traits.summary: Summarizing trait data

In brpetrucci/PaleoBuddy: Simulating Diversification Dynamics

Summarizing trait data

Description

Summarizes trait data from a sim object, usually the ouput of bd.sim in the case where diversification rates are trait-dependent. Returns a list of trait values at the present or the time of extinction (depending on whether the species is alive at present), and optionally returns values at the time of fossil sampling if provided with a fossil record object fossils, usually the output of sample.clade. Does not make assumptions on the number of traits described in the traits parameter, so that if that list has more than one trait per species, multiple vectors will be returned by the function.

Usage

traits.summary(sim, traits, fossils = NULL, selection = "all")

Arguments

sim	A sim object, containing extinction times, speciation times, parent, and status information for each species in the simulation. See ?sim.
traits	List of trait data frames, usually one of the returns of bd.sim. traits[[i]][[j]] should correspond to the jth trait data frame for species i. The data frames contain the following columns value A vector of trait values the species took at specific intervals of time. max A vector of time values corresponding to the upper bound of each interval. min A vector of time values corresponding to the lower bound of each interval
fossils	A data frame with a "Species" column and a SampT column, usually an output of the sample.clade function. Species names must contain only one number each, corresponding to the order of the sim vectors. Note that we require it to have a SampT column, i.e. fossils must have an exact age. This assumption might be relaxed in the future.
selection	Which subset of species to collect trait data for. If set to "all", it will return every trait value it has access to, i.e. either all species, living or dead, or all species plus fossils if fossils is supplied. If set to "extant", it will return only trait values for living species. If set to "extinct", it will return only trait values for extinct species, and fossils if fossils is supplied. If set to "fossil", it will return values for only the fossil species (and therefore requires a fossils parameter). If set to "sampled", it will function the same as in the case for "extant", except it will also return values for the fossils if fossils is supplied.

Value

A named list of named vectors of trait values. List element names refer to each trait, so i.e. res$traitN will correspond to the vector of trait values for trait N. Vector element names refer to the species, using the default naming convention of the package (tN is the Nth species in the simulation, and tN.M is the Mth sampled fossil of that species).

Author(s)

Bruno do Rosario Petrucci

Examples

###
# need a simple simulation to use as an example

# initial number of species
n0 <- 1

# maximum simulation time
tMax <- 40

# speciation, higher for state 1
lambda <- c(0.1, 0.2)

# extinction, trait-independent
mu <- 0.03

# number of traits and states (1 binary trait)
nTraits <- 1
nStates <- 2

# initial value of the trait
X0 <- 0

# transition matrix, with symmetrical transition rates
Q <- list(matrix(c(0, 0.1,
                   0.1, 0), ncol = 2, nrow = 2))

# set seed
set.seed(1)

# run the simulation
sim <- bd.sim.traits(n0, lambda, mu, tMax, nTraits = nTraits, 
                    nStates = nStates, X0 = X0, Q = Q, nFinal = c(2, Inf))
                    
# get all trait values
traitSummary <- traits.summary(sim$SIM, sim$TRAITS)
traitSummary

# could get only the extant values, instead
traitSummary <- traits.summary(sim$SIM, sim$TRAITS, selection = "extant")
traitSummary

# or all the extinct values
traitSummary <- traits.summary(sim$SIM, sim$TRAITS, selection = "extinct")
traitSummary

# set seed
set.seed(1)

# maybe we want to take a look at the traits of fossil records too
fossils <- sample.clade(sim$SIM, rho = 0.5, tMax = max(sim$SIM$TS))

# get the trait values for all extinct species, including fossil samples
traitSummary <- traits.summary(sim$SIM, sim$TRAITS, 
                               fossils = fossils, selection = "extinct")
traitSummary

# can also get the values for all sampled species, i.e. extant or fossils
traitSummary <- traits.summary(sim$SIM, sim$TRAITS, 
                               fossils = fossils, selection = "sampled")
traitSummary

# or just the fossil species
traitSummary <- traits.summary(sim$SIM, sim$TRAITS, 
                               fossils = fossils, selection = "fossil")
traitSummary

brpetrucci/PaleoBuddy documentation built on Feb. 28, 2025, 3:53 p.m.