Add guide on how to estimate clade frequencies

[huddlej]

Description of proposed changes

Adds the Jupyter notebook and corresponding restructured text version of a how-to guide to estimate clade frequencies from SARS-CoV-2 data.

An open question with this guide (and others like it in the future) is where we should source the data. The benefit to the current approach is that it does not require users to prepare any data in advance; data are fetched from the live Nextstrain builds. The disadvantages of this approach are that the guide's static figures quickly diverge from current data and we don't show users how to load their own local data which may be much more relevant.

Another potential issue is how we should maintain guides like this that we generate directly from a notebook environment. To prepare this guide for the docs, I had to manually copy images into the images directory and rename them for clarity. The HTML/CSS presentation of tables is also not ideal. We might want to standardize these steps for future guides, even if the standards are a checklist in the documentation's documentation.

Testing

The initial guide was tested by @kistlerk and this version reflects edits based on (most of) her comments. One comment I did not address here was a suggestion to allow users to source their own local data for the guide instead of fetching the live Nextstrain data (see discussion above).

The guide is available through this PR's RTD build.

[victorlin]

Suggested change

	tree_url = "https://data.nextstrain.org/ncov_global.json"
	frequencies_url = "https://data.nextstrain.org/ncov_global_tip-frequencies.json"
	tree_url = "https://data.nextstrain.org/ncov_open_global.json"
	frequencies_url = "https://data.nextstrain.org/ncov_open_global_tip-frequencies.json"

[victorlin]

Another potential issue is how we should maintain guides like this that we generate directly from a notebook environment.

What about an extension like nbsphinx or MyST-NB? We'd still have to run the notebook to generate new plots but less manual work than maintaining the same content in both .ipynb and .rst.

[huddlej]

During issue triage we also realized that this guide can be updated to use Nextstrain open data.