From b806ef141ae106d30e71304a0d0169820ae562a5 Mon Sep 17 00:00:00 2001 From: James Azam Date: Tue, 24 Sep 2024 09:22:00 +0100 Subject: [PATCH] Make `rt=NULL` settings explicit (#779) * Make rt=NULL settings explicit * Add NEWS item * Add reviewer Co-authored-by: Sebastian Funk * Rephrase and change "back calculaltion" to non-mechanistic --------- Co-authored-by: Sebastian Funk --- NEWS.md | 1 + R/create.R | 6 ++++-- man/create_rt_data.Rd | 6 ++++-- man/create_stan_data.Rd | 6 ++++-- man/epinow.Rd | 6 ++++-- man/estimate_infections.Rd | 6 ++++-- man/get_seeding_time.Rd | 6 ++++-- man/regional_epinow.Rd | 6 ++++-- man/run_region.Rd | 6 ++++-- 9 files changed, 33 insertions(+), 16 deletions(-) diff --git a/NEWS.md b/NEWS.md index bfdda9550..1c9450d90 100644 --- 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 index 154b28b86..6e0cf94e1 100644 --- 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 index 3c5233795..8349db1cf 100644 --- a/man/create_rt_data.Rd +++ b/man/create_rt_data.Rd @@ -8,8 +8,10 @@ create_rt_data(rt = rt_opts(), breakpoints = NULL, delay = 0, horizon = 0) } \arguments{ \item{rt}{A list of options as generated by \code{\link[=rt_opts]{rt_opts()}} defining Rt -estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. Set to \code{NULL} to switch to using back -calculation rather than generating infections using Rt.} +estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. To generate new infections using +the non-mechanistic model instead of the renewal equation model, use +\code{rt = NULL}. The non-mechanistic model internally uses the setting +\code{rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")}.} \item{breakpoints}{An integer vector (binary) indicating the location of breakpoints.} diff --git a/man/create_stan_data.Rd b/man/create_stan_data.Rd index e755fca8d..ed80f379e 100644 --- a/man/create_stan_data.Rd +++ b/man/create_stan_data.Rd @@ -23,8 +23,10 @@ create_stan_data( \code{\link[=get_seeding_time]{get_seeding_time()}}.} \item{rt}{A list of options as generated by \code{\link[=rt_opts]{rt_opts()}} defining Rt -estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. Set to \code{NULL} to switch to using back -calculation rather than generating infections using Rt.} +estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. To generate new infections using +the non-mechanistic model instead of the renewal equation model, use +\code{rt = NULL}. The non-mechanistic model internally uses the setting +\code{rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")}.} \item{gp}{A list of options as generated by \code{\link[=gp_opts]{gp_opts()}} to define the Gaussian process. Defaults to \code{\link[=gp_opts]{gp_opts()}}. Set to \code{NULL} to disable the diff --git a/man/epinow.Rd b/man/epinow.Rd index fd9b70b3c..6046dea56 100644 --- a/man/epinow.Rd +++ b/man/epinow.Rd @@ -49,8 +49,10 @@ used as the \code{truncation} argument here, thereby propagating the uncertainty in the estimate.} \item{rt}{A list of options as generated by \code{\link[=rt_opts]{rt_opts()}} defining Rt -estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. Set to \code{NULL} to switch to using back -calculation rather than generating infections using Rt.} +estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. To generate new infections using +the non-mechanistic model instead of the renewal equation model, use +\code{rt = NULL}. The non-mechanistic model internally uses the setting +\code{rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")}.} \item{backcalc}{A list of options as generated by \code{\link[=backcalc_opts]{backcalc_opts()}} to define the back calculation. Defaults to \code{\link[=backcalc_opts]{backcalc_opts()}}.} diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd index f77981a07..cab919f85 100644 --- a/man/estimate_infections.Rd +++ b/man/estimate_infections.Rd @@ -45,8 +45,10 @@ used as the \code{truncation} argument here, thereby propagating the uncertainty in the estimate.} \item{rt}{A list of options as generated by \code{\link[=rt_opts]{rt_opts()}} defining Rt -estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. Set to \code{NULL} to switch to using back -calculation rather than generating infections using Rt.} +estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. To generate new infections using +the non-mechanistic model instead of the renewal equation model, use +\code{rt = NULL}. The non-mechanistic model internally uses the setting +\code{rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")}.} \item{backcalc}{A list of options as generated by \code{\link[=backcalc_opts]{backcalc_opts()}} to define the back calculation. Defaults to \code{\link[=backcalc_opts]{backcalc_opts()}}.} diff --git a/man/get_seeding_time.Rd b/man/get_seeding_time.Rd index e240824fa..9be232e89 100644 --- a/man/get_seeding_time.Rd +++ b/man/get_seeding_time.Rd @@ -16,8 +16,10 @@ details.} For backwards compatibility a list of summary parameters can also be passed.} \item{rt}{A list of options as generated by \code{\link[=rt_opts]{rt_opts()}} defining Rt -estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. Set to \code{NULL} to switch to using back -calculation rather than generating infections using Rt.} +estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. To generate new infections using +the non-mechanistic model instead of the renewal equation model, use +\code{rt = NULL}. The non-mechanistic model internally uses the setting +\code{rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")}.} } \value{ An integer seeding time diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd index 64b150922..67ab215c5 100644 --- a/man/regional_epinow.Rd +++ b/man/regional_epinow.Rd @@ -48,8 +48,10 @@ used as the \code{truncation} argument here, thereby propagating the uncertainty in the estimate.} \item{rt}{A list of options as generated by \code{\link[=rt_opts]{rt_opts()}} defining Rt -estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. Set to \code{NULL} to switch to using back -calculation rather than generating infections using Rt.} +estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. To generate new infections using +the non-mechanistic model instead of the renewal equation model, use +\code{rt = NULL}. The non-mechanistic model internally uses the setting +\code{rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")}.} \item{backcalc}{A list of options as generated by \code{\link[=backcalc_opts]{backcalc_opts()}} to define the back calculation. Defaults to \code{\link[=backcalc_opts]{backcalc_opts()}}.} diff --git a/man/run_region.Rd b/man/run_region.Rd index 802b7b8f3..078a301d6 100644 --- a/man/run_region.Rd +++ b/man/run_region.Rd @@ -46,8 +46,10 @@ used as the \code{truncation} argument here, thereby propagating the uncertainty in the estimate.} \item{rt}{A list of options as generated by \code{\link[=rt_opts]{rt_opts()}} defining Rt -estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. Set to \code{NULL} to switch to using back -calculation rather than generating infections using Rt.} +estimation. Defaults to \code{\link[=rt_opts]{rt_opts()}}. To generate new infections using +the non-mechanistic model instead of the renewal equation model, use +\code{rt = NULL}. The non-mechanistic model internally uses the setting +\code{rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0")}.} \item{backcalc}{A list of options as generated by \code{\link[=backcalc_opts]{backcalc_opts()}} to define the back calculation. Defaults to \code{\link[=backcalc_opts]{backcalc_opts()}}.}