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feat: ✨ add include_podiatrist_services() with tests
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6eb2d35
docs: :memo: add podiatrist services logic
signekb de2cd32
build: :heavy_plus_sign: add lubridate
signekb dedd5e2
feat: :white_check_mark: add `yyww_to_date()` with tests
signekb 8bd888d
chore: :bento: run pipeline to include podiatrist services logic
signekb 1fb9dcb
feat: :white_check_mark: add `include_podiatrist_services()` with tests
signekb 495684c
docs: :memo: add and update function docs autogenerated by roxygen
signekb 7b0e2bc
docs: :pencil2: fix typo
signekb a78c218
chore: :bento: Re-generated roxygen2 documentation
signekb 9d188a6
test: :test_tube: add test for numeric year 2000
signekb ed910a9
fix: :bug: change paste0 to sprintf
signekb 4f52c23
feat: :sparkles: update based on #163
signekb 588e62d
test: :white_check_mark: add row with non-diabetes-specific podiatris…
signekb 128cdec
chore: :bento: Re-generated roxygen2 documentation
signekb d57a8c2
docs: pencil2: lower case comment
signekb d15ab93
refactor: :recycle: rename `yyww_to_date` to `yyww_to_yyyymmdd()` wit…
signekb 39efded
refactor: :truck: rename function and test file to `-yyyymmdd` instea…
signekb 4175fa2
chore: :bento: Re-generated roxygen2 documentation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| #' Include diabetes-specific podiatrist services. | ||
| #' | ||
| #' #' Uses the `sysi` or `sssy` registers as input to extract the dates of all | ||
| #' diabetes-specific podiatrist services. Removes duplicate services on the | ||
| #' same date. Only the two earliest dates per individual are kept. | ||
| #' | ||
| #' #' The output is passed to the `join_inclusions()` function for the final | ||
| #' step of the inclusion process. | ||
| #' | ||
| #' @param sysi The SYSI register. | ||
| #' @param sssy The SSSY register. | ||
| #' | ||
| #' @return The same type as the input data, default as a [tibble::tibble()], | ||
| #' with two columns and up to two rows for each individual: | ||
| #' | ||
| #' - `pnr`: Identifier variable | ||
| #' - `date`: The dates of the first and second diabetes-specific | ||
| #' podiatrist record | ||
| #' - `has_podiatrist_services`: A logical variable that acts as a helper | ||
| #' indicator for use in later functions. | ||
| #' | ||
| #' @keywords internal | ||
| #' @inherit algorithm seealso | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' include_podiatrist_services(register_data$sysi, register_data$sssy) | ||
| #' } | ||
| include_podiatrist_services <- function(sysi, sssy) { | ||
| verify_required_variables(sysi, "sysi") | ||
| verify_required_variables(sssy, "sssy") | ||
| criteria <- get_algorithm_logic("podiatrist_services") |> | ||
| # To convert the string into an R expression. | ||
| rlang::parse_expr() | ||
|
|
||
| column_names_to_lower(sysi) |> | ||
| dplyr::full_join(column_names_to_lower(sssy), | ||
| by = dplyr::join_by(pnr, barnmak, speciale, honuge) | ||
| ) |> | ||
| # filter based algorithm logic | ||
| dplyr::filter(!!criteria) |> | ||
| # remove duplicates | ||
| dplyr::distinct() |> | ||
| # keep only the two columns we need and transform `honuge` to date | ||
| dplyr::mutate( | ||
| pnr = .data$pnr, | ||
| date = yyww_to_yyyymmdd(.data$honuge), | ||
| .keep = "none" | ||
| ) |> | ||
| # FIXME: This might be computationally intensive. | ||
| dplyr::group_by(.data$pnr) |> | ||
| # keep earliest two dates per individual | ||
| dplyr::filter(dplyr::row_number(.data$date) %in% 1:2) |> | ||
| dplyr::ungroup() |> | ||
| # create Boolean helper variable | ||
