rm_multi_missing_species: Loops through the genera that have missing species and...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Loops through the genera that have missing species and removes the ones that are found in the missing genus list which have phylogenetic data. This is useful when wanting to know which missing species have not been assigned to the island_tbl using add_multi_missing_species().

Description

Loops through the genera that have missing species and removes the ones that are found in the missing genus list which have phylogenetic data. This is useful when wanting to know which missing species have not been assigned to the island_tbl using add_multi_missing_species().

Usage

rm_multi_missing_species(missing_species, missing_genus, island_tbl)

Arguments

missing_species	Numeric number of missing species from the phylogeny that belong to the colonising clade. For a clade with missing species this is n - 1, where n is the number of missing species in the clade. If the clade is an island singleton, the number of missing species is 0 because by adding the colonist it already counts as one automatically. If the clade has more than one species, the missing_species is n - 1 because adding the lineage already counts as one.
missing_genus	A list of character vectors containing the genera in each island clade
island_tbl	An instance of the Island_tbl class.

Value

Data frame

Examples

phylod <- create_test_phylod(test_scenario = 6)
island_tbl <- suppressWarnings(extract_island_species(
 phylod = phylod,
 extraction_method = "asr",
))
phylod <- create_test_phylod(test_scenario = 7)
island_tbl <- suppressWarnings(extract_island_species(
 phylod = phylod,
 extraction_method = "asr",
 island_tbl = island_tbl
))
missing_species <- data.frame(
  clade_name = "bird",
  missing_species = 1,
  endemicity_status = "endemic"
)
missing_genus <- list("bird", character(0))
rm_missing_species <- rm_multi_missing_species(
  missing_species = missing_species,
  missing_genus = missing_genus,
  island_tbl = island_tbl
)

DAISIEprep documentation built on April 3, 2025, 9:26 p.m.