div.rates | R Documentation |
Calculates diversification rates through time from shift.estimates() output.
div.rates(phylo, shift.res, combi = 1, part = "backbone",
time.interval = 1, backbone.option = "crown.shift")
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):
|
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. |
a list of matrix with two rows (speciation and extinction) and as many columns as million years from the root to the present.
Nathan Mazet
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
shift.estimates
# 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")
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