From 3cf2401778524a8456f87bdb5cc78d97a310a659 Mon Sep 17 00:00:00 2001 From: Rodrigo Zepeda-Tello Date: Wed, 24 Jul 2024 23:20:42 -0400 Subject: [PATCH] changed to 0.5.2 --- .Rbuildignore | 2 + DESCRIPTION | 2 +- NEWS.md | 6 +++ README.Rmd | 17 +++++++- README.md | 35 ++++++++-------- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/LICENSE.html | 2 +- docs/articles/Generating-your-token.html | 2 +- docs/articles/ICD-10.html | 2 +- docs/articles/ICD-11.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 6 +-- docs/index.html | 40 +++++++++---------- docs/news/index.html | 8 +++- docs/pkgdown.yml | 2 +- docs/reference/autocode.html | 2 +- docs/reference/check_names.html | 2 +- .../check_token_expiration_time.html | 2 +- docs/reference/code_info.html | 2 +- ...de_maternal_death_time_from_pregnancy.html | 2 +- docs/reference/code_place.html | 2 +- docs/reference/codify_ans.html | 2 +- docs/reference/codify_manner_of_death.html | 2 +- docs/reference/codify_sex.html | 2 +- docs/reference/doris.html | 2 +- .../reference/dot-icd10_search_recursive.html | 2 +- docs/reference/get_token.html | 2 +- docs/reference/icd10_blocks.html | 2 +- docs/reference/icd10_chapters.html | 2 +- docs/reference/icd10_code_search_release.html | 2 +- docs/reference/icd10_codes.html | 2 +- docs/reference/icd10_name_children.html | 2 +- docs/reference/icd10_parent.html | 2 +- docs/reference/icd10_release_info.html | 2 +- docs/reference/icd10_releases.html | 2 +- docs/reference/icd10_request_children.html | 2 +- docs/reference/icd10_search.html | 2 +- docs/reference/icd10_title.html | 2 +- docs/reference/icd11_linearization_info.html | 2 +- docs/reference/icd11_lookup.html | 2 +- docs/reference/icd11_release_info.html | 2 +- docs/reference/id.html | 2 +- docs/reference/index.html | 2 +- docs/reference/iso_8601.html | 2 +- docs/reference/make_request.html | 2 +- docs/reference/name_df.html | 2 +- docs/reference/order_columns.html | 2 +- docs/reference/request_WHO.html | 2 +- docs/reference/residual.html | 2 +- docs/reference/retrieve.html | 2 +- docs/reference/right_align_df.html | 2 +- docs/reference/search.html | 2 +- docs/search.json | 2 +- 54 files changed, 115 insertions(+), 93 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index d8cb3d3..cc62957 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,3 +8,5 @@ ^codecov\.yml$ ^\.github$ ^vignettes/articles$ +^_pkgdown\.yml +^\.Rhistory diff --git a/DESCRIPTION b/DESCRIPTION index fdf27c9..71436d0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: WHOicd Title: Retrieve data from the World Health Organization (WHO) International Classification of Diseases (ICD) API version 2 -Version: 0.5.1 +Version: 0.5.2 Authors@R: person("Rodrigo", "Zepeda-Tello", , "rzepeda17@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4471-5270")) diff --git a/NEWS.md b/NEWS.md index 955e367..528b17f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# WHOicd 0.5.2 + +* Added the site links to `DESCRIPTION`. +* Changed website version to bootstrap v5. +* Removed history from package. + # WHOicd 0.5.1 * Stopped exporting functions to `code_place` and `code_maternal`. diff --git a/README.Rmd b/README.Rmd index a314c37..1ff6297 100644 --- a/README.Rmd +++ b/README.Rmd @@ -56,7 +56,7 @@ token <- get_token(CLIENT_ID, CLIENT_SECRET) There are three main objectives for this package: -1. Use of the DORIS system to obtain underlying cause of death. +1. Use of the DORIS system to obtain underlying cause of death from death certificate information. 2. [Use of ICD-11 to codify causes of death](https://rodrigozepeda.github.io/WHOicd/articles/ICD-11.html). 