Add NEWS items for v0.4.0 release

NEWS.md

@@ -1,8 +1,44 @@
 # superspreading (development version)
 
+The fourth minor release of the _superspreading_ package contains new functionality, a new vignette and various minor improvements to documentation.
+
+With this release the development status of the package has been updated from _experimental_ to _stable_. 
+
+## New features
+
+* The `probability_emergence()` function has been added to calculate the probability that a pathogen introduced to humans can evolve and emerge to cause a sustained human-to-human outbreak, implementing and extending the framework of [Antia et al. (2003)](https://doi.org/10.1038/nature02104) (#124, #133).
+
+* A new vignette, `emergence.Rmd`, has been added that covers the functionality of `probability_emergence()` and reproduces the two figures from [Antia et al. (2003)](https://doi.org/10.1038/nature02104) as well as a figure using the multiple introductions extension (#124, #133).
+
+* Alt-text has been added to all plots across all vignettes (#129).
+
+## Breaking changes
+
+* The `percent_transmission` argument in `proportion_transmission()` has been renamed to `prop_transmission` (#130).
+
+## Minor changes
+
+* An `.aspell/` folder is added to the package including `defaults.R` and `superspreading.rds` to supply a wordlist to the CRAN spell checking to avoid quoting names in the `DESCRIPTION` (#127). 
+
+* Package and function documentation has been updated. Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the [Tidyverse style guide](https://style.tidyverse.org/documentation.html) (#131, #134).
+
+* Internal code style has been updated to adhere to current best practice (#125).
+
+* The package lifecycle badge has been updated from _experimental_ to _stable_. CRAN status, CRAN downloads, repo status and Zenodo DOI badges have been added to the `README` (#119, #132).
+
+* The {pkgdown} `development: mode` has been set to `auto` now the package is hosted on CRAN (#118).
+
+## Bug fixes
+
+* None
+
+## Deprecated and defunct
+
+* None
+
 # superspreading 0.3.0
 
-The third minor release of the _superspreading_ package contains enhancements to several functions and a new vignette. 
+The third minor release of the _superspreading_ package contains enhancements to several functions and a new vignette.
 
 We are also pleased to welcome Dillon Adam (@dcadam) as a new package author for his contributions towards this version.
 

inst/WORDLIST

@@ -31,6 +31,7 @@ Endo
 epiparameter
 Epiverse
 EVD
+experimental
 Faes
 Faye
 fitdistrplus
@@ -58,6 +59,7 @@ Koen
 Kremer
 Laure
 lfloor
+lifecycle
 Lifecycle
 Lim
 linetype
@@ -105,6 +107,7 @@ sim
 SJ
 Soropogui
 testthat
+Tidyverse
 Torneri
 Tsang
 u
@@ -120,4 +123,5 @@ Yeung
 yintercept
 ymax
 ymin
+Zenodo
 zika

vignettes/epidemic_risk.Rmd

@@ -227,7 +227,7 @@ ggplot(data = epidemic_params) +
 In the above plot we drop the uncertainty around each point and assume a known value
 of $R$ in order to more clearly show the pattern.
 
-These calculations enable us to understand epidemics and applications, such as Shiny apps, to explore this functionality and compare between existing parameter estimates of offspring distributions are also useful. An example application called [Probability of a large 2019-nCoV outbreak following introduction of cases](https://cmmid.github.io/visualisations/), that is no longer maintained, was developed by the Centre for Mathematical Modelling of Infectious diseases at the London School of Hygiene and Tropical Medicine, for comparing SARS-like and MERS-like scenarios, as well as random mixing during the COVID-19 pandemic.
+These calculations enable us to understand epidemics and applications, such as Shiny apps, to explore this functionality and compare between existing parameter estimates of offspring distributions are also useful. An example application called [Probability of a large 2019-nCoV outbreak following introduction of cases](https://cmmid.github.io/visualisations), that is no longer maintained, was developed by the Centre for Mathematical Modelling of Infectious diseases at the London School of Hygiene and Tropical Medicine, for comparing SARS-like and MERS-like scenarios, as well as random mixing during the COVID-19 pandemic.
 
 Conversely to the probability of an epidemic, the probability that an outbreak will 
 go extinct (i.e. transmission will subside), can also be plotted for different values of