delimtools (version 0.2.0)

delim_join: Join Multiple Species Delimitation Methods Outputs

Description

delim_join() returns a tbl_df of species delimitation outputs whose partitions are consistent across different methods.

Usage

delim_join(delim)

Value

an object of class tbl_df.

Arguments

delim

A list or data.frame of multiple species delimitation methods outputs.

Author

Pedro S. Bittencourt, Rupert A. Collins.

Details

delim_join() is a helper function to join multiple lists or columns of species delimitation outputs into a single tbl_df while keeping consistent identifications across multiple methods. Species delimitation outputs are in general a list or data frame of sample labels and its species partitions (Species 1, Species 2, etc.). These partition names may be or not the same across two or more methods. delim_join() standardizes partition names across two or more species delimitation outputs while keeping its underlying structure intact.

Examples

# \donttest{
## run GMYC
gmyc_res <- splits::gmyc(ape::as.phylo(geophagus_beast), method = "single")

# create a tibble
gmyc_df <- gmyc_tbl(gmyc_res)

## run bGMYC
bgmyc_res <- bGMYC::bgmyc.singlephy(ape::as.phylo(geophagus_beast),
  mcmc = 11000,
  burnin = 1000,
  thinning = 100,
  t1 = 2,
  t2 = ape::Ntip(ape::as.phylo(geophagus_beast)),
  start = c(1, 0.5, 50)
)

# create a tibble
bgmyc_df <- bgmyc_tbl(bgmyc_res, ppcutoff = 0.05)

## LocMin

# create a distance matrix
mat <- ape::dist.dna(geophagus, model = "raw", pairwise.deletion = TRUE)

# estimate local minima from `mat`
locmin_res <- spider::localMinima(mat)

# create a tibble
locmin_df <- locmin_tbl(mat,
  threshold = locmin_res$localMinima[1],
  haps = ape::as.phylo(geophagus_beast)$tip.label
)

# join delimitations
all_delims <- delim_join(list(gmyc_df, bgmyc_df, locmin_df))

# check
all_delims

# }