A_06_Predictors_phylogenetic_metrics.R

A - 06: Calculate phylogenetic distinctiveness

Source 00_Configuration.R

Code

source(here::here("Code/00_Configuration.R"))
x <- lapply(package_list, require, character = TRUE)
rm(x)

tax_path <-
  here("Data/input/Tax_lookup.csv")

Read tree and taxonomic data

Code

Tax <-
  read_csv(tax_path)

tree <-
  ape::read.tree(
  here::here("Data/input/MRC_consensus_BirdTree.tre"))

Calculate phylogenetic distinctiveness

Code

pd <-
  phyloregion::evol_distinct(
  tree,
  type = "fair.proportion",
  scale = FALSE,
  use.branch.lengths = TRUE) %>%
  as.data.frame() %>%
  tibble::rownames_to_column(var = "tip.label") %>%
  rename(pd = ".") %>%
  right_join(Tax) %>%
  select(verbatimIdentification, scientificName, pd)

Checks:

Code

pd %>% skimr::skim()

Data summary

Name	Piped data
Number of rows	890
Number of columns	3
_______________________
Column type frequency:
character	2
numeric	1
________________________
Group variables	None

Variable type: character

skim_variable	n_missing	complete_rate	min	max	empty	n_unique	whitespace
verbatimIdentification	0	1	9	32	0	762	0
scientificName	0	1	9	39	0	726	0

Variable type: numeric

skim_variable	n_missing	complete_rate	mean	sd	p0	p25	p50	p75	p100	hist
pd	9	0.99	8.18	6.17	1.11	4.38	6.24	9.55	56.96	▇▁▁▁▁

Save results to .rds

Code

# eval: false
saveRDS(pd,
        here::here("Data/output/A_predictors/Phylo_distinct.rds"))