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Remove Hmisc dependency #273

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Remove Hmisc dependency #273

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ntorresd
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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.

@ntorresd ntorresd changed the base branch from main to cran-fixes January 21, 2025 21:18
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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(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

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(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

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(Note that results may be inaccurate if you branched from an outdated version of the target branch.)

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codecov-commenter commented Jan 21, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (eeda3af) to head (afa6d3b).

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     

☔ View full report in Codecov by Sentry.
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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.)

Copy link

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.)

Copy link

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.)

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@Bisaloo Bisaloo left a comment

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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?

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3 participants