feat: add fill argument to incidence() for use when complete_dates TRUE

NAMESPACE

@@ -86,5 +86,6 @@ importFrom(tidyr,unnest)
 importFrom(tidyr,unpack)
 importFrom(ympes,assert_bool)
 importFrom(ympes,assert_scalar_character)
+importFrom(ympes,assert_scalar_numeric)
 importFrom(ympes,assert_scalar_numeric_not_na)
 importFrom(ympes,assert_scalar_whole)

NEWS.md

@@ -1,5 +1,12 @@
 # incidence2 (development version)
 
+- `incidence()` gains a `fill` parameter. This is passed to `complete_dates()`
+  so is only valid when the argument `complete_dates = TRUE`.
+
+- For convenience we now reexport `select()` from
+  [dplyr](https://cran.r-project.org/package=dplyr) as well as 
+  `unnest()` and `unpack()` from [tidyr](https://cran.r-project.org/package=tidyr).
+
 # incidence2 2.3.1
 
 - Temporarily remove the [ympes](https://cran.r-project.org/package=ympes)

R/assertions.R

@@ -17,6 +17,16 @@
     )
 }
 
+# -------------------------------------------------------------------------
+.assert_scalar_numeric <- function(x) {
+    assert_scalar_numeric(
+        x,
+        .arg = deparse(substitute(x)),
+        .call = sys.call(-1L),
+        .subclass = NULL
+    )
+}
+
 # -------------------------------------------------------------------------
 .assert_scalar_numeric_not_na <- function(x) {
     assert_scalar_numeric_not_na(

R/incidence.R

@@ -129,14 +129,23 @@
 #'
 #' Should the resulting object have the same range of dates for each grouping.
 #'
-#' Missing counts will be filled with `0L`.
+#' Missing counts will be filled with `0L` unless the `fill` argument is
+#' provided (and this value will take precedence).
 #'
 #' Will attempt to use `function(x) seq(min(x), max(x), by = 1)` on the
 #' resultant date_index column to generate a complete sequence of dates.
 #'
 #' More flexible completion is possible by using the `complete_dates()`
 #' function.
 #'
+#' @param fill `numeric`.
+#'
+#' Only applicable when `complete_dates = TRUE`.
+#'
+#' The value to replace missing counts caused by completing dates.
+#'
+#' If unset then will default to `0L`.
+#'
 #' @param ...
 #'
 #' Not currently used.
@@ -176,6 +185,7 @@ incidence <- function(
     interval = NULL,
     offset = NULL,
     complete_dates = FALSE,
+    fill = 0L,
     ...
 ) {
 
@@ -464,7 +474,16 @@ incidence <- function(
 
     # complete dates if flag set
     # TODO - this could be more efficient but this is safest for now
-    if (complete_dates) complete_dates(out) else out
+    if (complete_dates) {
+        if (missing(fill))
+            fill <- 0L
+        .assert_scalar_numeric(fill)
+        out <- complete_dates(out, fill = fill)
+    } else if (!missing(fill)) {
+        .stop_argument("`fill` can only be given when `complete_dates = TRUE`.")
+    }
+
+    out
 }
 
 

R/incidence2-package.R

@@ -7,5 +7,6 @@ NULL
 
 #' @rawNamespace import(data.table, except = c(isoweek, year))
 #' @import grates
-#' @importFrom ympes assert_bool assert_scalar_character assert_scalar_numeric_not_na assert_scalar_whole
+#' @importFrom ympes assert_bool assert_scalar_character assert_scalar_whole
+#' @importFrom ympes assert_scalar_numeric assert_scalar_numeric_not_na
 NULL

tests/testthat/test-incidence.R

@@ -476,7 +476,11 @@ test_that("miscellaneous incidence error messaging works as expected", {
         fixed = TRUE
     )
 
-
+    expect_error(
+        incidence(dat, c("dates","dates2"), fill = 9),
+        "`fill` can only be given when `complete_dates = TRUE`.",
+        fixed = TRUE
+    )
 
 
 })