Make rt=NULL settings explicit (#779)

* Make rt=NULL settings explicit * Add NEWS item * Add reviewer Co-authored-by: Sebastian Funk <[email protected]> * Rephrase and change "back calculaltion" to non-mechanistic --------- Co-authored-by: Sebastian Funk <[email protected]>
epiforecasts · Sep 24, 2024 · b806ef1 · b806ef1
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diff --git a/NEWS.md b/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.

diff --git a/R/create.R b/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.

diff --git a/man/create_rt_data.Rd b/man/create_rt_data.Rd
diff --git a/man/create_stan_data.Rd b/man/create_stan_data.Rd
diff --git a/man/epinow.Rd b/man/epinow.Rd
diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd
diff --git a/man/get_seeding_time.Rd b/man/get_seeding_time.Rd
diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
diff --git a/man/run_region.Rd b/man/run_region.Rd