time_type is getting nulled (possibly with rename) #682
Description
time_type gets nulled when (possibly) using rename. In my initial attempt to reproduce the error, it appears to work fine.
devtools::load_all(".")
#> ℹ Loading epiprocess
#> Loading required package: epidatasets
#>
#> Registered S3 method overwritten by 'tsibble':
#> method from
#> as_tibble.grouped_df dplyr
library(dplyr)
#>
#> Attaching package: 'dplyr'
#>
#> The following object is masked from 'package:epiprocess':
#>
#> between
#>
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#>
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(tibble)
# Create weekly data but label it as 'daily' ----
dates <- seq(as.Date("2020-01-01"), by = "week", length.out = 10)
edf_weekly <- tibble(
geo_value = "ca",
age = c(rep("1-5", 10), rep(">=5", 10)),
time_value = rep(dates, 2),
value = 1:20
) %>%
as_epi_df(other_keys = "age")
## Verify initial metadata
print(attr(edf_weekly, "metadata"))
#> $geo_type
#> [1] "state"
#>
#> $time_type
#> [1] "week"
#>
#> $as_of
#> [1] "2025-12-17 17:37:43 PST"
#>
#> $other_keys
#> [1] "age"
## Force time_type to 'day'
attr(edf_weekly, "metadata")$time_type <- "day"
## epi_slide on the original object
edf_weekly |>
epi_slide(cases_7sd = mean(value, na.rm = TRUE), .window_size = 14)
#> An `epi_df` object, 20 x 5 with metadata:
#> * geo_type = state
#> * time_type = day
#> * other_keys = age
#> * as_of = 2025-12-17 17:37:43.695804
#>
#> # A tibble: 20 × 5
#> geo_value age time_value value cases_7sd
#> <chr> <chr> <date> <int> <dbl>
#> 1 ca 1-5 2020-01-01 1 1
#> 2 ca 1-5 2020-01-08 2 1.5
#> 3 ca 1-5 2020-01-15 3 2.5
#> 4 ca 1-5 2020-01-22 4 3.5
#> 5 ca 1-5 2020-01-29 5 4.5
#> 6 ca 1-5 2020-02-05 6 5.5
#> 7 ca 1-5 2020-02-12 7 6.5
#> 8 ca 1-5 2020-02-19 8 7.5
#> 9 ca 1-5 2020-02-26 9 8.5
#> 10 ca 1-5 2020-03-04 10 9.5
#> 11 ca >=5 2020-01-01 11 11
#> 12 ca >=5 2020-01-08 12 11.5
#> 13 ca >=5 2020-01-15 13 12.5
#> 14 ca >=5 2020-01-22 14 13.5
#> 15 ca >=5 2020-01-29 15 14.5
#> 16 ca >=5 2020-02-05 16 15.5
#> 17 ca >=5 2020-02-12 17 16.5
#> 18 ca >=5 2020-02-19 18 17.5
#> 19 ca >=5 2020-02-26 19 18.5
#> 20 ca >=5 2020-03-04 20 19.5Works well
# Test Rename (Ungrouped) ---
## 'value' -> 'val'
(res_select <- edf_weekly %>% rename(val = value))
#> An `epi_df` object, 20 x 4 with metadata:
#> * geo_type = state
#> * time_type = day
#> * other_keys = age
#> * as_of = 2025-12-17 17:37:43.695804
#>
#> # A tibble: 20 × 4
#> geo_value age time_value val
#> * <chr> <chr> <date> <int>
#> 1 ca 1-5 2020-01-01 1
#> 2 ca 1-5 2020-01-08 2
#> 3 ca 1-5 2020-01-15 3
#> 4 ca 1-5 2020-01-22 4
#> 5 ca 1-5 2020-01-29 5
#> 6 ca 1-5 2020-02-05 6
#> 7 ca 1-5 2020-02-12 7
#> 8 ca 1-5 2020-02-19 8
#> 9 ca 1-5 2020-02-26 9
#> 10 ca 1-5 2020-03-04 10
#> 11 ca >=5 2020-01-01 11
#> 12 ca >=5 2020-01-08 12
#> 13 ca >=5 2020-01-15 13
#> 14 ca >=5 2020-01-22 14
#> 15 ca >=5 2020-01-29 15
#> 16 ca >=5 2020-02-05 16
#> 17 ca >=5 2020-02-12 17
#> 18 ca >=5 2020-02-19 18
#> 19 ca >=5 2020-02-26 19
#> 20 ca >=5 2020-03-04 20Correctly renamed
## Check if epi_slide still works on the renamed object
res_select |>
epi_slide(cases_7sd = mean(val, na.rm = TRUE), .window_size = 14)
#> An `epi_df` object, 20 x 5 with metadata:
#> * geo_type = state
#> * time_type = day
#> * other_keys = age
#> * as_of = 2025-12-17 17:37:43.695804
#>
