add cod_check_summary function and refactor outputs

NAMESPACE

@@ -12,6 +12,7 @@ export(cod_check_code_sex_icd11)
 export(cod_check_code_sex_icd11_)
 export(cod_check_code_structure_icd10)
 export(cod_check_code_structure_icd11)
+export(cod_check_code_summary)
 export(cod_check_code_unlikely_icd10)
 export(cod_check_code_unlikely_icd11)
 export(cod_check_codedit_input)

R/cod_check_code.R

@@ -50,7 +50,7 @@ cod_check_code <- function(cod, version = c("icd10", "icd11"), sex) {
     cod_check_code_unlikely, cod_check_code_sex
   ) |>
     dplyr::mutate(
-      cod_check = rowSums(
+      cod_check_code = rowSums(
         data.frame(
           .data$cod_check_structure,
           .data$cod_check_ill_defined,
@@ -59,7 +59,15 @@ cod_check_code <- function(cod, version = c("icd10", "icd11"), sex) {
         ),
         na.rm = TRUE
       ) |>
-        (\(x) ifelse(x == 0, 0, 1))()
+        (\(x) ifelse(x == 0, 0, 1))(),
+      cod_check_code_note = ifelse(
+        cod_check_code == 0,
+        "No issues found in CoD code",
+        "Issues found in CoD code"
+      ) |>
+        factor(
+          levels = c("No issues found in CoD code", "Issues found in CoD code")
+        )
     )
 }
 
@@ -239,20 +247,6 @@ cod_check_code_structure_icd11 <- function(cod) {
 #' @export
 #'
 cod_check_code_ill_defined_icd10 <- function(cod) {
-  # I46.1
-  # I46.9
-  # I50.-
-  #   I95.9
-  # I99
-  # J96.0
-  # J96.9
-  # P28.5
-  # R00-R57.1,
-  # R57.8-R64,
-  # R65.2-R65.3,
-  # R68.0-R94,
-  # R96-R99
-
   set1 <- ifelse(
     cod %in% c("I46.1", "I46.9", "I95.9", "I99", "J96.0", "P28.5"), 1L, 0L
   )
@@ -274,7 +268,16 @@ cod_check_code_ill_defined_icd10 <- function(cod) {
     "CoD code is an ill-defined code"
   )
 
-  tibble(cod_check, cod_check_note)
+  tibble(cod_check, cod_check_note) |>
+    dplyr::mutate(
+      cod_check_note = factor(
+        x = cod_check_note,
+        levels = c(
+          "No issues found in CoD code",
+          "CoD code is an ill-defined code"
+        )
+      )
+    )
 }
 
 
@@ -294,7 +297,16 @@ cod_check_code_ill_defined_icd11 <- function(cod) {
     "CoD code is an ill-defined code"
   )
 
-  tibble::tibble(cod_check, cod_check_note)
+  tibble(cod_check, cod_check_note) |>
+    dplyr::mutate(
+      cod_check_note = factor(
+        x = cod_check_note,
+        levels = c(
+          "No issues found in CoD code",
+          "CoD code is an ill-defined code"
+        )
+      )
+    )
 }
 
 
@@ -312,7 +324,16 @@ cod_check_code_unlikely_icd10 <- function(cod) {
     "CoD code is an unlikely cause-of-death"
   )
 
-  tibble(cod_check, cod_check_note)
+  tibble(cod_check, cod_check_note) |>
+    dplyr::mutate(
+      cod_check_note = factor(
+        x = cod_check_note,
+        levels = c(
+          "No issues found in CoD code",
+          "CoD code is an unlikely cause-of-death"
+        )
+      )
+    )
 }
 
 #'
@@ -331,7 +352,16 @@ cod_check_code_unlikely_icd11 <- function(cod) {
     "CoD code is an unlikely cause-of-death"
   )
 
-  tibble::tibble(cod_check, cod_check_note)
+  tibble(cod_check, cod_check_note) |>
+    dplyr::mutate(
+      cod_check_note = factor(
+        x = cod_check_note,
+        levels = c(
+          "No issues found in CoD code",
+          "CoD code is an unlikely cause-of-death"
+        )
+      )
+    )
 }
 
 #'
@@ -356,7 +386,16 @@ cod_check_code_sex_icd10_ <- function(cod, sex) {
     "CoD code is not appropriate for person's sex"
   )
 
-  tibble::tibble(cod_check, cod_check_note)
+  tibble::tibble(cod_check, cod_check_note) |>
+    dplyr::mutate(
+      cod_check_note = factor(
+        x = cod_check_note,
+        levels = c(
+          "No issues found in CoD code",
+          "CoD code is not appropriate for person's sex"
+        )
+      )
+    )
 }
 
 
@@ -397,7 +436,16 @@ cod_check_code_sex_icd11_ <- function(cod, sex) {
     "CoD code is not appropriate for person's sex"
   )
 
