Change expected type of reported_cases argument to numeric (#594)

* Revise doc to state expected type as numeric not integer * Add NEWS item
epiforecasts · Mar 4, 2024 · c5f2437 · c5f2437
1 parent 9d7c28d
commit c5f2437
Show file tree

Hide file tree

Showing 12 changed files with 12 additions and 11 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -16,6 +16,7 @@
 * Removed references to the no longer existing `forecast_infections` function. By @sbfnk in #460 and reviewed by @seabbs.
 * The contribution guide has been improved to include more detail on ways to contribute new features/enhancements, report bugs, and improve or suggest vignettes. By @jamesmbaazam in #464 and reviewed by @seabbs.
 * Updated the code in `inst/CITATION` and added a GitHub Actions workflow to auto-generate `citation.cff` so that the two citation files are always in sync with `DESCRIPTION`. By @jamesmbazam in #467, with contributions from @Bisaloo, and reviewed by @seabbs and @sbfnk.
+* Updated the documentation of the `reported_cases` argument in `estimate_infections()` and `confirm` column in the `obs` argument of `estimate_truncation()` to allow `numeric` types, not just `integer`. See #594, by @jamesmbaazam, and reviewed by @sbfnk.
 
 ## Package
 

diff --git a/R/estimate_infections.R b/R/estimate_infections.R
@@ -18,7 +18,7 @@
 #' estimate Rt for Covid-19 in a country from the ECDC data source.
 #'
 #' @param reported_cases A `<data.frame>` of confirmed cases (confirm) by date
-#' (date). confirm must be integer and date must be in date format.
+#' (date). confirm must be numeric and date must be in date format.
 #'
 #' @param generation_time A call to [generation_time_opts()] defining the
 #' generation time distribution used. For backwards compatibility a list of

diff --git a/R/estimate_truncation.R b/R/estimate_truncation.R
@@ -34,7 +34,7 @@
 #'  - Truncation is log normally distributed.
 #'
 #' @param obs A list of `<data.frame>`s each containing a date variable
-#' and a confirm (integer) variable. Each data set should be a snapshot
+#' and a confirm (numeric) variable. Each data set should be a snapshot
 #' of the reported data over time. All data sets must contain a complete vector
 #' of dates.
 #'

diff --git a/man/create_clean_reported_cases.Rd b/man/create_clean_reported_cases.Rd
diff --git a/man/create_shifted_cases.Rd b/man/create_shifted_cases.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/estimate_truncation.Rd b/man/estimate_truncation.Rd
diff --git a/man/save_input.Rd b/man/save_input.Rd
diff --git a/man/setup_dt.Rd b/man/setup_dt.Rd
diff --git a/man/update_horizon.Rd b/man/update_horizon.Rd