Add checks & test for additional_metadata format in epi_df

[mgyliu]

Action items

• Update examples in as_epi-df so that additional_metadata is always a list() type.
• Add example in as_epi_df with multiple other_keys

Related to issue cmu-delphi/epipredict#114

The problem

other_keys gets stored differently in epi_df if you initialize it as a vector vs. a list. The epi_df constructor expects additional_metadata to be a list but passing a vector still "works" (i.e., no error). Examples are shown below for each case. The examples are taken from the as_epi-df reference.

library(dplyr)
library(recipes)
library(epiprocess)

Example 1

ex1_input <- tibble::tibble(
  geo_value = rep(c("ca", "fl", "pa"), each = 2),
  county_code = c("06059","06061","06067",
                  "12111","12113","12117"),
  another_key = 1:6, # <- I added this additional key 
  time_value = rep(seq(as.Date("2020-06-01"), as.Date("2020-06-03"),
                       by = "day"), length.out = length(geo_value)),
  value = 1:length(geo_value) + 0.01 * rnorm(length(geo_value))) %>% 
  tsibble::as_tsibble(
    index = time_value, 
    key = c(geo_value, county_code, another_key))

# The `other_keys` metadata (`"county_code"` in this case) is automatically
# inferred from the `tsibble`'s `key`:
ex1 <- as_epi_df(x = ex1_input, geo_type = "state", time_type = "day", as_of = "2020-06-03")
attr(ex1,"metadata")

Output:

$geo_type
[1] "state"

$time_type
[1] "day"

$as_of
[1] "2020-06-03"

$other_keys
[1] "county_code" "another_key"

Example 2 (but ex3 from the as_epi_df documentation so we'll keep the names)

ex3_input <- jhu_csse_county_level_subset %>%
  dplyr::filter(time_value > "2021-12-01", state_name == "Massachusetts") %>%
  dplyr::slice_tail(n = 6) %>% 
  tsibble::as_tsibble() %>% # needed to add the additional metadata
  dplyr::mutate(state = rep("MA",6)) %>%
  dplyr::mutate(pol = rep(c("blue", "swing", "swing"), each = 2)) # extra key

# Note: additional_metadata is vector, not list
ex3 <- ex3_input %>%  as_epi_df(additional_metadata = c(other_keys = c("state", "pol")))
attr(ex3,"metadata")

Output:

$geo_type
[1] "county"

$time_type
[1] "day"

$as_of
[1] "2022-08-02 15:31:30 PDT"

$other_keys1
[1] "state"

$other_keys2
[1] "pol"

[mgyliu]

Closed via. PR #183