Merge pull request #329 from epiforecasts/develop

Develop

.devcontainer/Dockerfile

@@ -48,8 +48,8 @@ RUN Rscript -e 'devtools::install_github("milesmcbain/fnmate")'
 RUN Rscript -e 'devtools::install_github("milesmcbain/datapasta")'
 
 # install dependencies
-COPY DESCRIPTION /tmp/package/DESCRIPTION
+COPY . /tmp/package/
 RUN Rscript -e "devtools::install_dev_deps('/tmp/package')"
 
 ## Install the local version of EpiNow2
-Run R CMD INSTALL --no-multiarch --with-keep.source EpiNow2
+Run R CMD INSTALL  --no-multiarch --with-keep.source /tmp/package/

NEWS.md

@@ -2,7 +2,9 @@
 
 This release adds a range of new minor features, squashes bugs, enhances documentation, expands unit testing, implements some minor run-time optimisations, and removes some obsolete features.
 
-Thanks to @Bisaloo, @hsbadr, @LloydChapman, @medewitt, and @sbfnk.
+Thanks to @Bisaloo, @hsbadr, @LloydChapman, @medewitt, and @sbfnk for contributing to this release.
+
+Thanks to @sbfnk, @pearsonca, and @icholasdavies for regression testing this release against `1.3.2`.
 
 ## New features
 

R/adjust.R

@@ -17,6 +17,7 @@
 #' @importFrom data.table setorder data.table data.table 
 #' @importFrom lubridate wday
 #' @examples
+#' \donttest{
 #' # define example cases
 #' cases <- data.table::copy(example_confirmed)[, cases := as.integer(confirm)]
 #'
@@ -65,6 +66,7 @@
 #'   }
 #' )
 #' print(report_stochastic)
+#'}
 adjust_infection_to_report <- function(infections, delay_defs,
                                        reporting_model, reporting_effect,
                                        type = "sample",

R/dist.R

@@ -525,6 +525,7 @@ estimate_delay <- function(delays, ...) {
 #' @importFrom data.table data.table setorder
 #' @importFrom lubridate days
 #' @examples
+#' \donttest{
 #' cases <- example_confirmed
 #' cases <- cases[, cases := as.integer(confirm)]
 #' print(cases)
@@ -576,6 +577,7 @@ estimate_delay <- function(delays, ...) {
 #'   direction = "forwards",
 #'   type = "median"
 #' )
+#'}
 sample_approx_dist <- function(cases = NULL,
                                dist_fn = NULL,
                                max_value = 120,

README.Rmd

@@ -43,7 +43,7 @@ Forecasting is also supported for the time-varying reproduction number, infectio
 A simple example of using the package to estimate a national Rt for Covid-19 can be found [here](https://gist.github.com/seabbs/163d0f195892cde685c70473e1f5e867).
 
 
-`EpiNow2` also supports adjustment for truncated data via `estimate_truncation()` (though users may be interested in more flexibility and if so should check out the [`epinowcast`](https://www.epinowcast.org/epinowcast/) package), and for estimating dependent observations (i.e deaths based on hospital admissions) using `estimate_secondary()`.
+`EpiNow2` also supports adjustment for truncated data via `estimate_truncation()` (though users may be interested in more flexibility and if so should check out the [`epinowcast`](https://package.epinowcast.org/) package), and for estimating dependent observations (i.e deaths based on hospital admissions) using `estimate_secondary()`.
 
 ## Installation