draw.sim: Draw a sim object

In brpetrucci/paleobuddy: Simulating Diversification Dynamics

Draw a sim object

Description

Draws species longevities for a paleobuddy simulation (a sim object - see ?sim) in the graphics window. Allows for the assignment of speciation and sampling events, and further customization.

Usage

draw.sim(sim, fossils = NULL, sortBy = "TS", lwdLin = 4, showLabel = TRUE, ...)

Arguments

sim	A sim object, containing extinction times, speciation times, parent, and status information for each species in the simulation. See ?sim.
fossils	A data.frame containing the fossil occurrences of each lineage, e.g. as returned by the sample.clade function. The format of this argument will define the way fossils are drawn (see below).
sortBy	A single character or integer vector indicating how lineages should be sorted in the plot. If it is a string (see example 3), it indicates which element in the sim object that should be used to sort lineages in the plot. If it is a vector of integers, it directly specifies the order in which lineages should be drawn, from the bottom (i.e. the first integer) to the upper side (#th integer, with # = number of lineages in sim) of the figure. Default value of this parameter is "TS", so by default species will be sorted by order of origination in the simulation.
lwdLin	The relative thickness/size of all elements (i.e., lines and points in the plot. Default value is 4 (i.e. equal to lwd = 4 for the black horizontal lines).
showLabel	A logical on whether to draw species labels (i.e. species 1 being t1, species 2 t2 etc.). Default is TRUE.
...	Further arguments to be passed to plot

Value

A plot of the simulation in the graphics window. If the fossils data.frame is supplied, its format will dictate how fossil occurrences will be plotted. If fossils has a SampT column (i.e. the occurrence times are exact), fossil occurrences are assigned as dots. If fossils has columns MaxT and MinT (i.e. the early and late stage bounds associated with each occurrence), fossil occurrences are represented as slightly jittered, semitransparent bars indicating the early and late bounds of each fossil occurrence.

Author(s)

Matheus Januario

Examples

###
# we start drawing a simple simulation

# maximum simulation time
tMax <- 10

# set seed
set.seed(1)

# run a simulation
sim <- bd.sim(n0 = 1, lambda = 0.6, mu = 0.55, tMax = tMax, 
              nFinal = c(10,20)) 
              
# draw it
draw.sim(sim)

###
# we can add fossils to the drawing

# maximum simulation time
tMax <- 10

# set seed
set.seed(1)

# run a simulation
sim <- bd.sim(n0 = 1, lambda = 0.6, mu = 0.55, tMax = tMax, 
              nFinal = c(10,20)) 

# set seed
set.seed(1)

# simulate data resulting from a fossilization process
# with exact occurrence times
fossils <- sample.clade(sim = sim, rho = 4, tMax = tMax, returnTrue = TRUE)

# draw it
draw.sim(sim, fossils = fossils)

# we can order the vertical drawing of species based on
# any element of sim
draw.sim(sim, fossils = fossils, sortBy = "PAR")
# here we cluster lineages with their daughters by
# sorting them by the "PAR" list of the sim object

draw.sim(sim, fossils = fossils, sortBy = "TE")
# here we sort lineages by their extinction times

###
# try with fossil ranges

# maximum simulation time
tMax <- 10

# set seed
set.seed(1)

# run birth-death simulation
sim <- bd.sim(n0 = 1, lambda = 0.6, mu = 0.55, tMax = tMax, 
              nFinal = c(10,20)) 

# simulate data resulting from a fossilization process
# with fossil occurrence time ranges

# set seed
set.seed(20)

# create time bins randomly
bins <- c(tMax, 0, runif(n = rpois(1, lambda = 6), min = 0, max = tMax))

# set seed
set.seed(1)

# simulate fossil sampling
fossils <- sample.clade(sim = sim, rho = 2, tMax = tMax, 
                        returnTrue = FALSE, bins = bins)

# draw it, sorting lineages by their parent
draw.sim(sim, fossils = fossils, sortBy = "PAR")

# adding the bounds of the simulated bins
abline(v = bins, lty = 2, col = "blue", lwd = 0.5)

###
# we can control how to sort displayed species exactly

# maximum simulation time
tMax <- 10

# set seed
set.seed(1)

# run birth-death simulations
sim <- bd.sim(n0 = 1, lambda = 0.6, mu = 0.55, tMax = tMax, 
              nFinal = c(10,20)) 

# set seed
set.seed(1)  

# simulate fossil sampling
fossils <- sample.clade(sim = sim, rho = 4, tMax = tMax, returnTrue = TRUE)

# draw it with random sorting (in pratice this could be a trait
# value, for instance)
draw.sim(sim, fossils = fossils, sortBy = sample(1:length(sim$TS)))

brpetrucci/paleobuddy documentation built on July 26, 2023, 8:15 p.m.