More small bugfixes

[katy-sadowski]

Addresses #347 #461 #438

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (eb295b0) 86.19% compared to head (1f57b24) 85.97%.

❗ Current head 1f57b24 differs from pull request most recent head 16990b4. Consider uploading reports for the commit 16990b4 to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #502      +/-   ##
===========================================
- Coverage    86.19%   85.97%   -0.23%     
===========================================
  Files           16       16              
  Lines          884      884              
===========================================
- Hits           762      760       -2     
- Misses         122      124       +2     

Files	Coverage Δ
R/writeJsonResultsTo.R	76.78% <100.00%> (ø)

... and 2 files with indirect coverage changes

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