diff --git a/vignettes/cause_of_death_code_checks.Rmd b/vignettes/cause_of_death_code_checks.Rmd index 9fd37f2..028a14a 100644 --- a/vignettes/cause_of_death_code_checks.Rmd +++ b/vignettes/cause_of_death_code_checks.Rmd @@ -1,5 +1,6 @@ --- title: "Cause-of-death code checks" +author: Anita Makori and Ernest Guevarra output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Cause-of-death code checks} @@ -111,7 +112,9 @@ rbind( ) ) |> knitr::kable( - col.names = c("Score Combinations", "CoD Check Score", "CoD Check Note")) + col.names = c("Score Combinations", "CoD Check Score", "CoD Check Note"), + caption = "Cause-of-death code structure checks for ICD-10 version" + ) ``` ### Cause-of-death code structure checks for ICD-11 version @@ -141,7 +144,9 @@ rbind( ) ) |> knitr::kable( - col.names = c("Score Combinations", "CoD Check Score", "CoD Check Note")) + col.names = c("Score Combinations", "CoD Check Score", "CoD Check Note"), + caption = "Cause-of-death code structure checks for ICD-11 version" + ) ``` These cause-of-death code structure checks are meant to detect writing/typing/encoding issues and gives feedback as to what potentially needs correction by the person performing the coding. Hence, these checks are most useful during routine cause-of-death code data quality checks prior to finalisation of cause-of-death data for reporting and/or statistical analysis use. @@ -154,6 +159,8 @@ The cause-of-death coding steps/process for both ICD-10 and ICD-11 gives clear g Following are the ill-defined codes for the ICD-10^[World Health Organization. International Classification of Diseases Tenth Revision (ICD-10). Sixth Edition. Vol. 2 Instruction Manual. Geneva: World Health Organization, 2019. https://icd.who.int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf.] and ICD-11^[World Health Organization. International Classification of Disease Eleventh Revision (ICD-11). Geneva: World Health Organization, 2022. https://icdcdn.who.int/icd11referenceguide/en/html/index.html.] versions. +### Ill-defined codes for ICD_10 and ICD-11 + ```{r ill-defined-codes, echo = FALSE} data.frame( icd_version = c("ICD-10", "ICD-11"), @@ -162,13 +169,18 @@ data.frame( "BD10-BD1Z, BA2Z, BE2Y, BE2Z, CB41.0, CB41.2, KB2D, KB2E, Chapter 21 codes" ) ) |> - knitr::kable(col.names = c("ICD Version", "Ill-defined Codes")) + knitr::kable( + col.names = c("ICD Version", "Ill-defined Codes"), + caption = "Ill-defined codes for ICD-10 and ICD-11" + ) ``` Presence of ill-defined codes in the cause-of-death registry is critical as this can impact reported mortality statistics. This is the reason why one of the standard indicators for cause-of-death data quality is the proportion of ill-defined causes in cause-of-death registration^[https://www.who.int/data/gho/indicator-metadata-registry/imr-details/3057#:~:text=The%20following%20ICD%2D10%20codes,2%2C%20I49.]. The functions `cod_check_code_ill_defined_icd10()` and `cod_check_code_ill_defined_icd11()` classifies a cause-of-death code as follows: +### Checks for ill-defined cause-of-death codes + ```{r ill-defined-coding, echo = FALSE} data.frame( cod_check <- c(0L, 1L), @@ -178,7 +190,10 @@ data.frame( "CoD code is an ill-defined code" ) ) |> - knitr::kable(col.names = c("CoD Check Score", "CoD Check Note")) + knitr::kable( + col.names = c("CoD Check Score", "CoD Check Note"), + caption = "Checks for ill-defined cause-of-death codes" + ) ``` ## Unlikely cause-of-death codes @@ -189,7 +204,9 @@ Similar to issues with ill-defined codes, unlikely cause-of-death codes are prim Following are the unlikely cause-of-death codes for the ICD-10^[World Health Organization. International Classification of Diseases Tenth Revision (ICD-10). Sixth Edition. Vol. 2 Instruction Manual. Geneva: World Health Organization, 2019. https://icd.who.int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf.] and ICD-11^[https://icd.who.int/valuesets/viewer/582/en] versions. -```{r sex-specific-cod-codes, echo = FALSE} +### Unlikely cause-of-death codes for ICD-10 and ICD-11 + +```{r unlikely-cod-codes, echo = FALSE} data.frame( icd_version = c("ICD-10", "ICD-11"), ill_defined_codes = c( @@ -197,7 +214,10 @@ data.frame( paste(icd11_unlikely_cod$code, collapse = ", ") ) ) |> - knitr::kable(col.names = c("ICD Version", "Unlikely Cause-of-Death Codes")) + knitr::kable( + col.names = c("ICD Version", "Unlikely Cause-of-Death Codes"), + caption = "Unlikely cause-of-death codes for ICD-10 and ICD-11" + ) ``` The `codeditr` package comes with datasets for ICD-10 (`icd10_unlikely_cod`) and ICD-11 (`icd11_unlikely_cod`) unlikely codes as reference. @@ -206,7 +226,9 @@ Presence of unlikely