epiforecasts · seabbs · Jul 25, 2024 · Jul 25, 2024 · Jul 25, 2024 · Jul 25, 2024
diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,7 @@
 
 ## Documentation
 
+- 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.
 
 ## Model changes

diff --git a/R/epinow.R b/R/epinow.R
@@ -92,7 +92,7 @@ epinow <- function(data,
                    CrIs = c(0.2, 0.5, 0.9),
                    filter_leading_zeros = TRUE,
                    zero_threshold = Inf,
-                   return_output = FALSE,
+                   return_output = is.null(target_folder),
                    output = c("samples", "plots", "latest", "fit", "timing"),
                    plot_args = list(),
                    target_folder = NULL, target_date,
@@ -116,10 +116,6 @@ epinow <- function(data,
   assert_string(id)
   assert_logical(verbose)
 
-  if (is.null(target_folder)) {
-    return_output <- TRUE
-  }
-
   if (is.null(CrIs) || length(CrIs) == 0 || !is.numeric(CrIs)) {
     futile.logger::flog.fatal(
       "At least one credible interval must be specified",

diff --git a/R/regional_epinow.R b/R/regional_epinow.R
@@ -108,7 +108,7 @@ regional_epinow <- function(data,
                               "regions", "summary", "samples",
                               "plots", "latest"
                             ),
-                            return_output = FALSE,
+                            return_output = is.null(target_folder),
                             summary_args = list(),
                             verbose = FALSE,
                             logs = tempdir(check = TRUE), ...,
@@ -148,7 +148,6 @@ regional_epinow <- function(data,
     futile.logger::flog.info(
       "No target directory specified so returning output"
     )
-    return_output <- TRUE
   } else {
     futile.logger::flog.info("Saving estimates to : %s", target_folder)
   }

diff --git a/R/summarise.R b/R/summarise.R
@@ -26,12 +26,8 @@
 summarise_results <- function(regions,
                               summaries = NULL,
                               results_dir = NULL,
-                              target_date = NULL,
+                              target_date = "latest",
                               region_scale = "Region") {
-  if (is.null(target_date)) {
-    target_date <- "latest"
-  }
-
   if (is.null(results_dir)) {
     if (is.null(summaries)) {
       stop(
@@ -181,7 +177,7 @@ regional_summary <- function(regional_output = NULL,
                              target_date = NULL,
                              region_scale = "Region",
                              all_regions = TRUE,
-                             return_output = FALSE,
+                             return_output = is.null(summary_dir),
                              plot = TRUE,
                              max_plot = 10,
                              ...) {
@@ -190,7 +186,6 @@ regional_summary <- function(regional_output = NULL,
     futile.logger::flog.info(
       "No summary directory specified so returning summary output"
     )
-    return_output <- TRUE
   } else {
     futile.logger::flog.info("Saving summary to : %s", summary_dir)
   }

diff --git a/R/utilities.R b/R/utilities.R
@@ -13,10 +13,7 @@
 #' @importFrom futile.logger flog.info
 #' @return No return value, called for side effects
 #' @export
-clean_nowcasts <- function(date = NULL, nowcast_dir = ".") {
-  if (is.null(date)) {
-    date <- Sys.Date()
-  }
+clean_nowcasts <- function(date = Sys.Date(), nowcast_dir = ".") {
   dirs <- list.dirs(nowcast_dir, recursive = FALSE)
   purrr::walk(
     dirs,

diff --git a/man/clean_nowcasts.Rd b/man/clean_nowcasts.Rd
diff --git a/man/epinow.Rd b/man/epinow.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/summarise_results.Rd b/man/summarise_results.Rd