get.sampling.fractions: Sampling fractions of subclades

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Sampling fractions of subclades

Description

Provides the sampling fractions of a phylogenetic tree from a complete database.

Usage

  get.sampling.fractions(phylo, data, clade.size = 5, plot = F,
                         lad = T, text.cex = 1, pch.cex = 0.8, ...)

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.
clade.size	numeric. Define the minimum number of species in a subgroup. Default is 5.
plot	bolean. If TRUE, the tree is plotted and testable nodes are highlighted with red dots. Default is FALSE.
lad	bolean. Define which way the tree should be represented if plot = T. If TRUE, the smallest clade is at the bottom plot. If FALSE, it is at the top of the plot. Default is TRUE.
text.cex	numeric. Defines the size of the text in legend.
pch.cex	numeric. Defines the size of the red points at the crown of subclades.
...	further arguments to be passed to plot or to plot.phylo.

Details

All described species should be included to properly calculate sampling fractions. The example of Cetacea uses a taxonomic database but groups can be defined on geography or traits as soon as they are monophyletic. If the taxonomy of the studied group is difficult to establish (e.i. taxonomic uncertainty, etc.), a "fake" taxonomic database can be created with random species names (Gen1_sp1, Gen1_sp2, Gen2_sp1, etc.) to circumvent taxonomic difficulties. Note that sampling fractions of the backbones are calculated in the next step of the pipeline (function get.comb.shift()).

Value

a data.frame with as many rows as nodes in the phylogeny with the following informations in columns:

nodes	the node IDs
data	the name of the subclade from data
f	the sampling fraction for this subclade
sp_in	the number of species included in the tree
sp_tt	the number of species described in the data
to_test	the node IDs for nodes that are testable according to clade.size

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.comb.shift, 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"]

# calculating sampling fractions with a plot
f_cetacea <- get.sampling.fractions(phylo = Cetacea, lad = FALSE,
                                    data = taxo_cetacea_no_genus,
                                    plot = TRUE, cex = 0.3)

hmorlon/PANDA documentation built on April 24, 2024, 3:27 a.m.