Site-Based Estimation of Ancestral Range of Species

Usage

calc_sbears(
  x,
  phy,
  coords,
  method = c("single_site", "disp_assembly"),
  w_slope = 5,
  min_disp_prob = 0.8,
  compute.node.by.sites = TRUE,
  make.node.label = TRUE
)

Arguments

x: Matrix object with community/assemblage composition. Rows represent sites and columns represents species.
phy: A phylogenetic tree of phylo class object.
coords: A rectangular object (it can be a matrix, data.frame or tibble) containing two columns, one with longitude and another with latitude coordinates in this order.
method: character indicating how ancestral range probabilities are computed. The options are "single_site" or "disp_assembly"
w_slope: A scalar representing the slope of the dispersal kernel function.
compute.node.by.sites: Logical, TRUE (default) computes a matrix of node occurrence by site.
make.node.label: Logical, if TRUE (default) the nodes of the phylogeny will be named as the letter "N" preceding node number

Value

A list with two elements.

reconstruction: a matrix with ancestral nodes in rows and assemblages in columns. The numeric values represent the occupation probability of each ancestral node in each assemblage.

\item \code{site_node_composition}: a matrix with assemblage in rows and
    node names in columns. The values represent the presence of a given
    node in a given assemblage based on the occurrence of current species
    in the assemblages.

Details

SBEARS (Site-Based Estimation of Ancestral Range of Species) is a method for ancestral state reconstruction of species geographic ranges. It operates at fine spatial resolution and does not require predefined discrete biogeographic areas. The method estimates ancestral ranges under a maximum likelihood framework, using site-level occurrence information. For large matrix this function supports parallel computation with package future

the method used to compute ancestral range probabilities can be single_site or disp_assembly. For both methods SBEARS use the function fastAnc to reconstruct the the ancestral ranges. In single_site each site is taken as a binary categorical trait representing the presence (state 1) or the absence (state 0) of every species in the site, which is reconstructed along the nodes of the phylogeny. In disp_assembly option the single site reconstruction is carried out, producing a matrix describing standardized probabilities of occurrence of each node at each site. The difference here is that an additional step is performed to compute the probability of a cell being colonized by an ancestral species originating from a focal cell. The probability of colonization decreases increasing the distance from the focal cell. This probability of an ancestral species to disperse from a cell to any other can be defined using a dispersal kernel function proposed by Gravel et al (2006).

References

Gravel D., Canhan C.D., Beaudet M. and Messier C. Reconciling niche and neutrality: the continuum hypothesis. 2006. Ecology Letters doi:10.1111/j.1461-0248.2006.00884.x

Examples

# phylogenetic tree
phylo <- geiger::sim.bdtree(n = 10, seed = 42)
#> Error in loadNamespace(x): there is no package called ‘geiger’
phylo <- ape::makeNodeLabel(phy = phylo)
#> Error: object 'phylo' not found

# 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)
 )
#> Error: object 'phylo' not found

# 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")
        )
 )
#> Error: object 'comm' not found

# running sbears with "single_site" algorithm
out_sbears <- 
 calc_sbears(x = comm,
             phy = phylo, 
             coords = xy_coords, 
             method = "single_site")
#> Error: object 'phylo' not found

# matrix containing ancestral reconsturction, nodes are rows and columns are sites
anc_reconstruction <- out_sbears$reconstruction
#> Error: object 'out_sbears' not found