Document Preparation

[mmore500]

• [x] ~put graphicsx in "draft mode," add build option to Makefile to disable graphicsx "draft mode"~
  • ~due to limitations with overleaf, we won't be able to sync the figure graphics into the overleaf environment~
  • ~this means that the raw data for CSV includes won't be available there either, how to deal with that?~
  • new plan: the document just won't compile on overleaf
• [x] setup binder branch as submodule on tex branch
• [x] incorporate meeting feedback into introduction outline
• [x] turn introduction outline into very rough draft text
• [ ] refine introduction draft text
• [x] outline methods
• [x] turn methods outline into draft text
  • [x] phylometric definitions and intuitions go in this section
  • [x] find and cite scientific sofware dependencies
• [ ] build \{figure}'s for results
  • [ ] perfect phylogenies by regime
  • [x] plain regime phylogenies by reconstruction quality (probably in supplement for space)
  • [ ] raincloud plot of reconstruction qualities (plain for main text, others go in supplement)
  • [x] ~csvsimple reconstruction quality summary statistics tables~
    • ~create different table for each sensitivity analysis condition~
    • new plan: just make empty tables in supplement and then fill tables in later
  • [x] phylometrics by regime for perfect phylogenies
  • [x] phylometric "fingerprint" heatmap
  • [x] phylometrics by regime across reconstruction qualities
• [x] write figure captions
• [x] outline results
• [x] put statistics into results
• [x] turn results outline into draft text
  • [x] phylometrics by evolutionary regime
  • [x] phylometrics by evolutionary regime with spatial structure nuisance
  • [x] tree reconstruciton quality
  • [x] reconstruction phylometrics error
• [x] outline conclusion
• [x] turn conclusion outline into draft text
• [x] write abstract