get.comb.shift {RPANDA}

Combinations of shifts of diversification.

Description

Provides all the combinations of nodes of a phylogeny where shifts of diversification can be tested.

Usage

  get.comb.shift(phylo, data, sampling.fractions,
                 clade.size = 5, Ncores = 1)

Arguments

phylo

an object of type 'phylo' (see ape documentation)

data

a data.frame containing a database of monophyletic groups for which potential shifts can be tested. This database should be based on taxonomy, ecology or traits and must contain a column named "Species" with species names as in phylo.

sampling.fractions

the output resulting from get.sampling.fractions.

clade.size

numeric. Define the minimum number of species in a subgroup. Default is 5.

Ncores

numeric. Define the number of CPU cores to use for parallelizing the computation of combinations.

Details

clade.size argument should be the same value for the whole procedure (same that for get.sampling.fraction and shift.estimates).

Value

a vector of character summaryzing the combination of shifts as a concatenation of node IDs separated by "." or "/". Node IDs at the left of "/" correspond to shifts at the origin of subclades (monophyletic and ultrametric subtrees) while node IDs at the right of "/" correspond to shifts at the origin of backbone(s) (pruned trees).

Author(s)

Nathan Mazet

References

Mazet, N., Morlon, H., Fabre, P., Condamine, F.L., (2023). Estimating clade‐specific diversification rates and palaeodiversity dynamics from reconstructed phylogenies. Methods in Ecology and in Evolution 14, 2575–2591. https://doi.org/10.1111/2041-210X.14195

See Also

get.sampling.fractions, shift.estimates

Examples

# loading data
data("Cetacea")
data("taxo_cetacea")

# no shifts tested at genus level
taxo_cetacea_no_genus <- taxo_cetacea[names(taxo_cetacea) != "Genus"]

f_cetacea <- get.sampling.fractions(phylo = Cetacea,
                                    data = taxo_cetacea_no_genus)

comb.shift_cetacea <- get.comb.shift(phylo = Cetacea,
                                     data = taxo_cetacea_no_genus,
                                     sampling.fractions = f_cetacea,
                                     Ncores = 4)