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doc+test: update epix_merge tests and docs (#514)
Co-authored-by: rnayebi21 <[email protected]> Co-authored-by: Dmitry Shemetov <[email protected]>
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‎R/methods-epi_archive.R‎

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@@ -245,16 +245,75 @@ epix_fill_through_version <- function(x, fill_versions_end,
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#' be clobbered in either input archive.
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#'
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#' @examples
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#' # create two example epi_archive datasets
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#' x <- archive_cases_dv_subset$DT %>%
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#' dplyr::select(geo_value, time_value, version, case_rate_7d_av) %>%
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#' as_epi_archive(compactify = TRUE)
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#' y <- archive_cases_dv_subset$DT %>%
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#' dplyr::select(geo_value, time_value, version, percent_cli) %>%
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#' as_epi_archive(compactify = TRUE)
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#' # merge results stored in a third object:
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#' xy <- epix_merge(x, y)
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#' # Example 1
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#' # The s1 signal at August 1st gets revised from 10 to 11 on August 2nd
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#' s1 <- tibble::tibble(
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#' geo_value = c("ca", "ca", "ca"),
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#' time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-02")),
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#' version = as.Date(c("2024-08-01", "2024-08-02", "2024-08-02")),
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#' signal1 = c(10, 11, 7)
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#' )
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#'
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#' s2 <- tibble::tibble(
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#' geo_value = c("ca", "ca"),
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#' time_value = as.Date(c("2024-08-01", "2024-08-02")),
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#' version = as.Date(c("2024-08-03", "2024-08-03")),
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#' signal2 = c(2, 3)
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#' )
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#'
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#'
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#' s1 <- s1 %>% as_epi_archive()
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#' s2 <- s2 %>% as_epi_archive()
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#'
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#' merged <- epix_merge(s1, s2, sync = "locf")
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#' merged[["DT"]]
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#'
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#' # Example 2
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#' # The s1 signal at August 1st gets revised from 12 to 13 on August 3rd
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#' s1 <- tibble::tibble(
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#' geo_value = c("ca", "ca", "ca", "ca"),
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#' time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-02", "2024-08-03")),
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#' version = as.Date(c("2024-08-01", "2024-08-03", "2024-08-03", "2024-08-03")),
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#' signal1 = c(12, 13, 22, 19)
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#' )
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#'
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#' s2 <- tibble::tibble(
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#' geo_value = c("ca", "ca"),
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#' time_value = as.Date(c("2024-08-01", "2024-08-02")),
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#' version = as.Date(c("2024-08-02", "2024-08-02")),
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#' signal2 = c(4, 5),
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#' )
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#'
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#'
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#' s1 <- s1 %>% as_epi_archive()
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#' s2 <- s2 %>% as_epi_archive()
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#'
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#' merged <- epix_merge(s1, s2, sync = "locf")
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#' merged[["DT"]]
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#'
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#'
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#' # Example 3:
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#' s1 <- tibble::tibble(
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#' geo_value = c("ca", "ca", "ca"),
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#' time_value = as.Date(c("2024-08-01", "2024-08-02", "2024-08-03")),
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#' version = as.Date(c("2024-08-01", "2024-08-02", "2024-08-03")),
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#' signal1 = c(14, 11, 9)
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#' )
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#'
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#' # The s2 signal at August 1st gets revised from 3 to 5 on August 3rd
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#' s2 <- tibble::tibble(
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#' geo_value = c("ca", "ca", "ca"),
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#' time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-02")),
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#' version = as.Date(c("2024-08-02", "2024-08-03", "2024-08-03")),
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#' signal2 = c(3, 5, 2),
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#' )
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#'
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#' s1 <- s1 %>% as_epi_archive()
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#' s2 <- s2 %>% as_epi_archive()
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#'
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#' # Some LOCF for signal 1 as signal 2 gets updated
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#' merged <- epix_merge(s1, s2, sync = "locf")
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#' merged[["DT"]]
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#' @importFrom data.table key set setkeyv
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#' @export
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epix_merge <- function(x, y,

‎man/epiprocess.Rd‎

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‎man/epix_merge.Rd‎

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‎tests/testthat/test-epix_merge.R‎

