Computes the arrival ages of each species in the assemblages

Usage

calc_age_arrival(W, tree, ancestral.area, biogeo, age.no.ancestor = "recent")

Arguments

W: Occurrence matrix, rows are assemblages and columns are species
tree: Phylogenetic tree in newick format
ancestral.area: One column data frame, nodes in row and one column containing the occurrence of the nodes
biogeo: One column data frame, assemblages in rows and one column containing the region in which the assemblage is located
age.no.ancestor: a character string "recent" (default) or "half.edge" indicating how to deal with cases in which the most recent aancestor of a tip node are not on the same region. "recent" attributes a small age (10e-5), while "half.edge" attributes the age as half the length of the branch linking the ancestor to the tip.

Value

A list of length two.

age_arrival: A matrix with the arrival age of each species in each assemblage
mean_age_arrival: mean age values for each assemblage

Details

This function computes the mean arrival age of species in an assemblage based in an ancestral area reconstruction. For each assemblage we calculate the arrival and establishment of each ancestor of present-day species as showed in Van Dijk et al (2021). We consider an arrival event as being the arrival of an ancestor and the establishment of this ancestor until the present day. Arrival events that occurred between the last speciation event of that lineage and the present time can be assigned a small value or the age corresponding to the half of the lenght of the branch linking the ancestor and the present day species

References

Van Dijk, A.; Nakamura G,; Rodrigues, A.V.; Maestri, R. and Duarte, L.d.S. (2021). Imprints of tropical niche conservatism and historical dispersal in the radiation of Tyrannidae (Aves:Passeriformes). Biol. Journ. Linnean Soc., 134, 57-67.

Author

Gabriel Nakamura gabriel.nakamura.souza@gmail.com and Arthur Rodrigues

Examples

 # hypothetical occurrence matrix with species in columns and assemblages in lines
 W_toy<- matrix(c(0, 1, 1, 0, 1,
                  1, 0, 1, 0, 1, 
                  0, 0, 1, 0, 0),nrow= 3,
                  ncol= 5,dimnames=list(c("Comm 1", "Comm 2", "Comm 3"),
                  c(paste("s", 1:5, sep=""))))
 
 #toy tree
 data(toy_treeEx)
 
 # hypothetical data indicating the ecoregions of each assemblage
 biogeo_toy <- data.frame(Ecoregion= c("A", "B", "C"))
 
 # hypothetical data indicating the ancestral range of each node
 ancestral_area_toy <- data.frame(state= c("ABC", "B", "C", "ABC"))
 
 # caculating age of each assemblage
 age_assemblages <- calc_age_arrival(W_toy, toy_treeEx, ancestral_area_toy, biogeo_toy)