Clean up inline methods variables

[jasonratcliff]

Chapter Globals

Replace methods_variables list of inline R expressions, sequence vectors, and table data.

Tables

• [x] Table 2 | Specimens • 3d56adab90c6b41b539024023c4c73177d9c3ab9

  • $collections -> samples (858eb5e408b48c249ad3a3e757f6467e7a2c92d9)
  • $dna_footnote -> footnotes

• [x] Table 3 | DNA Primers • d673714be005fe64ab847ba1468fcd6386c36264

  • $primers -> primers

• [x] Table 4 | Phylogenetics • a2d0d19edcd751eb3783f1fdc6f6294a883fd41c

  • $star_beast -> species

Find

• Specimens

  • $seinet

• Biostrings

  • $fasta_paths
  • $fasta_msa

Occurrences

Find usages of global methods_variables list in Thesis scope files:

Targets
    Occurrences of 'methods_variables\$.+?(?=[^A-z])' in Thesis with mask '!*.R'
Found Occurrences in Thesis with mask '!*.R'  (13 usages found)
    Unclassified  (13 usages found)
        thesis  (13 usages found)
            docs/thesis/chapters  (13 usages found)
                methods.qmd  (13 usages found)
                    10 methods_variables$seinet <-
                    14 methods_variables$fasta_paths <-
                    21 methods_variables$fasta_msa <-
                    22 purrr::map(.x = methods_variables$fasta_paths, function(fasta) {
                    27 names(methods_variables$fasta_msa) <-
                    29 x = fs::path_file(methods_variables$fasta_paths))
                    76 `r nrow(methods_variables$seinet)` with specimen occurrence
                    136 `r length(methods_variables$fasta_msa$rITS)` specimens for the rITS locus,
                    137 `r length(methods_variables$fasta_msa$rps)` for the *rps*
                    138 intron, and `r length(methods_variables$fasta_msa$ycf1)` for *ycf1*.
                    489 multi-FASTA sequences (rITS: n=`r length(methods_variables$fasta_msa$rITS)`,
                    490 *rps*: n=`r length(methods_variables$fasta_msa$rps)`,
                    491 *ycf1*: n=`r length(methods_variables$fasta_msa$ycf1)`) and the subset of