From 18ba5c25fb8438b66751404a774874cd0d22da05 Mon Sep 17 00:00:00 2001 From: epiverse-trace-bot Date: Thu, 28 Aug 2025 23:38:11 +0000 Subject: [PATCH 1/3] Automated release blog post `simulist` - `v0.6.0` --- .../index/execute-results/html.json | 15 +++++ posts/simulist_v0.6.0/index.qmd | 59 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 _freeze/posts/simulist_v0.6.0/index/execute-results/html.json create mode 100644 posts/simulist_v0.6.0/index.qmd diff --git a/_freeze/posts/simulist_v0.6.0/index/execute-results/html.json b/_freeze/posts/simulist_v0.6.0/index/execute-results/html.json new file mode 100644 index 00000000..92572621 --- /dev/null +++ b/_freeze/posts/simulist_v0.6.0/index/execute-results/html.json @@ -0,0 +1,15 @@ +{ + "hash": "e1bae9d83bc5acee00020aee5515bb8f", + "result": { + "engine": "knitr", + "markdown": "---\ntitle: \"simulist v0.6.0\"\nauthor:\n - name: \"The Epiverse-TRACE development team\"\ndate: \"2025-08-28\"\ncategories: [new-release]\ncode-link: true\n---\n\n\nWe are very excited to announce the release of a new [simulist](https://epiverse-trace.github.io/simulist) version v0.6.0.\nHere is an automatically generated summary of the changes in this version.\n\n\n::: {.cell}\n\n```{.r .cell-code}\nlibrary(simulist)\n```\n:::\n\n\nIn this minor version release we have continued to make a range of improvements across the package. A new line list post-processing function, `censor_linelist()`, makes it easy to group dates into various intervals, `messy_linelist()` introduced in v0.5.0 is enhanced, and the package documentation is expanded to cover under-reporting in outbreak data and censoring dates. There are also a couple of minor bug fixes.\n\nThe development status of the package is updated to _stable_ from _experimental_ to reflect the long term stability and low probability of major changes. \n\n## New features\n\n* A new `censor_linelist()` function is added to the package. This is a new post-processing function for line list data to censor `` to daily, weekly and other user-defined time periods. The `censor_linelist()` also has a weekend-effect option to replicate the low reporting over weekends. This new feature also adds the {grates} package as a dependency (#240).\n\n* `messy_linelist()` can now accept a vector with multiple `missing_value`s to allow different values to represent missing data (#241).\n\n* A demonstration of how to replicate under-reporting of line list and contact tracing data is added to the `wrangling-linelist.Rmd` vignette. The demo contains examples for multiple types of under-reporting data found in real-world outbreaks (#244).\n\n## Breaking changes\n\n* The `$was_case` column in contact tracing data simulated by `sim_contacts()` now contains `logical` boolean values instead of `\"Y\"` and `\"N\"` `character` strings (#243).\n\n* The minimum R version required by the package is incremented to v4.2.0 due to a recursive dependency on {fastymd} (#235).\n\n## Minor changes\n\n* Documentation on censoring dates is added to `wrangling-linelist.Rmd` (#240). \n\n* Documentation on interoperability between {simulist} and {incidence2} for double precision ``s and warning for not specifying `interval` in `incidence2::incidence()` is added to `vis-linelist.Rmd` (#232).\n\n* The lifecycle of the package has been updated from _experimental_ to _stable_ (#229).\n\n* `@return` function documentation for exported functions is improved (#235).\n\n## Bug fixes\n\n* `truncate_linelist()` sets `$outcome` to `NA` if they are more recent than truncation time. This matches the way `$date_outcome` was handled in `truncate_linelist()` in v0.5.0 (#228).\n\n* Alt-text in vignettes is fixed to render correctly on pkgdown website (#230).\n\n## Deprecated and defunct\n\n* None\n\n\n## Acknowledgements\n\n[@joshwlambert](https://github.com/joshwlambert)\n", + "supporting": [], + "filters": [ + "rmarkdown/pagebreak.lua" + ], + "includes": {}, + "engineDependencies": {}, + "preserve": {}, + "postProcess": true + } +} \ No newline at end of file diff --git a/posts/simulist_v0.6.0/index.qmd b/posts/simulist_v0.6.0/index.qmd new file mode 100644 index 00000000..cab8f6e9 --- /dev/null +++ b/posts/simulist_v0.6.0/index.qmd @@ -0,0 +1,59 @@ +--- +title: "simulist v0.6.0" +author: + - name: "The Epiverse-TRACE development team" +date: "2025-08-28" +categories: [new-release] +code-link: true +--- + + +We are very excited to announce the release of a new [simulist](https://epiverse-trace.github.io/simulist) version v0.6.0. +Here is an automatically generated summary of the changes in this version. + +```{r} +library(simulist) +``` + +In this minor version release we have continued to make a range of improvements across the package. A new line list post-processing function, `censor_linelist()`, makes it easy to group dates into various intervals, `messy_linelist()` introduced in v0.5.0 is enhanced, and the package documentation is expanded to cover under-reporting in outbreak data and censoring dates. There are also a couple of minor bug