Apply quarto syntax for methods code cells

[jasonratcliff]

Breaking Changes

Data

Move methods chapter table data *.csv files from instdata/extdata/Methods to skip installing as external data:

• [x] Move to docs/thesis/tables/*.csv
  • [x] Table 2. samples.csv DNA sample specimens (3d56adab90c6b41b539024023c4c73177d9c3ab9, 858eb5e408b48c249ad3a3e757f6467e7a2c92d9)
  • [x] Table 3. primers.csv sequencing primer sets (d673714be005fe64ab847ba1468fcd6386c36264)
  • [x] Table 4. beast.csv *BEAST species hypotheses (a2d0d19edcd751eb3783f1fdc6f6294a883fd41c)

Deprecation

• [x] Useknitr to build table cross reference (857f3b3e3e706ed97ea9f9a081810da0b4f4fcf8)

  • knit_table_dna()
  • html_caption()

• [x] Remove utils.R functions (20fe8784dde5ae98b8ae4fae0f75e559d57bddc0)

  • save_plot()
  • capitalize()
  • italicize()

Chunks

• [x] Update chunk labels with prefixed quarto cross references

Renamed

bookdown	quarto
MethodsVariables	methods
TableDnaSpecimens	samples-table
TableDnaSpecimensLatex	tbl-samples-latex
TableDnaSpecimensLatexContinued	tbl-samples-continued
TableDnaSpecimensHtml	tbl-samples-html
TableSpeciesTreeHypotheses	beast-species
TableSpeciesTreeHypothesesLatex	tbl-species-tree
TableSpeciesTreeHypothesesLatexContinued	tbl-species-tree-continued

Notes

• [x] Utilize commonmark to handle markdown conversions (989e3d8cddc077f366f4b4ffc35f6f282f464058)

  • Use knitr::pandoc_to() to replace knit_variables globals

• 95