Remove Hmisc dependency

[ntorresd]

This PR removes Hmisc as a dependency. So far, we were using Hmisc::binconf to compute the binomial confidence interval according to the Clopper-Pearson method. As pointed out by @Bisaloo in #174, this is a very heavy dependency to be used only for this purpose.

Now, the binomial confidence interval is computed by means of dependencies already present in the packages, namely purrr and stats. I adapted the code from this post to our needs and it yields similar results as before.

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (eeda3af) to head (83407b1).

Additional details and impacted files

@@             Coverage Diff              @@
##           cran-fixes      #273   +/-   ##
============================================
  Coverage      100.00%   100.00%           
============================================
  Files               6         6           
  Lines            1015      1017    +2     
============================================
+ Hits             1015      1017    +2     

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[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

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

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

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

[Bisaloo]

Visual control indicates this change returns the same value as in main, as desired.

It might however be good to add a snapshot test on prepare_serosurvey_for_plotting() to formally confirm this here and in future changes. What do you think?

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

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

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

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

[ntorresd]

Visual control indicates this change returns the same value as in main, as desired.

It might however be good to add a snapshot test on prepare_serosurvey_for_plotting() to formally confirm this here and in future changes. What do you think?

Thanks a lot for the review and your suggestions, @Bisaloo! Regarding the snapshot test, I would rather have a direct comparison of the results with a benchmark obtained using Hmisc::binconf(); I did this in this branch. Let me know if you agree with this test so I can bring it here. I also found some warnings in the tests regarding the function purrr::lift_vd() that I used to replace Hmisc::binconf(), it seems like it's deprecated... do you know any workaround this?

Btw, do you know how to fix the problem with pandoc that is causing the R-CMD checks to fail for some Ubuntu distributions? I'm sure I've encountered this before, but I don't remember how (if) I solved it.

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

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

[Bisaloo]

Regarding the snapshot test, I would rather have a direct comparison of the results with a benchmark obtained using Hmisc::binconf(); I did this in this branch. Let me know if you agree with this test so I can bring it here

Yes, sounds good.

I also found some warnings in the tests regarding the function purrr::lift_vd() that I used to replace Hmisc::binconf(), it seems like it's deprecated... do you know any workaround this?

#274 contains a proposal for an alternative. Please double check before integrating it in case I missed anything.

Btw, do you know how to fix the problem with pandoc that is causing the R-CMD checks to fail for some Ubuntu distributions? I'm sure I've encountered this before, but I don't remember how (if) I solved it.

I cannot find mentions of pandoc in the CI failure logs. Could you link to the specific log / line you're referencing please?

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

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

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 7 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

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

[ntorresd]

Clean version in #277.