Separate plotting code from data prep

[pratikunterwegs]

This PR separates the data preparation for plotting into intermediate functions prefixed prep_plot_*().

Known issues:
- Two functions in burden_diagnostics.R are yet to be worked on; now removed.

• Some plotting preparation and plotting functions need better tests.

[github-actions]

This pull request:

• Adds 1 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 0 existing dependencies (direct and indirect)
• Removes 0 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

This pull request:

• Adds 1 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 2 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

This pull request:

• Adds 1 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 2 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

This pull request:

• Adds 1 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 2 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[xiangli313]

we also have deaths_cwyx, cases_cwyx, dalys_cwyx, yll_cwyx, rubella_deaths_congenital and rubella_cases_congenital.

[github-actions]

This pull request:

• Adds 1 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 2 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

This pull request:

• Adds 1 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 2 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[xiangli313]

I think this is looking good. I am approving it; and will be using it once merged (will feedback).

[pratikunterwegs]

@xiangli313 - I had a question regarding this function that prepares the FVP data for plotting. This function is used to generate the data for the FVPs-over-time plot (usually Fig. 2 in burden diagnostics reports). Where can I find an example of the FVPs dataset that is used to make the FVPs plot? The related plotting function is plot_fvp().

[kgaythorpe]

fantastic, thanks Pratik, happy to approve from my side

[pratikunterwegs]

@xiangli313 - similar question/request for some example coverage set data so that this function can be tested. This function prepares data that is used to generate the coverage set data (usually Fig. 1 in diagnostics reports). The related plotting function is plot_coverage_set().

[github-actions]

This pull request:

• Adds 1 new dependencies (direct and indirect)
• Adds 1 new system dependencies
• Removes 2 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

Reach out on slack (#code-review or #help channels) to double check if there are base R alternatives to the new dependencies.

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)