causes-of-death codes in the cause-of-death registry is cri The functions `cod_check_code_unlikely_icd10()` and `cod_check_code_unlikely_icd11()` classifies a cause-of-death code as follows: -```{r sex-specific-coding, echo = FALSE} +### Checks for unlikely cause-of-death codes + +```{r unlikely-coding, echo = FALSE} data.frame( cod_check <- c(0L, 1L), cod_check_note <- ifelse( @@ -215,7 +237,10 @@ data.frame( "CoD code is an unlikely cause-of-death" ) ) |> - knitr::kable(col.names = c("CoD Check Score", "CoD Check Note")) + knitr::kable( + col.names = c("CoD Check Score", "CoD Check Note"), + caption = "Checks for unlikely cause-of-death codes" + ) ``` ## Cause-of-death code not appropriate for sex @@ -224,6 +249,8 @@ Certain cause-of-death codes are limited to or more likely to occur only to a sp Following are cause-of-death codes for the ICD-10^[World Health Organization. International Classification of Diseases Tenth Revision (ICD-10). Sixth Edition. Vol. 2 Instruction Manual. Geneva: World Health Organization, 2019. https://icd.who.int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf.] and ICD-11^[https://icdcdn.who.int/icd11referenceguide/en/html/index.html#list-of-categories-limited-to-or-more-likely-to-occur-in-female-persons; https://icdcdn.who.int/icd11referenceguide/en/html/index.html#list-of-categories-limited-to-or-more-likely-to-occur-in-male-persons] versions specific to males and females. +### Male-specific cause-of-death codes + ```{r male-specific-codes, echo = FALSE} data.frame( icd_version = c("ICD-10", "ICD-11"), @@ -233,13 +260,13 @@ data.frame( ) ) |> knitr::kable( - col.names = c( - "ICD Version", - "Male-Specific Cause-of-Death Codes" - ) + col.names = c("ICD Version", "Cause-of-Death Codes"), + caption = "Male-specific cause-of-death codes" ) ``` +### Female-specific cause-of-death codes + ```{r female-specific-codes, echo = FALSE} data.frame( icd_version = c("ICD-10", "ICD-11"), @@ -249,10 +276,8 @@ data.frame( ) ) |> knitr::kable( - col.names = c( - "ICD Version", - "Female-Specific Cause-of-Death Codes" - ) + col.names = c("ICD Version", "Cause-of-Death Codes"), + caption = "Female-specific cause-of-death codes" ) ``` @@ -260,7 +285,9 @@ The `codeditr` package comes with datasets for ICD-10 (`icd10_cod_by_sex`) and I The functions `cod_check_code_sex_icd10()` and `cod_check_code_sex_icd11()` classifies a cause-of-death code as follows: -```{r unlikely-coding, echo = FALSE} +### Checks for sex-specific cause-of-death codes + +```{r sex-specific-coding, echo = FALSE} data.frame( cod_check <- c(0L, 1L), cod_check_note <- ifelse( @@ -269,7 +296,10 @@ data.frame( "CoD code is not appropriate for person's sex" ) ) |> - knitr::kable(col.names = c("CoD Check Score", "CoD Check Note")) + knitr::kable( + col.names = c("CoD Check Score", "CoD Check Note"), + caption = "Checks for sex-specific cause-of-death codes" + ) ``` ## Cause-of-death codes not appropriate for age @@ -278,6 +308,8 @@ Certain cause-of-death codes are limited to or more likely to occur only to a sp Following are cause-of-death codes for the ICD-10 and ICD-11 versions specific to neonates (less than 1 year old) and to children (less than 18 years old). +### Neonate-specific cause-of-death codes + ```{r neonate-specific-codes, echo = FALSE} data.frame( icd_version = c("ICD-10", "ICD-11"), @@ -287,13 +319,13 @@ data.frame( ) ) |> knitr::kable( - col.names = c( - "ICD Version", - "Neonate-Specific Cause-of-Death Codes" - ) + col.names = c("ICD Version", "Cause-of-Death Codes"), + caption = "Neonate-specific cause-of-death codes" ) ``` +### Child-specific cause-of-death codes + ```{r child-specific-codes, echo = FALSE} data.frame( icd_version = c("ICD-10", "ICD-11"), @@ -303,10 +335,8 @@ data.frame( ) ) |> knitr::kable( - col.names = c( - "ICD Version", - "Child-Specific Cause-of-Death Codes" - ) + col.names = c("ICD Version", "Cause-of-Death Codes"), + caption = "Child-specific cause-of-death codes" ) ``` @@ -314,6 +344,8 @@ The `codeditr` package comes with datasets for ICD-10 (`icd10_cod_neonate` and ` The functions `cod_check_code_age_icd10()` and `cod_check_code_age_icd11()` classifies a cause-of-death code as follows: +### Checks for age-specific cause-of-death codes + ```{r age-specific-coding, echo = FALSE} data.frame( cod_check <- c(0L, 1L), @@ -323,5 +355,12 @@ data.frame( "CoD code is not appropriate for person's age" ) ) |> - knitr::kable(col.names = c("CoD Check Score", "CoD Check Note")) + knitr::kable( + col.names = c("CoD Check Score", "CoD Check Note"), + caption = "Checks for age-specific cause-of-death codes" + ) ``` + + +
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