Merge branch 'main' into future-detect

.github/workflows/synthetic-validation.yaml

@@ -1,26 +1,34 @@
 name: "Synthetic validation check"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
 on:
-  push:
-    branches:
-      - main
-      - master
-      - develop
   pull_request:
-    branches:
-      - main
-      - master
-      - develop
+    paths:
+      # Directories with stan code and benchmarking code
+      - "inst/stan/**"
+      - "inst/dev/recover-synthetic/*"
+      # Benchmarking config file
+      - ".github/workflows/synthetic-validation.yaml"
+      # Manual trigger
+      - ".synthetic"
   workflow_dispatch:
 
 jobs:
-  synthetic-valiation:
+  synthetic-validation:
     runs-on: macos-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@master
 
-      - uses: r-lib/actions/setup-r@v2
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -30,12 +38,17 @@ jobs:
             here
             scoringutils
             loo
+            data.table
+            rstan
+            any::rmarkdown
             matrixStats
             local::.
       - name: Run synthetic validation
         run: |
-          source("inst/dev/recover-synthetic/rt.R")
-        shell: Rscript {0}
+          Rscript -e '
+          source("inst/dev/recover-synthetic/rt.R") 
+          source("inst/dev/recover-synthetic/eval_rt.R") 
+          '
 
       - name: Upload validation figures
         uses: actions/upload-artifact@v4
@@ -50,3 +63,29 @@ jobs:
           name: fits
           retention-days: 5
           path: synthetic.rds
+
+      - name: Render synthetic recovery md
+        run: |
+          rmarkdown::render("inst/dev/synthetic_recovery.md")
+        shell: Rscript {0}
+
+      - name: Upload markdown
+        uses: actions/upload-artifact@v4
+        with:
+          name: synthetic_recovery
+          retention-days: 5
+          path: inst/dev/synthetic_recovery.html
+
+      - name: Post the artifact
+        uses: CDCgov/cfa-actions/post-artifact@main
+        if: ${{ github.event_name == 'pull_request' }}
+        with:
+          artifact-name: synthetic_recovery
+          gh-token: ${{ secrets.GITHUB_TOKEN }}
+          message: 'Thank you for your contribution ${{ github.actor }} :rocket:! Your { artifact-name } markdown is ready for download :point_right: [here]({ artifact-url }) :point_left:!'
+
+
+
+
+
+

NEWS.md

@@ -33,6 +33,7 @@
 - Brought the docs on `alpha_sd` up to date with the code change from prior PR #853. By @zsusswein in #862 and reviewed by @jamesmbaazam.
 - The `...` argument in `estimate_secondary()` has been removed because it was not used. By @jamesmbaazam in #894 and reviewed by @.
 - All examples now use the natural parameters of distributions rather than the mean and standard deviation when specifying uncertain distributions. This is to eliminate warnings and encourage best practice. By @jamesmbaazam in #893 and reviewed by @sbfnk.
+- The ways that `dist_spec()` with certain/uncertain parameters can be constrained has been clarified. By @sbfnk in #940 and reviewed by @jamesmbaazam.
 
 # EpiNow2 1.6.1
 

R/checks.R

@@ -111,9 +111,10 @@ check_stan_delay <- function(dist) {
   if (any(is.infinite(max(dist))) && !(attr(dist, "cdf_cutoff") > 0)) {
     cli_abort(
       c(
-        "i" = "All distribution passed to the model need to have a
+        "i" = "All distributions passed to the model need to have a
       {col_blue(\"finite maximum\")}, which can be achieved either by
-      setting {.var max} or non-zero {.var cdf_cutoff}."
+      setting {.var max} or, if using a distribution with fixed parameters,
+      non-zero {.var cdf_cutoff}."
       )
     )
   }

R/dist_spec.R

@@ -751,8 +751,8 @@ plot.dist_spec <- function(x, samples = 50L, res = 1, cumulative = TRUE, ...) {
             c(
               "!" = "All distributions in {.var x} must have a finite
               maximum value.",
-              "i" = "You can set a finite maximum either as an
-              argument to {.fn plot} or when defining the distribution."
+              "i" = "You can set a finite maximum or CDF cutoff
+              when defining the distribution."
             )
           )
         }

R/estimate_infections.R

@@ -17,7 +17,7 @@
 #' for an example of using `estimate_infections` within the `epinow` wrapper to
 #' estimate Rt for Covid-19 in a country from the ECDC data source.
 #'
-#' @param data A `<data.frame>` of confirmed cases (confirm) by date (date).
+#' @param data A `<data.frame>` of disease reports (confirm) by date (date).
 #' `confirm` must be numeric and `date` must be in date format. Optionally
 #' this can also have a logical `accumulate` column which indicates whether
 #' data should be added to the next data point. This is useful when modelling

R/estimate_truncation.R

@@ -318,7 +318,7 @@ plot.estimate_truncation <- function(x, ...) {
   plot <- plot +
     ggplot2::theme_bw() +
     ggplot2::labs(
-      y = "Confirmed Cases", x = "Date", col = "Type", fill = "Type"
+      y = "Reports", x = "Date", col = "Type", fill = "Type"
     ) +
     ggplot2::scale_x_date(date_breaks = "day", date_labels = "%b %d") +
     ggplot2::scale_y_continuous(labels = scales::comma) +

R/opts.R

@@ -1197,7 +1197,8 @@ filter_opts <- function(opts, region) {
 #' @param dist A <dist_spec>
 #' @param default_cdf_cutoff Numeric; default CDF cutoff to be used if an
 #'   unconstrained distribution is passed as `dist`. If `dist` is already
-#'   constrained by having a maximum or CDF cutoff this is ignored.
+#'   constrained by having a maximum or CDF cutoff this is ignored. Note that
+#'   this can only be done for <dist_spec> objects with fixed parameters.
 #' @param cdf_cutoff_set Logical; whether the default CDF cutoff has been set by
 #'   the user; if yes and `dist` is constrained a warning is issued
 #' @importFrom cli cli_inform cli_warn

R/regional_epinow.R

@@ -20,7 +20,7 @@
 #' using [progressr::handlers()] and enable it in batch by setting
 #' `R_PROGRESSR_ENABLE=TRUE` as an environment variable.
 #'
-#' @param data A `<data.frame>` of confirmed cases (confirm) by date
+#' @param data A `<data.frame>` of disease reports (confirm) by date
 #' (date), and region (`region`).
 #'
 #' @param reported_cases Deprecated; use `data` instead.

README.Rmd

@@ -163,11 +163,12 @@ you can file an issue [here](https://github.com/epiforecasts/EpiNow2/issues). We
 ## Contributors
 
 
+
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
 
-All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
+All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [allcontributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
 
 ### Code
 
@@ -181,16 +182,17 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 <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=kaitejohnson">kaitejohnson</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=pearsonca">pearsonca</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=JAllen42">JAllen42</a>, 
-<a href="https://github.com/epiforecasts/EpiNow2/commits?author=kaitejohnson">kaitejohnson</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=adamkucharski">adamkucharski</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=andrjohns">andrjohns</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=Bisaloo">Bisaloo</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=LloydChapman">LloydChapman</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=medewitt">medewitt</a>, 
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=nikosbosse">nikosbosse</a>, 
-<a href="https://github.com/epiforecasts/EpiNow2/commits?author=sophiemeakin">sophiemeakin</a>
+<a href="https://github.com/epiforecasts/EpiNow2/commits?author=sophiemeakin">sophiemeakin</a>, 
+<a href="https://github.com/epiforecasts/EpiNow2/commits?author=zsusswein">zsusswein</a>
 
 
 
@@ -231,7 +233,7 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 <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%3Azsusswein">zsusswein</a>
+<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Amicahwiesner67">micahwiesner67</a>
 
 
 
@@ -250,3 +252,4 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
 
+

README.md

@@ -257,7 +257,7 @@ guide](https://github.com/epiforecasts/EpiNow2/blob/main/.github/CONTRIBUTING.md
 
 All contributions to this project are gratefully acknowledged using the
 [`allcontributors` package](https://github.com/ropensci/allcontributors)
-following the [all-contributors](https://allcontributors.org)
+following the [allcontributors](https://allcontributors.org)
 specification. Contributions of any kind are welcome!
 
 ### Code
@@ -271,16 +271,17 @@ specification. Contributions of any kind are welcome!
 <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=kaitejohnson">kaitejohnson</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=pearsonca">pearsonca</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=JAllen42">JAllen42</a>,
-<a href="https://github.com/epiforecasts/EpiNow2/commits?author=kaitejohnson">kaitejohnson</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=adamkucharski">adamkucharski</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=andrjohns">andrjohns</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=Bisaloo">Bisaloo</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=LloydChapman">LloydChapman</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=medewitt">medewitt</a>,
 <a href="https://github.com/epiforecasts/EpiNow2/commits?author=nikosbosse">nikosbosse</a>,
-<a href="https://github.com/epiforecasts/EpiNow2/commits?author=sophiemeakin">sophiemeakin</a>
+<a href="https://github.com/epiforecasts/EpiNow2/commits?author=sophiemeakin">sophiemeakin</a>,
+<a href="https://github.com/epiforecasts/EpiNow2/commits?author=zsusswein">zsusswein</a>
 
 ### Issue Authors
 
@@ -318,7 +319,7 @@ specification. Contributions of any kind are welcome!
 <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%3Azsusswein">zsusswein</a>
+<a href="https://github.com/epiforecasts/EpiNow2/issues?q=is%3Aissue+author%3Amicahwiesner67">micahwiesner67</a>
 
 ### Issue Contributors
 

inst/dev/recover-synthetic/plot.R

@@ -17,7 +17,8 @@ save_ggplot <- function(plot, name, prefix = "") {
   ggplot2::ggsave(
     here::here("inst", "dev", "figs", paste0(prefix, name, ".png")),
     plot,
-    dpi = 300, width = 9, height = 6
+    dpi = 300, width = 9, height = 6,
+    create.dir = TRUE
   )
 }
 

inst/dev/synthetic_recovery.md

@@ -0,0 +1,32 @@
+# Synthetic Recovery visual results
+
+This file combines the figures generated in `rt.R` into a single file, used to 
+confirm that the fits to synthetic data with different EpiNow2
+specifications work as expected. 
+
+In all figures, the black dots indicate the ground truth R(t) estimate, used to 
+generate the synthetic data used for model fitting. 
+
+### Estimate from the default Gaussian Process settings using the No-U-Turn (NUTS) sampler
+![](./figs/rt_gp_nuts.png)
+![](./figs/inf_gp_nuts.png)
+
+### Estimate from back-calculation
+![](./figs/rt_backcalc_nuts.png)
+![](./figs/inf_backcalc_nuts.png)
+
+### Estimate from a weekly random walk, with no Gaussian process
+![](./figs/rt_weekly_rw_nuts.png)
+![](./figs/inf_weekly_rw_nuts.png)
+
+### Estimate from a monthly random walk + a stationary Gaussian process
+![](./figs/rt_gp_rw_nuts.png)
+![](./figs/inf_gp_rw_nuts.png)
+
+
+### Comparison of different model specs
+CRPS over time evaluated against known R(t)
+![](./figs/rt_crps.png)
+CRPS over time evaluated against infections
+![](./figs/inf_crps.png)
+