lazyatom / cmmid.github.io

OVERVIEW

The source for the web page advertising assorted CMMID project work.

Adding NEW posts

To add a new post to the website, add a new markdown or html file to the correct category under /topic/category/_posts, e.g. /topic/covid19/_posts

Copy the /topics/YYYY-MM-DD-post-template.md as a template to work on.

Front-matter variables are optional, but the following are available:

title: Title of the post
description: Short description of post
status: paper-under-peer-review, paper-accepted-at-journal, paper-published-at-journal, etc (see template for full list)
update: YYYY-MM-DD when post was updated

Posts without the status 'paper-accepted-at-journal' or 'paper-published-at-journal' will automatically show the "Ths study is not peer-reviewed" message. To suppress this message, set suppress_peerreviewed: true

tags: [transmission-dynamics, severity, lmic-considerations, control-measures, mixing-patterns, healthcare-settings, comments-opinions, forecasts-and-projections]

Posts can appear in multiple sections; delete the tags as appropriate

authors:
  - id: author_1
  - id: author_2
  - id: author_3

If you want to use mathjax, tabs, or other objects regularly used in Rmarkdown html files:

1. set 'output: html_fragment' in your rmarkdown file
2. set rmarkdown_html_fragment: true in the front-matter of your post

Figures and attachments

Copy your figures and attachments into the /topics/covid19/figures and /topics/covid19/reports directories accordingly. Make sure they have a unique name (chances are someone else has already generated a figure1.png file), or create under /topics/covid19/figures specifically for your figures. The template contains some example markup demonstrating this.

Adding TRANSLATED posts

Post translations can be added alongside their English versions, but with the language variable set in the front-matter:

language: zh-cn

These posts can share the same images as the English versions.

Currently, only zh-cn is available. If unspecified, the language of the post will be set to en-gb automatically.

Adding R Shiny Apps

To add a new shiny app to the visualisations page, all you need to do is copy a file, and change two fields.

Detailed instructions:

1. copy the _shinyapp/template.md file to a new file name in the same directory
2. if using the Github interface, click raw to see the text to copy, then create a new file and paste that in; there is no simple way to duplicate a file in the web interface
3. edit the URL in the shinyurl: https://cmmid-lshtm.shinyapps.io/SOME_APP/ line to match the url where the application is hosted; this can be any url that serves up an R Shiny App
4. edit the title; this must be valid YAML, so no new lines and watch out for : and , in your title - those and other special characters can be addressed by quoting the whole entry
5. DON'T edit the ---s.
6. if using the Github web editing interface, you can check the preview to ensure proper entry. Should see a table-like thing
7. commit your changes

Adding new tags

To add a new tag, two things are required:

1. a topic page with the tag_filter matching that tag (see existing ones for an example)
2. an entry in _data/translations.yml (only the id, matching the tag, and an en-gb version are required).

Both of these must be in place before the new tag will be visible on the site.