Update ref files

[cristinamullin]

• updates reference files and flag functions to deal with all values
• wait to merge until after Tulsa training

[codecov-commenter]

Codecov Report

Merging #340 (40e8f58) into develop (ed9a2df) will decrease coverage by 0.58%.
The diff coverage is 60.00%.

❗ Current head 40e8f58 differs from pull request most recent head d5a267c. Consider uploading reports for the commit d5a267c to get more accurate results

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@@             Coverage Diff             @@
##           develop     #340      +/-   ##
===========================================
- Coverage    53.47%   52.89%   -0.58%     
===========================================
  Files           11       11              
  Lines         2891     2898       +7     
===========================================
- Hits          1546     1533      -13     
- Misses        1345     1365      +20     

Files Changed	Coverage Δ
R/Utilities.R	60.06% <ø> (ø)
R/ResultFlagsDependent.R	40.48% <46.15%> (ø)
R/GenerateRefTables.R	85.83% <62.50%> (-1.95%)	⬇️
R/ResultFlagsIndependent.R	57.83% <100.00%> (-0.49%)	⬇️

... and 1 file with indirect coverage changes

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