attempted child

ljwright · ljwright · commit 0165de9d00eb · 2023-12-24T07:03:21.000Z
diff --git a/.gitignore b/.gitignore
@@ -16,3 +16,6 @@ vendor/
 .Rproj.user
 
 /.quarto/
+
+# Ignore R environment
+.Renviron
diff --git a/README.md b/README.md
@@ -1,174 +1,12 @@
-# just-the-docs-template
+# Introduction
 
-This is a *bare-minimum* template to create a [Jekyll] site that:
+The Centre for Longitudinal Studies (CLS) manages four cohort studies for which data is currently available to researchers:
 
-- uses the [Just the Docs] theme;
-- can be built and published on [GitHub Pages];
-- can be built and previewed locally, and published on other platforms.
+1. [The National Child Development Study (NCDS)](https://doi.org/10.1093/ije/dyi183), a birth cohort of individuals born in Britain in a single week of March 1958.
+2. [The 1970 British Cohort Study (BCS70)](https://doi.org/10.1093/ije/dyac148), a birth cohort of individuals born in Britain in a single week of April 1970.
+3. [Next Steps](https://doi.org/10.5334/ohd.16), a cohort of English schoolchildren followed from age 13/14 and born in 1989/90.
+4. [The Millennium Cohort Study (MCS)](https://doi.org/10.1093/ije/dyu001), a birth cohort of individuals born in Britain in 2000/02.
 
-More specifically, the created site:
+This is the GitHub repository for the [cls-data.github.io/](https://cls-data.github.io/) website which provides `R` and `Stata` code for common data management tasks in each of the studies. This include merging files across survey sweeps, reshaping data from wide to long format, and identifying correct identifier variables for observational units in each study (e.g., cohort members, families, parents, and so on);
 
