Phylogenetic diversity decomposition

Usage

PD_decomposition(comm, sbears.obj, phy, threshold, make.node.label = TRUE)

Arguments

comm: a community matrix with sites in rows and species in columns
sbears.obj: an object calculated from calc_sbears containing ancestral community reconstruction
phy: A phylo object containing phylogenetic relationships among species
threshold: Scalar indicating the threshold used to consider the presence of a species in a community
make.node.label: Logical. If TRUE (the default) the nodes of the phylogeny will be named with the letter N preceding the number of the node

Value

a list of length two.

decomp_potential: is a list with results of PD decomposition considering the range area model reconstruction. This list contains:

PD_decomposition: A data frame with three colums. partition is a character indicating the component of PD, value is a numeric columns with respective PD compoent and community is a character column with the name of the community

 \item \code{decomp_faith}: is a list with the same structure of
     \code{decomp_potential}, but contains the results of PD decomposition
     considering only the current occurrence of lineages in communities

Examples

# phylogenetic tree
set.seed(42)
phylo <- ape::rcoal(n = 10)
phylo <- ape::makeNodeLabel(phy = phylo)

# community composition matrix
comm <- 
  matrix(sample(c(0, 1), size = 10*20, replace = TRUE),
         nrow = 20, 
         ncol = 10, 
         dimnames = list(paste("comm", 1:20), phylo$tip.label)
  )

# coordinates - this is necessary for "disperal_assembly" algorithm
xy_coords <- 
  matrix(runif(1:10), 
         nrow = nrow(comm),
         ncol = 2, 
         dimnames = list(rownames(comm), c("lng", "lat")
         )
  )

# running sbears with "single_site" algorithm
out_sbears <- 
  calc_sbears(x = comm,
              phy = phylo, 
              coords = xy_coords, 
              method = "single_site")

# sbears object can be used directly in PD_decomposition function

out_decomp <- 
  PD_decomposition(comm = comm,
                   sbears.obj = out_sbears, 
                   phy = phylo, 
                   threshold = 0.5)
#> 
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# Data frame with results from PD decomposition
out_pd_decomposition <- out_decomp$decomp_potential$PD_decomposition