div.rates {RPANDA}

Diversification rates through time

Description

Calculates diversification rates through time from shift.estimates() output.

Usage

  div.rates(phylo, shift.res, combi = 1, part = "backbone",
            time.interval = 1, backbone.option = "crown.shift")

Arguments

phylo

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

shift.res

the output resulting from shift.estimates.

combi

numeric. The combination of shifts defined by its rank in the global comparison.

part

character. Specifies for which parts of the combination diversification rates has to be calculated. Default is "backbone" and provides only the backbone rate. Can be "all" for all the parts of a combination or "subclades" for subclades only.

backbone.option

type of the backbone analysis (see backbone.option in shift.estimates for more details):

• "stem.shift": rates are calculated from the stem age for subclades.

• "crown.shift": rates are calculated from the crown age for subclades.

time.interval

numeric. Define the time interval (in million years) at which diversification rates are calculated. Default is 1 for a value at each million year.

Value

a list of matrix with two rows (speciation and extinction) and as many columns as million years from the root to the present.

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

shift.estimates

Examples

# loading data
data("Cetacea")
data("shifts_cetacea")

# with shifts_cetacea the output from shift.estimates()
rates <- div.rates(phylo = Cetacea, shift.res = shifts_cetacea,
                   combi = 1, part = "all")