| dplyr::mutate(has_podiatrist_services = TRUE) | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| #' Convert date format YYWW to YYYY-MM-DD | ||
| #' | ||
| #' Since the exact date isn't given in the input, this function will set the | ||
| #' date to Monday of the week. | ||
| #' | ||
| #' As a precaution, a leading zero is added if it has been removed | ||
| #' This can e.g., happen if the input was "0107" and has been converted to a | ||
| #' numeric 107. | ||
| #' | ||
| #' @param yyww Character(s) of the format yyww | ||
| #' | ||
| #' @returns Date(s) in the format YYYY-MM-DD. | ||
| #' | ||
| #' @keywords internal | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' yyww_to_yyyymmdd("0102") | ||
| #' yyww_to_yyyymmdd(c("0102", "0304")) | ||
| #' } | ||
| yyww_to_yyyymmdd <- function(yyww) { | ||
| # ensure input is zero-padded to length 4 | ||
| yyww <- sprintf("%04d", as.numeric(yyww)) | ||
|
|
||
| year <- stringr::str_sub(yyww, 1, 2) | ||
| week <- stringr::str_sub(yyww, 3, 4) | ||
|
|
||
| # define helper variables | ||
| first_day_of_iso_year <- lubridate::ymd(paste(year, "-01-04")) | ||
| n_weekday_start_of_year <- lubridate::wday(first_day_of_iso_year, week_start = 1) | ||
|
|
||
| # calculate date | ||
| date <- first_day_of_iso_year | ||
| lubridate::week(date) <- as.numeric(week) | ||
| date <- date - n_weekday_start_of_year + 1 # adjust date to be Monday in that week | ||
|
|
||
| return(date) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name,logic | ||
| hba1c,(analysiscode == 'NPU27300' AND value >= 48) OR (analysiscode == 'NPU03835' AND value >= 6.5) | ||
| gld,atc =~ '^A10' | ||
|
|
||
| podiatrist_services,speciale =~ '^54' AND barnmak != 0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| sysi <- tibble::tribble( | ||
| ~pnr, ~barnmak, ~speciale, ~honuge, | ||
| 1000000000, 0, 54711, "1879", # removed since barnmark = 0 | ||
| 2000000000, 1, 54800, "9207", # kept but deduplicated | ||
| 2000000000, 1, 54800, "9207", # kept but deduplicated | ||
| 3000000000, 1, 54005, "0752", # kept bc it's the first date for this person | ||
| 3000000000, 1, 54005, "2430", # removed bc it's the third date for this person | ||
| 4000000000, 1, 55000, "0044" # removed since speciale doesn't start with 54 | ||
| ) | ||
|
|
||
| sssy <- tibble::tribble( | ||
| ~pnr, ~barnmak, ~speciale, ~honuge, | ||
| 2000000000, 1, 54800, "9207", # kept but deduplicated | ||
| 3000000000, 0, 10000, "1801", # removed since barnmark = 0 | ||
| 3000000000, 1, 54005, "0830", # kept bc it's the second date for this person | ||
| 4000000000, 1, 76255, "1123", # removed since speciale doesn't start with 54 | ||
| ) | ||
|
|
||
| expected <- tibble::tribble( | ||
| ~pnr, ~date, ~has_podiatrist_services, | ||
| 2000000000, lubridate::ymd("1992-02-10"),TRUE, | ||
| 3000000000, lubridate::ymd("2007-12-24"),TRUE, | ||
| 3000000000, lubridate::ymd("2008-07-21"),TRUE | ||
| ) | ||
|
|
||
|
|
||
| test_that("sysi needs expected variables", { | ||
| sysi <- sysi[-2] | ||
| expect_error(include_podiatrist_services(sysi, sssy)) | ||
| }) | ||
|
|
||
| test_that("ssy needs expected variables", { | ||
| sssy <- sssy[-2] | ||
| expect_error(include_podiatrist_services(sysi, sssy)) | ||
| }) | ||
|
|
||
|
|
||
| test_that("those with inclusion are kept", { | ||
| actual <- include_podiatrist_services(sysi, sssy) | ||
| expect_equal(actual, expected) | ||
| }) | ||
|
|
||
| test_that("casing of input variables doesn't matter", { | ||
| sysi <- sysi |> | ||
| dplyr::rename_with(\(columns) toupper(columns)) | ||
| sssy <- sssy |> | ||
| dplyr::rename_with(\(columns) toupper(columns)) | ||
