remove references to "confirmed" cases (#936)

epiforecasts · Jan 30, 2025 · b1771c9 · b1771c9
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Showing 25 changed files with 29 additions and 30 deletions.
diff --git a/R/estimate_infections.R b/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

diff --git a/R/estimate_truncation.R b/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) +

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

diff --git a/man/add_breakpoints.Rd b/man/add_breakpoints.Rd
diff --git a/man/apply_zero_threshold.Rd b/man/apply_zero_threshold.Rd
diff --git a/man/clean_regions.Rd b/man/clean_regions.Rd
diff --git a/man/create_clean_reported_cases.Rd b/man/create_clean_reported_cases.Rd
diff --git a/man/create_forecast_data.Rd b/man/create_forecast_data.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/default_fill_missing_obs.Rd b/man/default_fill_missing_obs.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/filter_leading_zeros.Rd b/man/filter_leading_zeros.Rd
diff --git a/man/forecast_opts.Rd b/man/forecast_opts.Rd
diff --git a/man/get_regions_with_most_reports.Rd b/man/get_regions_with_most_reports.Rd
diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
diff --git a/man/regional_summary.Rd b/man/regional_summary.Rd
diff --git a/man/run_region.Rd b/man/run_region.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/setup_future.Rd b/man/setup_future.Rd
diff --git a/man/update_horizon.Rd b/man/update_horizon.Rd
diff --git a/vignettes/estimate_infections_workflow.Rmd b/vignettes/estimate_infections_workflow.Rmd
@@ -21,7 +21,7 @@ See other vignettes for a more thorough exploration of [alternative model varian
 # Data
 
 Obtaining a good and full understanding of the data being used is an important first step in any inference procedure such as the one applied here. 
-_EpiNow2_ expects data in the format of a data frame with two columns, `date` and `confirm`, where `confirm` stands for the number of confirmed counts - although in reality this can be applied to any data including suspected cases and lab-confirmed outcomes.
+_EpiNow2_ expects data in the format of a data frame with two columns, `date` and `confirm`, where `confirm` stands for the number of reports - which could be confirmed case counts although in reality this can be applied to any data including suspected cases and lab-confirmed outcomes.
 The user might already have the data as such a time series provided, for example, on public dashboards or directly from public health authorities.
 Alternatively, they can be constructed from individual-level data, for example using the [incidence2](https://CRAN.R-project.org/package=incidence2) R package.
 An example data set called `example_confirmed`  is included in the package:

diff --git a/vignettes/estimate_infections_workflow.Rmd.orig b/vignettes/estimate_infections_workflow.Rmd.orig
@@ -30,7 +30,7 @@ See other vignettes for a more thorough exploration of [alternative model varian
 # Data
 
 Obtaining a good and full understanding of the data being used is an important first step in any inference procedure such as the one applied here. 
-_EpiNow2_ expects data in the format of a data frame with two columns, `date` and `confirm`, where `confirm` stands for the number of confirmed counts - although in reality this can be applied to any data including suspected cases and lab-confirmed outcomes.
+_EpiNow2_ expects data in the format of a data frame with two columns, `date` and `confirm`, where `confirm` stands for the number of reports - which could be confirmed case counts although in reality this can be applied to any data including suspected cases and lab-confirmed outcomes.
 The user might already have the data as such a time series provided, for example, on public dashboards or directly from public health authorities.
 Alternatively, they can be constructed from individual-level data, for example using the [incidence2](https://CRAN.R-project.org/package=incidence2) R package.
 An example data set called `example_confirmed`  is included in the package: