- use epireview functions to get parameters

[cm401]

• add notes & limitations on review data

• Please check if the PR fulfills these requirements

• I have read the CONTRIBUTING guidelines
• A new item has been added to NEWS.md
• Tests for the changes have been added (for bug fixes / features)
• Docs have been added / updated (for bug fixes / features)
• Checks have been run locally and pass

• What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)
  In the data_from_epireview vignette we use epireview functions to get and filter parameters
  We add notes on epireview data for users.

• What is the current behavior? (You can also link to an open issue here)
  No change in behaviour.

• What is the new behavior (if this is a feature change)?
  No change in behaviour.

• Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)
  No

• Other information:

@annecori, @patcatgit, @kellymccain28, @ruthmccabe - please review, in particular notes + limitations on epireview.

[kellymccain28]

Notes and limitations look great to me. I have a few editing suggestions:

• Update the sentence under Multi-row epireview entries to:

• "We are trying to avoid this as linking these entries is very challenging, but there are still some cases in which there are linked parameters on different rows."

• A few small edits to the limitations section:

• The database schema of {epireview} has evolved over time as the Imperial PERG team has extracted more pathogens.
• A list of parameter types is available in the {epireview} package
• It is important to differentiate between variability of the sample (e.g. sample standard deviation) and uncertainty of the estimate (e.g. 95% confidence interval or credible interval). From the database version of {epireview} of Zika, we will explicitly expose this to remove any ambiguity of the extracted data. Please note that in the Marburg, Lassa, and Ebola datasets, there may be some ambiguity between variability and uncertainty.
• This is functionality in {epireview} which will be developed and improved over the coming months.

[joshwlambert]

Thanks for this contribution @cm401 & @kellymccain28. The {epireview} -> {epiparameter} vignette has change quite a bit since this PR was opened, but I think the updates are still valuable.

I think the use of epireview::get_parameters() is not needed for the vignette as subsetting with brackets ([) works fine. However, the edits to the text and the limitations are useful additions. Therefore I propose to try and rebase this branch on to the main branch to get all of the recent updates to this vignette and then merge these changes. If the rebase does not work because of too many conflicts then I will make a new branch and commit these additions, with Kelly's comments, with you both added as commit co-authors to ensure your contributions are recorded.

[joshwlambert]

The rebase worked so everything is now up-to-date.

I've updated the text with @kellymccain28's suggestions, and I think everything is ready to be merged.

Thanks both for your contribution. Apologies it took so long to get it merged into the package.