-- uses a gem-based approach, i.e. uses a `Gemfile` and loads the `just-the-docs` gem;
-- uses the [GitHub Pages / Actions workflow] to build and publish the site on GitHub Pages.
-
-To get started with creating a site, simply:
-
-1. click "[use this template]" to create a GitHub repository
-2. go to Settings > Pages > Build and deployment > Source, and select GitHub Actions
-
-If you want to maintain your docs in the `docs` directory of an existing project repo, see [Hosting your docs from an existing project repo](#hosting-your-docs-from-an-existing-project-repo).
-
-After completing the creation of your new site on GitHub, update it as needed:
-
-## Replace the content of the template pages
-
-Update the following files to your own content:
-
-- `index.md` (your new home page)
-- `README.md` (information for those who access your site repo on GitHub)
-
-## Changing the version of the theme and/or Jekyll
-
-Simply edit the relevant line(s) in the `Gemfile`.
-
-## Adding a plugin
-
-The Just the Docs theme automatically includes the [`jekyll-seo-tag`] plugin.
-
-To add an extra plugin, you need to add it in the `Gemfile` *and* in `_config.yml`. For example, to add [`jekyll-default-layout`]:
-
-- Add the following to your site's `Gemfile`:
-
-  ```ruby
-  gem "jekyll-default-layout"
-  ```
-
-- And add the following to your site's `_config.yml`:
-
-  ```yaml
-  plugins:
-    - jekyll-default-layout
-  ```
-
-Note: If you are using a Jekyll version less than 3.5.0, use the `gems` key instead of `plugins`.
-
-## Publishing your site on GitHub Pages
-
-1.  If your created site is `YOUR-USERNAME/YOUR-SITE-NAME`, update `_config.yml` to:
-
-    ```yaml
-    title: YOUR TITLE
-    description: YOUR DESCRIPTION
-    theme: just-the-docs
-
-    url: https://YOUR-USERNAME.github.io/YOUR-SITE-NAME
-
-    aux_links: # remove if you don't want this link to appear on your pages
-      Template Repository: https://github.com/YOUR-USERNAME/YOUR-SITE-NAME
-    ```
-
-2.  Push your updated `_config.yml` to your site on GitHub.
-
-3.  In your newly created repo on GitHub:
-    - go to the `Settings` tab -> `Pages` -> `Build and deployment`, then select `Source`: `GitHub Actions`.
-    - if there were any failed Actions, go to the `Actions` tab and click on `Re-run jobs`.
-
-## Building and previewing your site locally
-
-Assuming [Jekyll] and [Bundler] are installed on your computer:
-
-1.  Change your working directory to the root directory of your site.
-
-2.  Run `bundle install`.
-
-3.  Run `bundle exec jekyll serve` to build your site and preview it at `localhost:4000`.
-
-    The built site is stored in the directory `_site`.
-
-## Publishing your built site on a different platform
-
-Just upload all the files in the directory `_site`.
-
-## Customization
-
-You're free to customize sites that you create with this template, however you like!
-
-[Browse our documentation][Just the Docs] to learn more about how to use this theme.
-
-## Hosting your docs from an existing project repo
-
-You might want to maintain your docs in an existing project repo. Instead of creating a new repo using the [just-the-docs template](https://github.com/just-the-docs/just-the-docs-template), you can copy the template files into your existing repo and configure the template's Github Actions workflow to build from a `docs` directory. You can clone the template to your local machine or download the `.zip` file to access the files.
-
-### Copy the template files
-
-1.  Create a `.github/workflows` directory at your project root if your repo doesn't already have one. Copy the `pages.yml` file into this directory. GitHub Actions searches this directory for workflow files.
-
-2.  Create a `docs` directory at your project root and copy all remaining template files into this directory.
-
-### Modify the GitHub Actions workflow
-
-The GitHub Actions workflow that builds and deploys your site to Github Pages is defined by the `pages.yml` file. You'll need to edit this file to that so that your build and deploy steps look to your `docs` directory, rather than the project root.
-
-1.  Set the default `working-directory` param for the build job.
-
-    ```yaml
-    build:
-      runs-on: ubuntu-latest
-      defaults:
-        run:
-          working-directory: docs
-    ```
-
-2.  Set the `working-directory` param for the Setup Ruby step.
-
-    ```yaml
-    - name: Setup Ruby
-        uses: ruby/setup-ruby@v1
-        with:
-          ruby-version: '3.1'
-          bundler-cache: true
-          cache-version: 0
-          working-directory: '${{ github.workspace }}/docs'
-    ```
-
-3.  Set the path param for the Upload artifact step:
-
-    ```yaml
-    - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
-        with:
-          path: "docs/_site/"
-    ```
-
-4.  Modify the trigger so that only changes within the `docs` directory start the workflow. Otherwise, every change to your project (even those that don't affect the docs) would trigger a new site build and deploy.
-
-    ```yaml
-    on:
-      push:
-        branches:
-          - "main"
-        paths:
-          - "docs/**"
-    ```
-
-## Licensing and Attribution
-
-This repository is licensed under the [MIT License]. You are generally free to reuse or extend upon this code as you see fit; just include the original copy of the license (which is preserved when you "make a template"). While it's not necessary, we'd love to hear from you if you do use this template, and how we can improve it for future use!
-
-The deployment GitHub Actions workflow is heavily based on GitHub's mixed-party [starter workflows]. A copy of their MIT License is available in [actions/starter-workflows].
-
-----
-
-[^1]: [It can take up to 10 minutes for changes to your site to publish after you push the changes to GitHub](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/creating-a-github-pages-site-with-jekyll#creating-your-site).
-
-[Jekyll]: https://jekyllrb.com
-[Just the Docs]: https://just-the-docs.github.io/just-the-docs/
-[GitHub Pages]: https://docs.github.com/en/pages
-[GitHub Pages / Actions workflow]: https://github.blog/changelog/2022-07-27-github-pages-custom-github-actions-workflows-beta/
-[Bundler]: https://bundler.io
-[use this template]: https://github.com/just-the-docs/just-the-docs-template/generate
-[`jekyll-default-layout`]: https://github.com/benbalter/jekyll-default-layout
-[`jekyll-seo-tag`]: https://jekyll.github.io/jekyll-seo-tag
-[MIT License]: https://en.wikipedia.org/wiki/MIT_License
-[starter workflows]: https://github.com/actions/starter-workflows/blob/main/pages/jekyll.yml
-[actions/starter-workflows]: https://github.com/actions/starter-workflows/blob/main/LICENSE
+For background on these studies, please see cohort profile papers (linked above) and the [CLS website](https://cls.ucl.ac.uk/cls-studies/). Queries on the data can be sent to the [CLS Data team](mailto:clsdata@ucl.ac.uk).
diff --git a/docs/mcs.md b/docs/mcs.md
@@ -1,6 +1,7 @@
 ---
 layout: default
 title: MCS
+has_children: true
 nav_order: 5
 ---
 