#> # A tibble: 20 × 5
#> geo_value age time_value val cases_7sd
#> <chr> <chr> <date> <int> <dbl>
#> 1 ca 1-5 2020-01-01 1 1
#> 2 ca 1-5 2020-01-08 2 1.5
#> 3 ca 1-5 2020-01-15 3 2.5
#> 4 ca 1-5 2020-01-22 4 3.5
#> 5 ca 1-5 2020-01-29 5 4.5
#> 6 ca 1-5 2020-02-05 6 5.5
#> 7 ca 1-5 2020-02-12 7 6.5
#> 8 ca 1-5 2020-02-19 8 7.5
#> 9 ca 1-5 2020-02-26 9 8.5
#> 10 ca 1-5 2020-03-04 10 9.5
#> 11 ca >=5 2020-01-01 11 11
#> 12 ca >=5 2020-01-08 12 11.5
#> 13 ca >=5 2020-01-15 13 12.5
#> 14 ca >=5 2020-01-22 14 13.5
#> 15 ca >=5 2020-01-29 15 14.5
#> 16 ca >=5 2020-02-05 16 15.5
#> 17 ca >=5 2020-02-12 17 16.5
#> 18 ca >=5 2020-02-19 18 17.5
#> 19 ca >=5 2020-02-26 19 18.5
#> 20 ca >=5 2020-03-04 20 19.5Still working
## Rename other key 'age' -> 'age_group'
(res_select <- edf_weekly %>% rename(age_group = age))
#> An `epi_df` object, 20 x 4 with metadata:
#> * geo_type = state
#> * time_type = day
#> * other_keys = age_group
#> * as_of = 2025-12-17 17:37:43.695804
#>
#> # A tibble: 20 × 4
#> geo_value age_group time_value value
#> * <chr> <chr> <date> <int>
#> 1 ca 1-5 2020-01-01 1
#> 2 ca 1-5 2020-01-08 2
#> 3 ca 1-5 2020-01-15 3
#> 4 ca 1-5 2020-01-22 4
#> 5 ca 1-5 2020-01-29 5
#> 6 ca 1-5 2020-02-05 6
#> 7 ca 1-5 2020-02-12 7
#> 8 ca 1-5 2020-02-19 8
#> 9 ca 1-5 2020-02-26 9
#> 10 ca 1-5 2020-03-04 10
#> 11 ca >=5 2020-01-01 11
#> 12 ca >=5 2020-01-08 12
#> 13 ca >=5 2020-01-15 13
#> 14 ca >=5 2020-01-22 14
#> 15 ca >=5 2020-01-29 15
#> 16 ca >=5 2020-02-05 16
#> 17 ca >=5 2020-02-12 17
#> 18 ca >=5 2020-02-19 18
#> 19 ca >=5 2020-02-26 19
#> 20 ca >=5 2020-03-04 20Correctly renamed
## Check if epi_slide still works on the renamed object
res_select |>
epi_slide(cases_7sd = mean(value, na.rm = TRUE), .window_size = 14)
#> An `epi_df` object, 20 x 5 with metadata:
#> * geo_type = state
#> * time_type = day
#> * other_keys = age_group
#> * as_of = 2025-12-17 17:37:43.695804
#>
#> # A tibble: 20 × 5
#> geo_value age_group time_value value cases_7sd
#> <chr> <chr> <date> <int> <dbl>
#> 1 ca 1-5 2020-01-01 1 1
#> 2 ca 1-5 2020-01-08 2 1.5
#> 3 ca 1-5 2020-01-15 3 2.5
#> 4 ca 1-5 2020-01-22 4 3.5
#> 5 ca 1-5 2020-01-29 5 4.5
#> 6 ca 1-5 2020-02-05 6 5.5
#> 7 ca 1-5 2020-02-12 7 6.5
#> 8 ca 1-5 2020-02-19 8 7.5
#> 9 ca 1-5 2020-02-26 9 8.5
#> 10 ca 1-5 2020-03-04 10 9.5
#> 11 ca >=5 2020-01-01 11 11
#> 12 ca >=5 2020-01-08 12 11.5
#> 13 ca >=5 2020-01-15 13 12.5
#> 14 ca >=5 2020-01-22 14 13.5
#> 15 ca >=5 2020-01-29 15 14.5
#> 16 ca >=5 2020-02-05 16 15.5
#> 17 ca >=5 2020-02-12 17 16.5
#> 18 ca >=5 2020-02-19 18 17.5
#> 19 ca >=5 2020-02-26 19 18.5
#> 20 ca >=5 2020-03-04 20 19.5Still working
# Test Rename grouped ----
## Grouping by geo_value
edf_grouped <- edf_weekly %>% group_by(geo_value, age)
## Verify grouped metadata and class
attr(edf_grouped, "metadata")
print(class(edf_grouped)
## Rename on grouped data
res_select_grouped <- edf_grouped %>% rename(val = value)
# Check if sliding works after grouped rename
res_select_grouped |>
epi_slide(cases_7sd = mean(val, na.rm = TRUE), .window_size = 14)
#> Error in parse(text = input): <text>:11:1: unexpected symbol
#> 10: ## Rename on grouped data
#> 11: res_select_grouped
#> ^Work as expected
# Final check of metadata
attr(res_select_grouped, "metadata")
#> Error: object 'res_select_grouped' not foundCreated on 2025-12-17 with reprex v2.1.1