2.1 Set directories for saving data

Set a list containing directories for easiness of reference:

directories <- list(
  # where you raw data is
  data = "data", 
  # where to save transformed compositional data (CoDa)
  transCoDa = "transformed_CoDa", 
  # where to save files concerning protocol workflow
  prot1 = "Protocol_1_geochemical_data",
  prot2 = "Protocol_2_petrographic_data",
  prot3 = "Protocol_3_geochemical_and_petrographic_data",
  prot4 = "Protocol_4_provenance_data",
  prot4_Shipwreck = "Protocols_4_provenance_data_with_shipwrecks"
)

Create the respective folders in the current R session working directory, if they do not exist:

lapply(directories, dir.create, showWarnings = FALSE)