diff --git a/docs/misc-sweep_folders.md b/docs/misc-sweep_folders.md
@@ -0,0 +1,48 @@
+---
+layout: default
+title: "Creating Per-Sweep Folders"
+nav_order: 1
+parent: Miscellaneous
+format: docusaurus-md
+---
+
+# Introduction {#introduction}
+
+This page shows code for taking UKDS zipped files, unzipping them and
+placing in per-sweep folders. For this code to work, you should download
+UKDS Stata files for a single study.
+
+To begin you will need to create a folder, XX. Alternatively, this code
+can be downloaded by cloning the this GitHub repository, saving, opening
+the `.Rpoj` file
+
+Why is this not working?
+
+``` r
+df <- read_dta("3y/mcs2_cm_interview.dta")
+df
+```
+
+``` text
+# A tibble: 15,778 × 56
+   MCSID   BCNUM00       BCMEAS00 BCHSER00  BCHPOU00 BCHCOU00 BCBKHT00 BCHTCM00 
+   <chr>   <dbl+lbl>     <dbl+lb> <dbl+lbl> <dbl+lb> <dbl+lb> <dbl+lb> <dbl+lbl>
+ 1 M10001N 1 [1st Cohor… 1 [Both…  26        1 [Par…  1 [Chi… -1 [Not…  97      
+ 2 M10002P 1 [1st Cohor… 1 [Both… 159        1 [Par…  1 [Chi… -1 [Not…  96      
+ 3 M10007U 1 [1st Cohor… 1 [Both…  74        1 [Par…  1 [Chi… -1 [Not… 102      
+ 4 M10008V 1 [1st Cohor… 0 [No m…  -2 [No … -2 [No … -2 [No … -2 [No …  -2 [No …
+ 5 M10008V 2 [2nd Cohor… 0 [No m…  -2 [No … -2 [No … -2 [No … -2 [No …  -2 [No …
+ 6 M10011Q 1 [1st Cohor… 1 [Both…  96        1 [Par…  1 [Chi… -1 [Not… 106      
+ 7 M10014T 1 [1st Cohor… 1 [Both… 246        1 [Par…  1 [Chi… -1 [Not…  97      
+ 8 M10015U 1 [1st Cohor… 1 [Both…  28        1 [Par…  1 [Chi… -1 [Not…  94      
+ 9 M10016V 1 [1st Cohor… 1 [Both… 153        1 [Par…  1 [Chi… -1 [Not… 102      
+10 M10017W 1 [1st Cohor… 1 [Both… 125        1 [Par…  1 [Chi… -1 [Not…  99      
+# ℹ 15,768 more rows
+# ℹ 48 more variables: BCHTMM00 <dbl+lbl>, BCHCMC00 <dbl+lbl>,
+#   BCHMMC00 <dbl+lbl>, BCHTOC00 <dbl+lbl>, BCHTAM00 <dbl+lbl>,
+#   BCHBKD00 <dbl+lbl>, BCHBKM00 <dbl+lbl>, BCHBKY00 <dbl+lbl>,
+#   BCHTAT00 <dbl+lbl>, BCHTTM00 <dbl+lbl>, BCHTIM00 <dbl+lbl>,
+#   BCHTRL0A <dbl+lbl>, BCHTRL0B <dbl+lbl>, BCHTRL0C <dbl+lbl>,
+#   BCHTRL0D <dbl+lbl>, BCHTRL0E <dbl+lbl>, BCHTRL0F <dbl+lbl>, …
+```
+
diff --git a/docs/misc.md b/docs/misc.md
@@ -0,0 +1,8 @@
+---
+layout: default
+title: Miscellaneous
+has_children: true
+nav_order: 6
+---
+
+This section contains code that is applicable to all cohorts.
diff --git a/docs/next_steps-test.md b/docs/next_steps-test.md
diff --git a/docs/next_steps.md b/docs/next_steps.md
@@ -1,7 +1,6 @@
 ---
 layout: default
 title: Next Steps
-has_children: true
 nav_order: 4
 ---
 
diff --git a/docs/test.md b/docs/test.md
diff --git a/quarto/README.txt b/quarto/README.txt
@@ -0,0 +1,3 @@
+Use the following command to save and render into the correct folder:
+
+quarto_render("quarto/next_steps-test.qmd", output_file = "next_steps-test.md")
diff --git a/quarto/misc-sweep_folders.qmd b/quarto/misc-sweep_folders.qmd
@@ -0,0 +1,35 @@
+---
+layout: default
+title: "Creating Per-Sweep Folders"
+nav_order: 1
+parent: Miscellaneous
+format: docusaurus-md
+---
+
+# Introduction
+
+This page shows code for taking UKDS zipped files, unzipping them and placing in per-sweep folders. For this code to work, you should download UKDS Stata files for a single study.
+
+To begin you will need to create a folder, XX. Alternatively, this code can be downloaded by cloning the this GitHub repository, saving, opening the `.Rpoj` file
+
+```{r}
+#| echo: false
+#| include: false
+# curr_dir <- getwd()
+# setwd(Sys.getenv("mcs_fld"))
+```
+
+```{r}
+#| include: false
+
+library(tidyverse)
+library(haven)
+```
+
+Why is this not working?
+
+```{r}
+df <- read_dta("3y/mcs2_cm_interview.dta")
+df
+```
+

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+Use the following command to save and render into the correct folder:`
	`2`	`+`
	`3`	`+quarto_render("quarto/next_steps-test.qmd", output_file = "next_steps-test.md")`