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Original file line numberDiff line numberDiff line change
@@ -62,6 +62,95 @@ test_that("epix_merge merges and carries forward updates properly", {
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)
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expect_identical(xy, xy_expected)
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s1 <- tibble(
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geo_value = c("ca", "ca", "ca"),
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time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-02")),
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version = as.Date(c("2024-08-01", "2024-08-02", "2024-08-02")),
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signal1 = c("XA", "XB", "XC")
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)
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s2 <- tibble(
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geo_value = c("ca", "ca"),
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time_value = as.Date(c("2024-08-01", "2024-08-02")),
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version = as.Date(c("2024-08-03", "2024-08-03")),
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signal2 = c("YA", "YB")
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)
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s1 <- s1 %>% as_epi_archive()
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s2 <- s2 %>% as_epi_archive()
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merge1_expected <- tibble(
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geo_value = rep("ca", 5),
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time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-01", "2024-08-02", "2024-08-02")),
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version = as.Date(c("2024-08-01", "2024-08-02", "2024-08-03", "2024-08-02", "2024-08-03")),
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signal1 = c("XA", "XB", "XB", "XC", "XC"),
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signal2 = c(NA, NA, "YA", NA, "YB")
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) %>% as_epi_archive()
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merged1 <- epix_merge(s1, s2, sync = "locf")
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expect_identical(merged1, merge1_expected)
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s1 <- tibble(
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geo_value = c("ca", "ca", "ca", "ca"),
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time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-02", "2024-08-03")),
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version = as.Date(c("2024-08-01", "2024-08-03", "2024-08-03", "2024-08-03")),
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signal1 = c("XA", "XB", "XC", "XD")
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)
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s2 <- tibble(
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geo_value = c("ca", "ca"),
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time_value = as.Date(c("2024-08-01", "2024-08-02")),
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version = as.Date(c("2024-08-02", "2024-08-02")),
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signal2 = c("YA", "YB"),
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)
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s1 <- s1 %>% as_epi_archive()
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s2 <- s2 %>% as_epi_archive()
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merge2_expected <- tibble(
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geo_value = rep("ca", 6),
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time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-01", "2024-08-02", "2024-08-02", "2024-08-03")),
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version = as.Date(c("2024-08-01", "2024-08-02", "2024-08-03", "2024-08-02", "2024-08-03", "2024-08-03")),
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signal1 = c("XA", "XA", "XB", NA, "XC", "XD"),
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signal2 = c(NA, "YA", "YA", "YB", "YB", NA)
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) %>% as_epi_archive()
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merged2 <- epix_merge(s1, s2, sync = "locf")
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expect_identical(merged2, merge2_expected)
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s1 <- tibble(
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geo_value = c("ca", "ca", "ca"),
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time_value = as.Date(c("2024-08-01", "2024-08-02", "2024-08-03")),
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version = as.Date(c("2024-08-01", "2024-08-02", "2024-08-03")),
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signal1 = c("XA", "XB", "XC")
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)
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s2 <- tibble(
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geo_value = c("ca", "ca", "ca"),
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time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-02")),
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version = as.Date(c("2024-08-02", "2024-08-03", "2024-08-03")),
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signal2 = c("YA", "YB", "YC"),
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)
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s1 <- s1 %>% as_epi_archive()
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s2 <- s2 %>% as_epi_archive()
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merge3_expected <- tibble(
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geo_value = rep("ca", 6),
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time_value = as.Date(c("2024-08-01", "2024-08-01", "2024-08-01", "2024-08-02", "2024-08-02", "2024-08-03")),
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version = as.Date(c("2024-08-01", "2024-08-02", "2024-08-03", "2024-08-02", "2024-08-03", "2024-08-03")),
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signal1 = c("XA", "XA", "XA", "XB", "XB", "XC"),
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signal2 = c(NA, "YA", "YB", NA, "YC", NA)
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) %>% as_epi_archive()
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merged3 <- epix_merge(s1, s2, sync = "locf")
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expect_identical(merged3, merge3_expected)
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})
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test_that("epix_merge forbids and warns on metadata and naming issues", {

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