Example of using contentid

contentid_fern_example.R

library(tidyverse)

#' Parse fossil calibration data in Sundue and Testo 2016 SI
#'
#' Testo WL, Sundue MA (2016) A 4000-species dataset provides new insight into
#' the evolution of ferns. Molecular Phylogenetics and Evolution 105:200–211.
#' https://doi.org/10.1016/j.ympev.2016.09.003
#'
#' @param testo_sundue_2016_si_path Path to Sundue and Testo 2016 SI file
#' (xlsx format).
#'
#' @return Tibble with fossil calibration dates
#'
parse_ts_calibrations <- function(testo_sundue_2016_si_path) {
readxl::read_excel(
  testo_sundue_2016_si_path,
  # Divergence dates are in the 3rd sheet
  sheet = 3
) %>%
  janitor::clean_names() %>%
  mutate(
    stem_crown = str_to_lower(stem_crown),
    clade =
      str_replace_all(clade, "Aglaomorpha heraclea", "Drynaria heraclea") %>%
      str_replace_all("Alsophila/Cyathea clade", "Alsophila+Cyathea") %>%
      str_replace_all("Isoetales", "Isoëtales") %>%
      str_replace_all(" ", "_")) %>%
  transmute(
    minimum_age = age,
    node_calibrated = paste(stem_crown, clade),
    fossil_taxon = fossil,
    affinities_group = stem_crown,
    affinities = clade
  ) %>%
  mutate(across(
    c(node_calibrated, affinities),
    ~str_replace_all(., "Polypodium", "Polypodium s.l.")))
}

ts_fossil_calibration_points <- parse_ts_calibrations(
    testo_sundue_2016_si_path = contentid::resolve(
      # hash corresponds to the URL of the file on github
      "hash://sha256/c629f4617e7e2329a10cb1b207b82a6720653a67eafcaaa97cc6ee891ae7fdf7"
    )
  )