Issue #4: Setup vignette

[kaitejohnson]

Description

This PR closes #4.

Here we introduce the Getting Started vignette. We start by using epinowcast package data, which itself uses the truth data from the German hospitalization nowcast hub. It contains daily data indexed by reference date and report date. enw_preprocess_data() is used, and we transform the output of the triangle to a matrix where the rows are the time points and the columns are the delays.

We then use this reporting triangle to estimate the delay. The subsequent sections for applying the delay, estimating the uncertainty, and generating the nowcast are outlined.

Additional tests are required for internal functions, e.g. handle_neg_values() and validate_triangle().

In future versions, we can modify the data we use for the vignette (e.g. another nice place to start might be from visit-level line list data as in https://github.com/kassteele/Nowcasting/blob/master/data/measles_NL_2013_2014.dat)

Checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have included the target issue or issues in the PR title in the for Issue(s) issue-numbers: PR title
• I have read the contribution guidelines.
• I have tested my changes locally.
• I have added or updated unit tests where necessary.
• I have updated the documentation if required.
• My code follows the established coding standards.
• I have added a news item linked to this PR.
• I have reviewed CI checks for this PR and addressed them as far as I am able.

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[kaitejohnson]

@seabbs A little stuck on the linting error (I see the warnings, one is for a global variable and the other falsely thinks a grep is a file path. But exit code 31 is about storage space so not sure.