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Merge pull request #24 from oxford-pharmacoepi/mah_dev2
Change summariseTableCount() name to summariseRecordCounts()
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| #' @noRd | ||
| checkAgeGroup <- function(ageGroup, overlap = FALSE) { | ||
| checkmate::assertList(ageGroup, min.len = 1, null.ok = TRUE) | ||
| if (!is.null(ageGroup)) { | ||
| if (is.numeric(ageGroup[[1]])) { | ||
| ageGroup <- list("age_group" = ageGroup) | ||
| } | ||
| for (k in seq_along(ageGroup)) { | ||
| invisible(checkCategory(ageGroup[[k]], overlap)) | ||
| if (any(ageGroup[[k]] |> unlist() |> unique() < 0)) { | ||
| cli::cli_abort("ageGroup can't contain negative values") | ||
| } | ||
| } | ||
| if (is.null(names(ageGroup))) { | ||
| names(ageGroup) <- paste0("age_group_", 1:length(ageGroup)) | ||
| } | ||
| if ("" %in% names(ageGroup)) { | ||
| id <- which(names(ageGroup) == "") | ||
| names(ageGroup)[id] <- paste0("age_group_", id) | ||
| } | ||
| } | ||
| return(invisible(ageGroup)) | ||
| } | ||
|
|
||
| #' @noRd | ||
| checkOmopTable <- function(omopTable){ | ||
| assertClass(omopTable, "omop_table") | ||
| omopTable |> | ||
| omopgenerics::tableName() |> | ||
| assertChoice(choices = tables$table_name) | ||
| } | ||
|
|
||
| #' @noRd | ||
| checkUnit <- function(unit){ | ||
| inherits(unit, "character") | ||
| assertLength(unit, 1) | ||
| if(!unit %in% c("year","month")){ | ||
| cli::cli_abort("units value is not valid. Valid options are year or month.") | ||
| } | ||
| } | ||
|
|
||
| #' @noRd | ||
| checkUnitInterval <- function(unitInterval){ | ||
| inherits(unitInterval, c("numeric", "integer")) | ||
| assertLength(unitInterval, 1) | ||
| if(unitInterval < 1){ | ||
| cli::cli_abort("unitInterval input has to be equal or greater than 1.") | ||
| } | ||
| if(!(unitInterval%%1 == 0)){ | ||
| cli::cli_abort("unitInterval has to be an integer.") | ||
| } | ||
| } | ||
|
|
||
|
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||
| #' @noRd | ||
| checkCategory <- function(category, overlap = FALSE, type = "numeric") { | ||
| checkmate::assertList( | ||
| category, | ||
| types = type, any.missing = FALSE, unique = TRUE, | ||
| min.len = 1 | ||
| ) | ||
|
|
||
| if (is.null(names(category))) { | ||
| names(category) <- rep("", length(category)) | ||
| } | ||
|
|
||
| # check length | ||
| category <- lapply(category, function(x) { | ||
| if (length(x) == 1) { | ||
| x <- c(x, x) | ||
| } else if (length(x) > 2) { | ||
| cli::cli_abort( | ||
| paste0( | ||
| "Categories should be formed by a lower bound and an upper bound, ", | ||
| "no more than two elements should be provided." | ||
| ), | ||
| call. = FALSE | ||
| ) | ||
| } | ||
| invisible(x) | ||
| }) | ||
|
|
||
| # check lower bound is smaller than upper bound | ||
| checkLower <- unlist(lapply(category, function(x) { | ||
| x[1] <= x[2] | ||
| })) | ||
| if (!(all(checkLower))) { | ||
| cli::cli_abort("Lower bound should be equal or smaller than upper bound") | ||
| } | ||
|
|
||
| # built tibble | ||
| result <- lapply(category, function(x) { | ||
| dplyr::tibble(lower_bound = x[1], upper_bound = x[2]) | ||
| }) |> | ||
| dplyr::bind_rows() |> | ||
| dplyr::mutate(category_label = names(.env$category)) |> | ||
| dplyr::mutate(category_label = dplyr::if_else( | ||
| .data$category_label == "", | ||
| dplyr::case_when( | ||
| is.infinite(.data$lower_bound) & is.infinite(.data$upper_bound) ~ "any", | ||
| is.infinite(.data$lower_bound) ~ paste(.data$upper_bound, "or below"), | ||
| is.infinite(.data$upper_bound) ~ paste(.data$lower_bound, "or above"), | ||
| TRUE ~ paste(.data$lower_bound, "to", .data$upper_bound) | ||
| ), | ||
| .data$category_label | ||
| )) |> | ||
| dplyr::arrange(.data$lower_bound) | ||
|
|
||
| # check overlap | ||
| if (!overlap) { | ||
| if (nrow(result) > 1) { | ||
| lower <- result$lower_bound[2:nrow(result)] | ||
| upper <- result$upper_bound[1:(nrow(result) - 1)] | ||
| if (!all(lower > upper)) { | ||
| cli::cli_abort("There can not be overlap between categories") | ||
| } | ||
| } | ||
| } | ||
|
|
||
| invisible(result) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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@@ -76,4 +76,3 @@ test_that("tableOmopTable() works", { | |
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| }) | ||
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