R code and datasets to replicate analyses in Clark et al (in review)

R code and raw excel spreadsheets needed to replicate analyses in Clark et al (in review). The excel dataset contains a number of sheets that are required for analysis, including a sheet of parasite infection statuses for individual birds (sheet 1: birds), a sheet containing information on parasite lineage names, MalAvi names and cytochrome-b sequences (sheet 2: lineages) and a sheet that links parasite ID numbers in sheet 1 with parasite lineage names in sheet 2 (sheet 3: link). R scripts in the 'Functions' folder are used in analysis. Please follow steps in the Appendices to replicate the workflow used in the manuscript. A number of libraries are needed along the way, and it is important to follow the file structure shown in the Appendices to ensure smooth replication