| actual <- include_podiatrist_services(sysi, sssy) | ||
| expect_equal(actual, expected) | ||
| }) | ||
|
|
||
| test_that("verification works for DuckDB Database", { | ||
| skip_on_cran() | ||
| skip_if_not_installed("duckplyr") | ||
|
|
||
| sysi <- duckplyr::as_duckplyr_tibble(sysi) | ||
| sssy <- duckplyr::as_duckplyr_tibble(sssy) | ||
| actual <- include_podiatrist_services(sysi, sssy) | ||
|
|
||
| actual_rows <- actual |> | ||
| dplyr::count() |> | ||
| dplyr::pull(n) | ||
|
|
||
| expect_equal(actual_rows, nrow(expected)) | ||
| expect_equal(colnames(actual), colnames(expected)) | ||
| }) | ||
|
|
||
| test_that("verification works for Arrow Tables (from Parquet)", { | ||
| # FIXME: This test fails because of some issue with the criteria and colnames | ||
| skip() | ||
| skip_on_cran() | ||
| skip_if_not_installed("arrow") | ||
|
|
||
| sysi <- arrow::as_arrow_table(sysi) | ||
| sssy <- arrow::as_arrow_table(sssy) | ||
| actual <- include_podiatrist_services(sysi, sssy) | ||
|
|
||
| actual_rows <- actual |> | ||
| dplyr::count() |> | ||
| dplyr::pull(n) | ||
|
|
||
| expect_equal(actual_rows, nrow(expected)) | ||
| # TODO: Arrow doesn't work with colname(), fix? | ||
| expect_equal(names(actual), colnames(expected)) | ||
| }) | ||
|
|
||
| test_that("verification works for data.frame", { | ||
| sysi <- as.data.frame(sysi) | ||
| ssy <- as.data.frame(sssy) | ||
| actual <- include_podiatrist_services(sysi, sssy) | ||
|
|
||
| actual_rows <- actual |> | ||
| dplyr::count() |> | ||
| dplyr::pull(n) | ||
|
|
||
| expect_equal(actual_rows, nrow(expected)) | ||
| expect_equal(colnames(actual), colnames(expected)) | ||
| }) | ||
|
|
||
| test_that("verification works for data.table", { | ||
| skip_on_cran() | ||
| skip_if_not_installed("data.table") | ||
| sysi <- data.table::as.data.table(sysi) | ||
| sssy <- data.table::as.data.table(sssy) | ||
| actual <- include_podiatrist_services(sysi, sssy) | ||
|
|
||
| actual_rows <- actual |> | ||
| dplyr::count() |> | ||
| dplyr::pull(n) | ||
|
|
||
| expect_equal(actual_rows, nrow(expected)) | ||
| expect_equal(colnames(actual), colnames(expected)) | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| test_that("conversion works when 01-01 is Monday in week 1", { | ||
| expect_equal(yyww_to_yyyymmdd("2439"), lubridate::ymd("2024-09-23")) | ||
| }) | ||
|
|
||
| test_that("conversion works when 01-01 is Friday in week 52 of the prior year", { | ||
| expect_equal(yyww_to_yyyymmdd("9307"), lubridate::ymd("1993-02-15")) | ||
| }) | ||
|
|
||
| test_that("conversion works for week 53", { | ||
| expect_equal(yyww_to_yyyymmdd("1853"), lubridate::ymd("2018-12-31")) | ||
| }) | ||
|
|
||
| test_that("conversion works for zero-padded year and week (i.e., numbers < 10)", { | ||
| expect_equal(yyww_to_yyyymmdd("0107"), lubridate::ymd("2001-02-12")) | ||
| }) | ||
|
|
||
| test_that("conversion works for numeric one digit year", { | ||
| # This could happen if the input was "0107" and has been converted to numeric | ||
| expect_equal(yyww_to_yyyymmdd(107), lubridate::ymd("2001-02-12")) | ||
| }) | ||
|
|
||
| test_that("conversion works for numeric year 2000", { | ||
| expect_equal(yyww_to_yyyymmdd(0007), lubridate::ymd("2000-02-14")) | ||
| }) | ||
|
|
||
| test_that("conversion works for multiple inputs", { | ||
| expect_equal(yyww_to_yyyymmdd(c("0107", "2439")), lubridate::ymd("2001-02-12", "2024-09-23")) | ||
| }) |
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After explicitly adding the columns to join by, I get a note from
devtools::check():I'm not sure how to fix this, since
join_by()doesn't seem to allow the use of.data$