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,
  traits = NULL,
  fossils = NULL,
  lineageColors = NULL,
  sortBy = "TS",
  lwdLin = 4,
  tipLabels = NULL,
  showLabel = TRUE,
  traitID = 1,
  traitColors = c("#a40000", "#16317d", "#007e2f", "#ffcd12", "#b86092", "#721b3e",
    "#00b7a7"),
  traitLegendPlacement = "topleft",
  fossilsFormat = "exact",
  fossilRangeAlpha = 100,
  restoreOldPar = TRUE,
  ...
)

Arguments

sim	A sim object, containing extinction times, speciation times, parent, and status information for each species in the simulation. See ?sim.
traits	A list of data frames enconding the value of one or more traits during the lifetime of each species, usually coming from the TRAITS member of the output of bd.sim.traits. It should have length equal to the number of species in sim, and the traitIDth trait (see below) (i.e. the data frame of number traitID for each species) will be used to draw trait values.
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).
lineageColors	Character vector giving the colors of all lineages, sorted by the original lineage order (the one in the sim object). Must have same length as the number of lineages in the sim object. If NULL (default value) all lineages are plotted as black. this parameter has no effect if traits is also provided.
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).
tipLabels	Character vector manually assigning the tip labels of all lineages, sorted by the original lineage order (the one in the sim object). Must have same length as the number of lineages in the sim object. If NULL (default value) all lineages are plotted as "t#", with "#" being the position of that lineage in the sim object.
showLabel	A logical on whether to draw species labels (i.e. species 1 being t1, species 2 t2 etc.). Default is TRUE.
traitID	Numerical giving the trait which will be plotted. this parameter is only useful when multiple traits were simulated in the same sim object, i.e. when traits has more than one data frame per species.
traitColors	Character vector providing colors for the states of a given trait, so its length must equal or exceed the number of states. Default values provide 7 colors (and so they can plot up to 7 states).
traitLegendPlacement	Placement of state legend. Accepted values are "topleft" (default value), "bottomleft", "bottomright", "topright", and "none".
fossilsFormat	Character assigning if fossils will be represented by exact time placements ("exact", default value), by horizontal bars giving range information ("ranges"), or by both forms ("all").
fossilRangeAlpha	Numerical giving color transparency for fossil range representation. Integers between 0 and 255 are preferred, but any float between 0 and 1 is also accepted. Default value is 100.
restoreOldPar	Logical assigning if plot default values show be restored after function finalizes plotting. Deafult is TRUE, but users interesting in using plot additions (e.g. abline() to highlight a certain age) should assign this as FALSE to use the x and y values in the plot. If false, x-axis follows time, and y-axis follows the number of species plotted, with 1 being the bottom lineage, and the upper y-limit being the Nth lineage in the sim.
...	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

###
# fossils can also be represented by 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)

# get old par
oldPar <- par(no.readonly = TRUE)

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

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

# alternatively, we can draw lineages varying colors and tip labels
# (note how they are sorted)
draw.sim(sim, fossils = fossils, fossilsFormat = "ranges",
         tipLabels = paste0("spp_", 1:length(sim$TS)), 
         lineageColors = rep(c("red", "green", "blue"), times = 5))
         
# restore old par
par(oldPar)

###
# 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)))

###
# we can display trait values as well

# initial number of species
n0 <- 1

# maximum simulation time
tMax <- 20

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

# extinction, lowest for state 0
mu <- c(0.01, 0.03)

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

# initial value of both traits
X0 <- 0

# transition matrix, with symmetrical transition rates for trait 1,
# and asymmetrical (and higher) for trait 2
Q <- list(matrix(c(0, 0.1,
                   0.1, 0), ncol = 2, nrow = 2),
          matrix(c(0, 1,
                   0.5, 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, 10))

# 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), 
                        returnAll = TRUE, bins = seq(0, 20, by = 1))
                         
draw.sim(sim$SIM, traits = sim$TRAITS, sortBy = "PAR",
         fossils = fossils, fossilsFormat = "all",
         traitLegendPlacement = "bottomleft")
# note how fossil ranges are displayed above and below the true
# occurrence times, but we could also draw only one or the other

# just ranges
draw.sim(sim$SIM, traits = sim$TRAITS, sortBy = "PAR",
         fossils = fossils, fossilsFormat = "ranges",
         traitLegendPlacement = "bottomleft")
         
# just true occurrence times
draw.sim(sim$SIM, traits = sim$TRAITS, sortBy = "PAR", traitID = 2,
         fossils = fossils, fossilsFormat = "exact",
         traitLegendPlacement = "bottomleft")
# note the different traitID, so that segments are colored
# following the value of the second trait

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