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Merge pull request #127 from OxfordIHTM/dev
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update pkgdown.yml to sandstone - primary
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@ernestguevarra
ernestguevarra authored Oct 31, 2024
2 parents 8c150ac + 9084fff commit c5bd9a1
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -52,7 +52,7 @@ This use case are for those that prefer not to use Microsoft Access (either beca

## Installation

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

```{r install, eval = FALSE}
install.packages(
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53 changes: 27 additions & 26 deletions README.md
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Expand Up @@ -84,7 +84,7 @@ potentially large scale cause-of-death data quality checks.
## Installation

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

``` r
install.packages(
Expand Down Expand Up @@ -114,20 +114,21 @@ structure before using with the CoDEdit tool.
``` r
cod_check_codedit_input(icd10_example)
#> # A tibble: 3,613 × 8
#> sex_check sex_check_note age_check age_check_note code_check code_check_note
#> <int> <fct> <int> <fct> <int> <chr>
#> 1 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 2 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 3 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 4 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 5 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 6 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 7 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 8 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 9 0 No issues with… 0 No issues wit… 0 Cause of death…
#> 10 0 No issues with… 0 No issues wit… 0 Cause of death…
#> sex_check sex_check_note age_check age_check_note code_check
#> <int> <fct> <int> <fct> <int>
#> 1 0 No issues with sex value 0 No issues with age… 0
#> 2 0 No issues with sex value 0 No issues with age… 0
#> 3 0 No issues with sex value 0 No issues with age… 0
#> 4 0 No issues with sex value 0 No issues with age… 0
#> 5 0 No issues with sex value 0 No issues with age… 0
#> 6 0 No issues with sex value 0 No issues with age… 0
#> 7 0 No issues with sex value 0 No issues with age… 0
#> 8 0 No issues with sex value 0 No issues with age… 0
#> 9 0 No issues with sex value 0 No issues with age… 0
#> 10 0 No issues with sex value 0 No issues with age… 0
#> # ℹ 3,603 more rows
#> # ℹ 2 more variables: dod_check <int>, dod_check_note <fct>
#> # ℹ 3 more variables: code_check_note <chr>, dod_check <int>,
#> # dod_check_note <fct>
```

2. Structure raw cause-of-death data for input into CoDEdit tool
Expand Down Expand Up @@ -220,18 +221,18 @@ cod_check_code(
cod_check_code_summary()
#> $`Code structure`
#> # A tibble: 65 × 2
#> cod_check_note n
#> <fct> <int>
#> 1 No issues found in CoD code 20
#> 2 CoD code has a period (`.`) character in the wrong place 0
#> 3 CoD code starts with `O` or `I` 0
#> 4 CoD code has a period (`.`) character in the wrong place; CoD code sta… 0
#> 5 CoD code has a number as its second value 0
#> 6 CoD code has a period (`.`) character in the wrong place; CoD code has… 0
#> 7 CoD code starts with `O` or `I`; CoD code has a number as its second v… 0
#> 8 CoD code has a period (`.`) character in the wrong place; CoD code sta… 0
#> 9 CoD code has `O` or `I` as its second value 0
#> 10 CoD code has a period (`.`) character in the wrong place; CoD code has… 0
#> cod_check_note n
#> <fct> <int>
#> 1 No issues found in CoD code 20
#> 2 CoD code has a period (`.`) character in the wrong place 0
#> 3 CoD code starts with `O` or `I` 0
#> 4 CoD code has a period (`.`) character in the wrong place; CoD code s… 0
#> 5 CoD code has a number as its second value 0
#> 6 CoD code has a period (`.`) character in the wrong place; CoD code h… 0
#> 7 CoD code starts with `O` or `I`; CoD code has a number as its second… 0
#> 8 CoD code has a period (`.`) character in the wrong place; CoD code s… 0
#> 9 CoD code has `O` or `I` as its second value 0
#> 10 CoD code has a period (`.`) character in the wrong place; CoD code h… 0
#> # ℹ 55 more rows
#>
#> $`Ill-defined code`
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4 changes: 2 additions & 2 deletions pkgdown/_pkgdown.yml
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Expand Up @@ -7,7 +7,7 @@ development:

template:
bootstrap: 5
bootswatch: journal
bootswatch: sandstone
theme: breeze-light
ganalytics: G-919S6XG78B

Expand All @@ -19,7 +19,7 @@ home:
href: https://www.who.int/standards/classifications/classification-of-diseases/services/codedit-tool

navbar:
bg: info
bg: primary
type: light
structure:
left: [home, intro, reference, articles, news]
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