From 9084fff68fafbdb58a7417c4dd52f79a44d154bf Mon Sep 17 00:00:00 2001 From: Ernest Guevarra Date: Thu, 31 Oct 2024 14:39:19 +0000 Subject: [PATCH] update pkgdown.yml to sandstone - primary --- README.Rmd | 2 +- README.md | 53 ++++++++++++++++++++++---------------------- pkgdown/_pkgdown.yml | 4 ++-- 3 files changed, 30 insertions(+), 29 deletions(-) diff --git a/README.Rmd b/README.Rmd index d7a96df..99ae1f1 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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( diff --git a/README.md b/README.md index d02b293..21b79cd 100644 --- a/README.md +++ b/README.md @@ -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( @@ -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 -#> -#> 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 +#> +#> 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 , dod_check_note +#> # ℹ 3 more variables: code_check_note , dod_check , +#> # dod_check_note ``` 2. Structure raw cause-of-death data for input into CoDEdit tool @@ -220,18 +221,18 @@ cod_check_code( cod_check_code_summary() #> $`Code structure` #> # A tibble: 65 × 2 -#> cod_check_note n -#> -#> 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 +#> +#> 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` diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index f15a57b..0d55538 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -7,7 +7,7 @@ development: template: bootstrap: 5 - bootswatch: journal + bootswatch: sandstone theme: breeze-light ganalytics: G-919S6XG78B @@ -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]