Helper fns support start dates

R/helpers.R

@@ -235,7 +235,7 @@ new_infections <- function(data,
  )
  checkmate::assert_names(
  colnames(data),
- must.include = c("time", "demography_group", "compartment", "value")
+ must.include = c("time", "date", "demography_group", "compartment", "value")
  )
  checkmate::assert_character(
  compartments_from_susceptible,
@@ -256,7 +256,7 @@ new_infections <- function(data,
  # cast data wide, this makes a copy
  data <- data.table::dcast(
  data,
- time + demography_group ~ compartment,
+ time + date + demography_group ~ compartment,
  value.var = "value"
  )
 
@@ -281,9 +281,11 @@ new_infections <- function(data,
  # return data in long format, by demographic group by default,
  # or aggregated otherwise; do not return other compartments
  # subsetting below creates a copy - input `data` is safe
- data <- data[, c("time", "demography_group", "new_infections")]
+ data <- data[, c("time", "date", "demography_group", "new_infections")]
  if (!by_group) {
- data <- data[, list(new_infections = sum(new_infections)), by = "time"]
+ data <- data[, list(
+ new_infections = sum(new_infections)
+ ), by = c("time", "date")]
  }
 
  # return data

R/tools.R

@@ -25,7 +25,7 @@
  # basic input checking only
  stopifnot(
  "`x` must be a list with vector elements" =
- is.list(x) && all(vapply(x, is.vector, TRUE))
+ checkmate::test_list(x, types = c("numeric", "Date"))
  )
  lens <- lengths(x)
  not_scalar <- lens != 1L