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update README
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@ernestguevarra
ernestguevarra committed Jul 2, 2024
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18 changes: 15 additions & 3 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ This use case are for those that prefer not to use Microsoft Access (either beca

## Installation

`coeditr` is not yet on CRAN but can be installed through the [Oxford IHTM R-universe](https://oxfordihtm.r-universe.dev) with:
`coeditr` is not yet on CRAN but can be installed through the [Oxford IHTM R Universe](https://oxfordihtm.r-universe.dev) with:

```{r install, eval = FALSE}
install.packages(
Expand Down Expand Up @@ -98,13 +98,19 @@ The output is a data.frame that can then be saved as an `.xlsx` file for use as
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$code, version = "icd11", sex = "sex")
cod_check_code(
cod_data_raw_example$code, version = "icd11",
sex = cod_data_raw_example$sex, age = cod_data_raw_example$age
)
```

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$code, version = "icd11", sex = "sex") |>
cod_check_code(
cod_data_raw_example$code, version = "icd11",
sex = cod_data_raw_example$sex, age = cod_data_raw_example$age
) |>
cod_check_code_summary()
```

Expand All @@ -121,6 +127,12 @@ 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)
### Perform check for cause-of-death codes inappropriate for specific sex ----
cod_check_code_sex_icd11(cod_data_raw_example$code, cod_data_raw_example$sex)
### Perform check for cause-of-death codes inappropriate for specific age ----
cod_check_code_age_icd11(cod_data_raw_example$code, cod_data_raw_example$age)
```

## Citation
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79 changes: 72 additions & 7 deletions README.md
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Expand Up @@ -81,7 +81,7 @@ potentially large scale cause-of-death data quality checks.
## Installation

`coeditr` is not yet on CRAN but can be installed through the [Oxford
IHTM R-universe](https://oxfordihtm.r-universe.dev) with:
IHTM R Universe](https://oxfordihtm.r-universe.dev) with:

``` r
install.packages(
Expand Down Expand Up @@ -173,8 +173,11 @@ The `cod_check_code()` function performs all the checks implemented by
the CoDEdit tool.

``` r
cod_check_code(cod_data_raw_example$code, version = "icd11", sex = "sex")
#> # A tibble: 20 × 10
cod_check_code(
cod_data_raw_example$code, version = "icd11",
sex = cod_data_raw_example$sex, age = cod_data_raw_example$age
)
#> # A tibble: 20 × 12
#> cod_check_structure cod_check_note_structure cod_check_ill_defined
#> <int> <fct> <int>
#> 1 0 No issues found in CoD code 0
Expand All @@ -197,17 +200,20 @@ cod_check_code(cod_data_raw_example$code, version = "icd11", sex = "sex")
#> 18 0 No issues found in CoD code 0
#> 19 0 No issues found in CoD code 0
#> 20 0 No issues found in CoD code 0
#> # ℹ 7 more variables: cod_check_note_ill_defined <fct>,
#> # ℹ 9 more variables: cod_check_note_ill_defined <fct>,
#> # cod_check_unlikely <int>, cod_check_note_unlikely <fct>,
#> # cod_check_sex <int>, cod_check_note_sex <fct>, cod_check_code <dbl>,
#> # cod_check_code_note <fct>
#> # cod_check_sex <int>, cod_check_note_sex <fct>, cod_check_age <int>,
#> # cod_check_note_age <fct>, cod_check_code <dbl>, cod_check_code_note <fct>
```

Results of the per row cause-of-death checks can also be summarised to
give a count of issues found in the dataset.

``` r
cod_check_code(cod_data_raw_example$code, version = "icd11", sex = "sex") |>
cod_check_code(
cod_data_raw_example$code, version = "icd11",
sex = cod_data_raw_example$sex, age = cod_data_raw_example$age
) |>
cod_check_code_summary()
#> $`Code structure`
#> # A tibble: 65 × 2
Expand Down Expand Up @@ -246,6 +252,13 @@ cod_check_code(cod_data_raw_example$code, version = "icd11", sex = "sex") |>
#> 1 No issues found in CoD code 20
#> 2 CoD code is not appropriate for person's sex 0
#>
#> $`Code not appropriate for age`
#> # A tibble: 2 × 2
#> cod_check_note n
#> <fct> <int>
#> 1 No issues found in CoD code 20
#> 2 CoD code is not appropriate for person's age 0
#>
#> $Overall
#> # A tibble: 2 × 2
#> cod_check_note n
Expand Down Expand Up @@ -328,6 +341,58 @@ cod_check_code_unlikely_icd11(cod_data_raw_example$code)
#> 18 0 No issues found in CoD code
#> 19 0 No issues found in CoD code
#> 20 0 No issues found in CoD code

### Perform check for cause-of-death codes inappropriate for specific sex ----
cod_check_code_sex_icd11(cod_data_raw_example$code, cod_data_raw_example$sex)
#> # A tibble: 20 × 2
#> cod_check cod_check_note
#> <int> <fct>
#> 1 0 No issues found in CoD code
#> 2 0 No issues found in CoD code
#> 3 0 No issues found in CoD code
#> 4 0 No issues found in CoD code
#> 5 0 No issues found in CoD code
#> 6 0 No issues found in CoD code
#> 7 0 No issues found in CoD code
#> 8 0 No issues found in CoD code
#> 9 0 No issues found in CoD code
#> 10 0 No issues found in CoD code
#> 11 0 No issues found in CoD code
#> 12 0 No issues found in CoD code
#> 13 0 No issues found in CoD code
#> 14 0 No issues found in CoD code
#> 15 0 No issues found in CoD code
#> 16 0 No issues found in CoD code
#> 17 0 No issues found in CoD code
#> 18 0 No issues found in CoD code
#> 19 0 No issues found in CoD code
#> 20 0 No issues found in CoD code

### Perform check for cause-of-death codes inappropriate for specific age ----
cod_check_code_age_icd11(cod_data_raw_example$code, cod_data_raw_example$age)
#> # A tibble: 20 × 2
#> cod_check cod_check_note
#> <int> <fct>
#> 1 0 No issues found in CoD code
#> 2 0 No issues found in CoD code
#> 3 0 No issues found in CoD code
#> 4 0 No issues found in CoD code
#> 5 0 No issues found in CoD code
#> 6 0 No issues found in CoD code
#> 7 0 No issues found in CoD code
#> 8 0 No issues found in CoD code
#> 9 0 No issues found in CoD code
#> 10 0 No issues found in CoD code
#> 11 0 No issues found in CoD code
#> 12 0 No issues found in CoD code
#> 13 0 No issues found in CoD code
#> 14 0 No issues found in CoD code
#> 15 0 No issues found in CoD code
#> 16 0 No issues found in CoD code
#> 17 0 No issues found in CoD code
#> 18 0 No issues found in CoD code
#> 19 0 No issues found in CoD code
#> 20 0 No issues found in CoD code
```

## Citation
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