From 42fbb2230250dd2e79b81c7bfea90041b6d7752f Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Wed, 9 Oct 2024 17:51:31 +0100 Subject: [PATCH] Update `NEWS.md` for v0.3.0 release (#392) * updated NEWS with v0.3.0 bullets * updated WORDLIST --- NEWS.md | 36 ++++++++++++++++++++++++++++++++++++ inst/WORDLIST | 2 ++ 2 files changed, 38 insertions(+) diff --git a/NEWS.md b/NEWS.md index 7266571cf..ce595d781 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,41 @@ # epiparameter (development version) +The third minor release of the {epiparameter} R package contains a range of updates and improvements to the package. The principal aim of this release is to simplify, clarify and enhance the classes and class methods when working with epidemiological parameters in R. + +The are a large number of ***breaking changes*** in this release, primarily functions and function arguments being renamed or restructured, see the _Breaking changes_ section for an overview. + +## New features + +* The library of epidemiological parameters has been updated to include 3 new Chikungunya parameter entries. The Mpox parameters previously missing from the Guzzetta et al. entry have been added (PR #346 & #374). +* A `c()` method has been added for `` and `` objects. +* An `aggregate()` method has been added for `` to enable consensus distributions to be built utilising the mixture distribution class from [{distributional}](https://cran.r-project.org/web/packages/distributional/index.html) (PR #388). +* Infrastructure has been added to the package to allow translations of messages/warnings/errors printed to the console. (@Bisaloo, PR #367). +* `convert_summary_stats_to_params()` can now convert from median and dispersion for a lognormal distribution (PR #378). +* The `data_dictionary.json` has been enhanced to improve validation of the library of epidemiological parameters (`parameters.json`) (PR #379). +* An interactive network showing all of the `` S3 methods has been added to the `design_principles.Rmd` vignette (PR #383). +* The `data_from_epireview.Rmd` article has been improved and updated with new changes from {epireview} (@CarmenTamayo & @cm401 & @kellymccain28, PR #305 & #373). +* Parameter units have been added to every entry in the {epiparameter} library (`parameters.json`) and to the `$metadata` element in `` objects. The `create_metadata()` function now has a `units` argument to construct metadata lists (PR #391). +* Improved `database.Rmd` vignette by adding a short citation to the reference column (@jamesmbaazam, PR #348). + +## Breaking changes + +* The `` class has been renamed `` to avoid confusion with the similar R package [{epidist}](https://github.com/epinowcast/epidist) (PR #360). +* Many functions that used `epidist` in their names have been renamed to use `epiparameter` due to the renaming of the class (PR #360). +* The function signatures of `epiparameter()` and `new_epiparameter()` functions (previously `epidist()` and `new_epidist()`) have been updated to collapse the `prob_dist`, `prob_dist_params`, `discretise` and `truncation` arguments into `prob_distribution`, which accepts the output of `create_prob_distribution()` (PR #381). +* The `epi_dist` argument has been renamed `epi_name`. This is to clarify that {epiparameter} can work with epidemiological parameters that take a variety of forms (e.g. point estimates, ranges, probability distributions, etc.) (PR #390). +* The `` class and it's methods have been removed from the package. It was not being used and was increasing the complexity and maintenance load of the package (PR #359). +* `create_prob_dist()` has been renamed to `create_prob_distribution()` (PR #381). +* `validate_epiparameter()` (previously `validate_epidist()`) has been renamed `assert_epiparameter()`, and `test_epiparameter()` has been added, with the aim to harmonise design with [{contactmatrix}](https://github.com/socialcontactdata/contactmatrix) (PR #366). +* The minimum version of R required by the package is now 4.1.0 due to the use of the base R pipe (`|>`) in dependencies (PR #384). + +## Bug fixes + +* Epidemiological parameter entries in the library stored with lognormal distributions, parameterised as median and dispersion are now converted to meanlog and sdlog correctly when creating an `` (when `auto_calc_params = TRUE`) (PR #381). + +## Deprecated and defunct + +* `epidist_db()` has been deprecated. It is replaced by `epiparameter_db()`. + # epiparameter 0.2.0 The second release of the {epiparameter} R package focuses on interoperability with the [{epireview} R package](https://mrc-ide.github.io/epireview/). Several functions have been refactored and enhanced. diff --git a/inst/WORDLIST b/inst/WORDLIST index 52837b509..d58628ed6 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -12,6 +12,7 @@ Discretises distcrete dplyr ebola +epidist EpiParameter epiparameters epireview @@ -21,6 +22,7 @@ estimat etc EVD facetted +Guzzetta jsonlite Lassa Lifecycle