-  tibble::tibble(cod_check, cod_check_note)
+  tibble::tibble(cod_check, cod_check_note) |>
+    dplyr::mutate(
+      cod_check_note = factor(
+        x = cod_check_note,
+        levels = c(
+          "No issues found in CoD code",
+          "CoD code is not appropriate for person's sex"
+        )
+      )
+    )
 }
 
 

R/cod_structure_input.R

@@ -43,7 +43,7 @@ cod_structure_input <- function(df, sex, sex_code = c(1, 2),
   if (is.null(id)) {
     FreeId <- seq(from = 1, to = nrow(df))
   } else {
-    FreeId <- id
+    FreeId <- df[[id]]
   }
 
   Sex <- cod_recode_sex(sex_value = df[[sex]], sex_code = sex_code)

R/cod_summary.R

@@ -0,0 +1,57 @@
+#'
+#' Summarise cause-of-death check results
+#'
+#' @param cod_check A data.frame output of the various `cod_check_code_*`
+#'   functions
+#' @param simplify Logical. Should output be converted into a data.frame?
+#'   Default is FALSE.
+#'
+#' @returns If `simplify` is FALSE (default), a list of summary check outputs.
+#'   Otherwise, a tabulated summary of check outputs.
+#'
+#' @examples
+#' cod_check_code(cod_data_raw_example$code, version = "icd11", sex = "sex") |>
+#'   cod_check_code_summary()
+#'
+#' @rdname cod_check_code_summary
+#' @export
+#'
+
+cod_check_code_summary <- function(cod_check, simplify = FALSE) {
+  cod_check_list <- list(
+    cod_check |> dplyr::select(dplyr::contains("note_structure")),
+    cod_check |> dplyr::select(dplyr::contains("note_ill")),
+    cod_check |> dplyr::select(dplyr::contains("note_unlikely")),
+    cod_check |> dplyr::select(dplyr::contains("note_sex")),
+    cod_check |> dplyr::select(dplyr::all_of("cod_check_code_note"))
+  ) |>
+    (\(x)
+      {
+        names(x) <- c(
+          "Code structure", "Ill-defined code",
+          "Unlikely cause-of-death code", "Code not appropriate for sex",
+          "Overall"
+        )
+        x
+      }
+    )()
+
+  cod_check_summary <- lapply(
+    X = cod_check_list,
+    FUN = function(x) dplyr::count(
+      x,
+      dplyr::across(
+        dplyr::everything()
+      ),
+      .drop = FALSE
+    ) |>
+      dplyr::rename_with(.fn = function(x) c("cod_check_note", "n"))
+  )
+
+  if (simplify) {
+    cod_check_summary <- cod_check_summary |>
+      dplyr::bind_rows(.id = "cod_check_type")
+  }
+
+  cod_check_summary
+}

README.Rmd

@@ -74,14 +74,55 @@ library(codeditr)
 
 Using the `icd10_example` dataset which is a dataset already formatted into a compatible structure required by the CoDEdit tool, we can perform a check on this dataset to see possible issues in its formatting and structure before using with the CoDEdit tool.
 
-```{r use-case-1}
+```{r use-case-1a}
 cod_check_codedit_input(icd10_example)
 ```
 
+2. Structure raw cause-of-death data for input into CoDEdit tool
 
+Using the `cod_data_raw_example` dataset, we can format it into a compatible structure required by the CoDEdit tool.
+
+```{r use-case-2a}
+cod_structure_input(
+  df = cod_data_raw_example, 
+  sex = "sex", dob = "dob", dod = "dod", code = "code", id = "id"
+)
+```
+
+The output is a data.frame that can then be saved as an `.xlsx` file for use as input into the CoDEdit tool.
 
 ### CoDEdit tool replacement workflow
 
+1. Perform all checks on cause-of-death data
+
+The `cod_check_code()` function performs all the checks implemented by the CoDEdit tool.
+
+```{r use-case-3}
+cod_check_code(cod_data_raw_example$code, version = "icd11", sex = "sex")
+```
+
+Results of the per row cause-of-death checks can also be summarised to give a count of issues found in the dataset.
+
+```{r use-case-4}
+cod_check_code(cod_data_raw_example$code, version = "icd11", sex = "sex") |>
+  cod_check_code_summary()
+```
+
+2. Perform specific check types on cause-of-death data
+
+The family of `cod_check_code_*` functions can be used to perform specific check types on the cause-of-death data.
+
+```{r use-case-5}
+### Perform code structure check on cause-of-death data ----
+cod_check_code_structure_icd10(icd10_example$Code)
+
+### Perform check for ill-defined codes on cause-of-death data ----
+cod_check_code_ill_defined_icd11(cod_data_raw_example$code)
+
+### Perform check for unlikely cause-of-death codes ----
+cod_check_code_unlikely_icd11(cod_data_raw_example$code)
+```
+
 ## Citation
 
 If you find the `codeditr` package useful please cite using the suggested citation provided by a call to the `citation()` function as follows: