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Accessing site-files

Accessing-site-files.Rmd

Downloading a site file

To access a site file - a collated set of data for a specific country - you will need to follow these steps:

  1. Sign up for a github account, single user accounts are free.

  2. Send an email to to ask for site file access. Please include the following details:

  • Your name
  • Your institution
  • Your github username
  • A short description of the project you will use the site files for
  1. You will then be added to the malariaverse github team.

When you receive confirmation of this (look out for a notification on github), you can then use the site package inbuilt functionality to download site files.

You can call fetch_site(), specifying the ISO3c country code of your country of interest. For example, for Nigeria: fetch_site(iso3c = "NGA", admin_level = 1, urban_rural = TRUE).

The first time you do this, you will see interactive authentication instructions asking you to access a github link and providing an authentication code. Open the link and copy the code to authorise access. This process should cache your credentials so that you don’t have to authorise every time.

Updates and versioning

Site files are periodically updated. You can check which version you have by inspecting the site metadata. The function available_sites() lists all site files currently available on the server.

By default, fetch_site(iso3c = ...) downloads the latest version of a site file. For reproducibility, you can also specify admin_level, urban_rural, and version to fetch a particular file.

For stable workflows, we recommend downloading and storing the site files you use once, rather than always pulling the latest version. Otherwise, downstream pipelines may break if new site file options become available.

News on new updates will be posted here.

Issues

If you encounter any issues with this process, please post an issue, with as much detail as possible on the site package issue page.