3. [Use of ICD-10 to search for causes of death](https://rodrigozepeda.github.io/WHOicd/articles/ICD-10.html). @@ -64,7 +64,7 @@ There are three main objectives for this package: The [Digital Open Rule Integrated Cause of Death Selection](https://icd.who.int/doris/en), DORIS, provides a framework for obtaining the underlying cause of death from a death certificate. DORIS -functionality has been implemented in the `doris` function. +functionality has been implemented in the `doris()` function. The following example considers a 60 year old female whose primary cause of death was `2D42`: `Malignant neoplasms of ill-defined sites` due to `2E03`: `Malignant neoplasm metastasis in bone or bone marrow` due to `CB41.0Z`: `Acute respiratory failure, unspecified`. @@ -108,19 +108,32 @@ Additional information on ICD-11 can be found in the [ICD-11 article](https://ro The main function relating to ICD-10 is `icd10_search()` which searches for the titles and parents of codes, blocks of chapters. As an example, we can search for the following vector and obtain a `data.frame`: ```{r} +#| results: false #Search for code, specific code, chapter and block codes <- c("D60", "IX", "I10-I15") icd10_search(token, codes) ``` +```{r} +#| echo: false +icd10_search(token, codes) |> tibble::as_tibble() +``` + If you only want to get the title of the current code/chapter/block you can use `icd10_title` which is faster as it requires less requests to the API: ```{r} +#| results: false #Search for code, specific code, chapter and block codes <- c("D60", "IX", "I10-I15") icd10_title(token, codes) ``` +```{r} +#| echo: false +#Search for code, specific code, chapter and block +icd10_title(token, codes) |> tibble::as_tibble() +``` + Additional information on ICD-10 can be found in the [ICD-10 article](https://rodrigozepeda.github.io/WHOicd/articles/ICD-10.html) ## Support diff --git a/README.md b/README.md index 1f5d788..e776c6c 100644 --- a/README.md +++ b/README.md @@ -52,7 +52,8 @@ token <- get_token(CLIENT_ID, CLIENT_SECRET) There are three main objectives for this package: -1. Use of the DORIS system to obtain underlying cause of death. +1. Use of the DORIS system to obtain underlying cause of death from + death certificate information. 2. [Use of ICD-11 to codify causes of death](https://rodrigozepeda.github.io/WHOicd/articles/ICD-11.html). 3. [Use of ICD-10 to search for causes of @@ -63,7 +64,7 @@ There are three main objectives for this package: The [Digital Open Rule Integrated Cause of Death Selection](https://icd.who.int/doris/en), DORIS, provides a framework for obtaining the underlying cause of death from a death certificate. -DORIS functionality has been implemented in the `doris` function. +DORIS functionality has been implemented in the `doris()` function. The following example considers a 60 year old female whose primary cause of death was `2D42`: `Malignant neoplasms of ill-defined sites` due to @@ -152,20 +153,15 @@ we can search for the following vector and obtain a `data.frame`: #Search for code, specific code, chapter and block codes <- c("D60", "IX", "I10-I15") icd10_search(token, codes) -#> searched code code_title block -#> 1 D60 D60 Acquired pure red cell aplasia [erythroblastopenia] D60-D64 -#> 2 IX -#> 3 I10-I15 I10-I15 -#> block_title chapter -#> 1 Aplastic and other anaemias III -#> 2 IX -#> 3 Hypertensive diseases IX -#> chapter_title -#> 1 Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism -#> 2 Diseases of the circulatory system -#> 3 Diseases of the circulatory system ``` + #> # A tibble: 3 × 7 + #> searched code code_title block block_title chapter chapter_title + #> + #> 1 D60 D60 Acquired pure red cell… D60-… Aplastic a… III Diseases of … + #> 2 IX IX Diseases of … + #> 3 I10-I15 I10-… Hypertensi… IX Diseases of … + If you only want to get the title of the current code/chapter/block you can use `icd10_title` which is faster as it requires less requests to the API: @@ -174,12 +170,15 @@ the API: #Search for code, specific code, chapter and block codes <- c("D60", "IX", "I10-I15") icd10_title(token, codes) -#> searched title -#> 1 D60 Acquired pure red cell aplasia [erythroblastopenia] -#> 2 IX Diseases of the circulatory system -#> 3 I10-I15 Hypertensive diseases ``` + #> # A tibble: 3 × 2 + #> searched title + #> + #> 1 D60 Acquired pure red cell aplasia [erythroblastopenia] + #> 2 IX Diseases of the circulatory system + #> 3 I10-I15 Hypertensive diseases + Additional information on ICD-10 can be found in the [ICD-10 article](https://rodrigozepeda.github.io/WHOicd/articles/ICD-10.html) diff --git a/docs/404.html b/docs/404.html index 6f952a0..d5d391f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -20,7 +20,7 @@ WHOicd - 0.5.1 + 0.5.2