View source: R/get.comb.shift.R
get.comb.shift | R Documentation |
Provides all the combinations of nodes of a phylogeny where shifts of diversification can be tested.
get.comb.shift(phylo, data, sampling.fractions,
clade.size = 5, Ncores = 1)
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. |
clade.size argument should be the same value for the whole procedure (same that for get.sampling.fraction and shift.estimates).
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).
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
get.sampling.fractions
, shift.estimates
# 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)
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