Merge branch 'main' into move-to-suggest

.github/workflows/touchstone-receive.yaml

@@ -52,7 +52,7 @@ jobs:
         with:
           cache-version: 1
           extra-packages: stan-dev/cmdstanr
-          touchstone_ref: '@6cbc622'
+          touchstone_ref: '@289cfc7'
           benchmarking_repo: ${{ matrix.config.benchmarking_repo }}
           benchmarking_ref: ${{ matrix.config.benchmarking_ref }}
           benchmarking_path: ${{ matrix.config.benchmarking_path }}

NAMESPACE

@@ -187,6 +187,7 @@ importFrom(ggplot2,ggsave)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_color_brewer)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_x_date)
 importFrom(ggplot2,scale_y_continuous)

NEWS.md

@@ -2,6 +2,7 @@
 
 ## Documentation
 
+- The documentation of the `rt` argument has been expanded in the case where `rt = NULL` to make explicit the settings that are applied in that case. By @jamesmbaazam in #779 and reviewed by @sbfnk.
 - The README has been updated to link to the free course on nowcasting and forecasting. The availability of variational inference, Laplace approximation, and Pathfinder through `cmdstanr` has also be surfaced. By @jamesmbaazam in #753 and reviewed by @seabbs.
 - Some implicit argument defaults have been made explicit in the function definition. By @Bisaloo in #729.
 - The installation guide in the README has been updated to provide instructions for configuring the C toolchain of Windows, MacOS, and Linux. By @jamesmbaazam in #707 and reviewed by @sbfnk.
@@ -28,6 +29,7 @@
 ## Package changes
 
 - `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.
 - The use of the `{progressr}` package for displaying progress bars is now optional, as is the use of `{future}` and `{future.apply}` for parallelisation. By @sbfnk in By @sbfnk in
 
 ## Bug fixes

R/create.R

@@ -239,8 +239,10 @@ create_future_rt <- function(future = c("latest", "project", "estimate"),
 #' Takes the output from [rt_opts()] and converts it into a list understood by
 #' stan.
 #' @param rt A list of options as generated by [rt_opts()] defining Rt
-#' estimation. Defaults to [rt_opts()]. Set to `NULL` to switch to using back
-#' calculation rather than generating infections using Rt.
+#' estimation. Defaults to [rt_opts()]. To generate new infections using
+#' the non-mechanistic model instead of the renewal equation model, use
+#' `rt = NULL`. The non-mechanistic model internally uses the setting
+#' `rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")`.
 #'
 #' @param breakpoints An integer vector (binary) indicating the location of
 #' breakpoints.

R/dist_spec.R

@@ -617,6 +617,7 @@ print.dist_spec <- function(x, ...) {
 #'   addition to the probability mass function
 #' @param ... ignored
 #' @importFrom ggplot2 aes geom_col geom_step facet_wrap vars theme_bw
+#' scale_color_brewer
 #' @importFrom data.table data.table rbindlist
 #' @importFrom cli cli_abort
 #' @export
@@ -699,11 +700,12 @@ plot.dist_spec <- function(x, samples = 50L, res = 1, cumulative = TRUE, ...) {
 
   # Plot PMF and CDF as facets in the same plot
   plot <- ggplot(
-    pmf_data, mapping = aes(x = x, y = p, group = sample, linetype = type)
+    pmf_data, mapping = aes(x = x, y = p, group = sample, color = type)
   ) +
     geom_line() +
     facet_wrap(vars(distribution)) +
     labs(x = "x", y = "Probability") +
+    scale_color_brewer(palette = "Dark2") +
     theme_bw()
   if (cumulative) {
     cmf_data <- pmf_data[,

README.Rmd

@@ -167,6 +167,7 @@ you can file an issue [here](https://github.com/epiforecasts/EpiNow2/issues). We
 
 
 
+
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
@@ -183,8 +184,8 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=hsbadr">hsbadr</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=dependabot[bot]">dependabot[bot]</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=pitmonticone">pitmonticone</a>, 
-<a href="https://github.com/epiforecasts/EpiNow2/commits?author=actions-user">actions-user</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=github-actions[bot]">github-actions[bot]</a>, 
+<a href="https://github.com/epiforecasts/EpiNow2/commits?author=actions-user">actions-user</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=ellisp">ellisp</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=jdmunday">jdmunday</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=pearsonca">pearsonca</a>, 
@@ -235,7 +236,8 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 <a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Alorenzwalthert">lorenzwalthert</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Anlinton">nlinton</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Amartinamcm">martinamcm</a>, 
-<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Aadrian-lison">adrian-lison</a>
+<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Aadrian-lison">adrian-lison</a>, 
+<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Akaitejohnson">kaitejohnson</a>
 
 
 
@@ -256,3 +258,4 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 
 
 
+

README.md

@@ -274,8 +274,8 @@ Contributions of any kind are welcome!
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=hsbadr">hsbadr</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=dependabot[bot]">dependabot\[bot\]</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=pitmonticone">pitmonticone</a>,
-<a href="https://github.com/epiforecasts/EpiNow2/commits?author=actions-user">actions-user</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=github-actions[bot]">github-actions\[bot\]</a>,
+<a href="https://github.com/epiforecasts/EpiNow2/commits?author=actions-user">actions-user</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=ellisp">ellisp</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=jdmunday">jdmunday</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=pearsonca">pearsonca</a>,
@@ -323,7 +323,8 @@ Contributions of any kind are welcome!
 <a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Alorenzwalthert">lorenzwalthert</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Anlinton">nlinton</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Amartinamcm">martinamcm</a>,
-<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Aadrian-lison">adrian-lison</a>
+<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Aadrian-lison">adrian-lison</a>,
+<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Akaitejohnson">kaitejohnson</a>
 
 ### Issue Contributors