNow2) [![GitHub commits](https://img.shields.io/github/commits-since/epiforecasts/EpiNow2/v1.4.0.svg?color=orange)](https://GitHub.com/epiforecasts/EpiNow2/commit/main/) [![DOI](https://zenodo.org/badge/272995211.svg)](https://zenodo.org/badge/latestdoi/272995211)
+[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epiforecasts/EpiNow2/blob/main/LICENSE.md/)   [![GitHub contributors](https://img.shields.io/github/contributors/epiforecasts/EpiNow2)](https://github.com/epiforecasts/EpiNow2/graphs/contributors)  [![universe](https://epiforecasts.r-universe.dev/badges/EpiNow2)](http://epiforecasts.r-universe.dev/#package:EpiNow2) [![GitHub commits](https://img.shields.io/github/commits-since/epiforecasts/EpiNow2/v1.4.0.svg?color=orange)](https://GitHub.com/epiforecasts/EpiNow2/commit/main/) [![DOI](https://zenodo.org/badge/272995211.svg)](https://zenodo.org/badge/latestdoi/272995211)
 
 ## Summary