fixes. + +The development status of the package is updated to _stable_ from _experimental_ to reflect the long term stability and low probability of major changes. + +## New features + +* A new `censor_linelist()` function is added to the package. This is a new post-processing function for line list data to censor `` to daily, weekly and other user-defined time periods. The `censor_linelist()` also has a weekend-effect option to replicate the low reporting over weekends. This new feature also adds the {grates} package as a dependency (#240). + +* `messy_linelist()` can now accept a vector with multiple `missing_value`s to allow different values to represent missing data (#241). + +* A demonstration of how to replicate under-reporting of line list and contact tracing data is added to the `wrangling-linelist.Rmd` vignette. The demo contains examples for multiple types of under-reporting data found in real-world outbreaks (#244). + +## Breaking changes + +* The `$was_case` column in contact tracing data simulated by `sim_contacts()` now contains `logical` boolean values instead of `"Y"` and `"N"` `character` strings (#243). + +* The minimum R version required by the package is incremented to v4.2.0 due to a recursive dependency on {fastymd} (#235). + +## Minor changes + +* Documentation on censoring dates is added to `wrangling-linelist.Rmd` (#240). + +* Documentation on interoperability between {simulist} and {incidence2} for double precision ``s and warning for not specifying `interval` in `incidence2::incidence()` is added to `vis-linelist.Rmd` (#232). + +* The lifecycle of the package has been updated from _experimental_ to _stable_ (#229). + +* `@return` function documentation for exported functions is improved (#235). + +## Bug fixes + +* `truncate_linelist()` sets `$outcome` to `NA` if they are more recent than truncation time. This matches the way `$date_outcome` was handled in `truncate_linelist()` in v0.5.0 (#228). + +* Alt-text in vignettes is fixed to render correctly on pkgdown website (#230). + +## Deprecated and defunct + +* None + + +## Acknowledgements + +[@joshwlambert](https://github.com/joshwlambert) From 296f1c70008178917f9b32a00dc7464146164235 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Fri, 29 Aug 2025 17:46:57 +0100 Subject: [PATCH 2/3] Add contributors to acknowledgements in simulist v0.6.0 --- posts/simulist_v0.6.0/index.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/posts/simulist_v0.6.0/index.qmd b/posts/simulist_v0.6.0/index.qmd index cab8f6e9..edb3eb38 100644 --- a/posts/simulist_v0.6.0/index.qmd +++ b/posts/simulist_v0.6.0/index.qmd @@ -56,4 +56,4 @@ The development status of the package is updated to _stable_ from _experimental_ ## Acknowledgements -[@joshwlambert](https://github.com/joshwlambert) +[@joshwlambert](https://github.com/joshwlambert) [@avallecam](https://github.com/avallecam) [@TimTaylor](https://github.com/TimTaylor) [@sbfnk](https://github.com/sbfnk) [@seabbs](https://github.com/seabbs) From acfd51a8e34e82f82a552dd6dea09eb12111b3d8 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Fri, 29 Aug 2025 17:50:02 +0100 Subject: [PATCH 3/3] linting simulist v0.6.0 release post --- posts/simulist_v0.6.0/index.qmd | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/posts/simulist_v0.6.0/index.qmd b/posts/simulist_v0.6.0/index.qmd index edb3eb38..dbe10b18 100644 --- a/posts/simulist_v0.6.0/index.qmd +++ b/posts/simulist_v0.6.0/index.qmd @@ -17,7 +17,7 @@ library(simulist) In this minor version release we have continued to make a range of improvements across the package. A new line list post-processing function, `censor_linelist()`, makes it easy to group dates into various intervals, `messy_linelist()` introduced in v0.5.0 is enhanced, and the package documentation is expanded to cover under-reporting in outbreak data and censoring dates. There are also a couple of minor bug fixes. -The development status of the package is updated to _stable_ from _experimental_ to reflect the long term stability and low probability of major changes. +The development status of the package is updated to _stable_ from _experimental_ to reflect the long term stability and low probability of major changes. ## New features @@ -35,7 +35,7 @@ The development status of the package is updated to _stable_ from _experimental_ ## Minor changes -* Documentation on censoring dates is added to `wrangling-linelist.Rmd` (#240). +* Documentation on censoring dates is added to `wrangling-linelist.Rmd` (#240). * Documentation on interoperability between {simulist} and {incidence2} for double precision ``s and warning for not specifying `interval` in `incidence2::incidence()` is added to `vis-linelist.Rmd` (#232). @@ -53,7 +53,6 @@ The development status of the package is updated to _stable_ from _experimental_ * None - ## Acknowledgements [@joshwlambert](https://github.com/joshwlambert) [@avallecam](https://github.com/avallecam) [@TimTaylor](https://github.com/TimTaylor) [@sbfnk](https://github.com/sbfnk) [@seabbs](https://github.com/seabbs)