Merge branch 'main' into joss

Author: joshwlambert

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "simulist" in publications use:'
 type: software
 license: MIT
 title: 'simulist: Simulate Disease Outbreak Line List and Contacts Data'
-version: 0.6.0.9000
+version: 0.7.0
 doi: 10.5281/zenodo.10471458
 identifiers:
 - type: doi

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: simulist
 Title: Simulate Disease Outbreak Line List and Contacts Data
-Version: 0.6.0.9000
+Version: 0.7.0
 Authors@R: c(
     person("Joshua W.", "Lambert", , "[email protected]", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-5218-3046")),

NEWS.md

@@ -1,4 +1,34 @@
-# simulist (development version)
+# simulist 0.7.0
+
+This minor version release contains a range of minor updates and accompanies the _simulist_ publication in the [Journal of Open Source Software (JOSS)](https://joss.theoj.org/).
+
+## New features
+
+* The sampling of sex for line list and contacts data can now be weighted instead of assuming a uniform probability via `prob_male` in `config` (#255).
+
+* The `reporting_delay` argument in `sim_linelist()` and `sim_outbreak()` now supports `<epiparameter>` objects, matching the functionality of the other delay distribution arguments (#262).
+
+* A new line list events plot has been added to the `vis-linelist.Rmd` vignette (#278).
+
+## Breaking changes
+
+* None
+
+## Minor changes
+
+* Added `dependabot` (#258).
+
+* GitHub actions versions are updated (multiple PRs).
+
+* `.lintr` is updated to include more linters (#279) and the `# nolint` flag syntax is fixed (#263).
+
+## Bug fixes
+
+* None
+
+## Deprecated and defunct
+
+* None
 
 # simulist 0.6.0
 

README.Rmd

@@ -267,4 +267,4 @@ Some packages are related to {simulist} but do not simulate line list data. Thes
 
 The {outbreaks} package is useful if data from a past outbreak data or generic line list data is required. The {ringbp} and {epichains} packages can be used to generate case data over time which can then be converted into a line list with some manual post-processing.
 
-Another package for creating messy data is the [{messy}](https://CRAN.R-project.org/package=messy) package. This can be used, either independently or in combination with `messy_linelist()`, to create messy line list and contacts data. 
+Another package for creating messy data is the [{messy}](https://CRAN.R-project.org/package=messy) package. This can be used, either independently or in combination with `messy_linelist()`, to create messy line list and contacts data.

cran-comments.md

@@ -1,7 +1,5 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 0 notes
+0 errors | 0 warnings | 1 note
 
 * Running R CMD check (with _R_CHECK_INCOMING_REMOTE_) flags 403 warnings for LSHTM URLs but these are valid URLs and are not flagged on winbuilder.
-
-* There are no papers describing the methods used in this package.

inst/WORDLIST

@@ -52,6 +52,7 @@ Kobo
 lifecycle
 Lifecycle
 linelist
+linters
 lintr
 LLsim
 lognormally
@@ -73,6 +74,7 @@ pkgdown
 Poisson
 Pratik
 primarycensored
+PRs
 px
 qPCR
 R's

vignettes/time-varying-cfr.Rmd

@@ -128,7 +128,7 @@ To visualise the incidence of cases and deaths over time we will use the [{incid
 For more information on using {incidence2} to plot line list data see the [Visualising simulated data](vis-linelist.html) vignette.
 :::
 
-Before converting the line list `<data.frame>` to an `<incidence>` object we need to ungroup the outcome columns into their own columns using the [{tidyr}](https://tidyr.tidyverse.org/) and [{dplyr}](https://dplyr.tidyverse.org/) R packages from the [Tidyverse](https://www.tidyverse.org/).
+Before converting the line list `<data.frame>` to an `<incidence>` object we need to ungroup the outcome columns into their own columns using the [{tidyr}](https://tidyr.tidyverse.org/) and [{dplyr}](https://dplyr.tidyverse.org/) R packages from the [Tidyverse](https://tidyverse.org/).
 
 ```{r, reshape-linelist}
 linelist <- linelist |>

vignettes/wrangling-linelist.Rmd

@@ -23,7 +23,7 @@ library(dplyr)
 library(epicontacts)
 ```
 
-This vignette provides data wrangling examples using both functions available in the R language (commonly called "base R") as well as using [tidyverse R packages](https://www.tidyverse.org/), which are commonly applied to data science tasks in R. The tidyverse examples are shown by default, but select the "Base R" tab to see the equivalent functionality using base R. There are many other tools for wrangling data in R which are not covered by this vignette (e.g. [{data.table}](https://rdatatable.gitlab.io/data.table/)).
+This vignette provides data wrangling examples using both functions available in the R language (commonly called "base R") as well as using [tidyverse R packages](https://tidyverse.org/), which are commonly applied to data science tasks in R. The tidyverse examples are shown by default, but select the "Base R" tab to see the equivalent functionality using base R. There are many other tools for wrangling data in R which are not covered by this vignette (e.g. [{data.table}](https://rdatatable.gitlab.io/data.table/)).
 
 ::: {.alert .alert-info}
 See these great resources for more information on general data wrangling in R: