eco.scape: eco.space scape simulation with a macro-ecological focus

In pez: Phylogenetics for the Environmental Sciences

eco.space scape simulation with a macro-ecological focus

Description

eco.scape is a modified version of the Helmus et al. method implemented in scape. It produces phylogenetically structured communities. It allows phylogenetic signals in niche optima, but unlike scape, does not include the ability to specify niche optima signal type (attraction/repulsion) or phylogenetic signal in range size. Instead, the focus is on having more control over the macroecological characteristics of the resulting landscapes. In particular, eco.scape produces landscapes with fixed mean range sizes, reasonable range size and abundance distributions, and control over whether species present on a tree must be present in the landscape.

Usage

eco.scape(
  tree,
  scape.size = 10,
  g.center = 1,
  wd.all = 0.2 * (scape.size + 1)^2,
  signal.center = TRUE,
  center.scale = 1,
  site.stoch.scale = 0,
  sd.center = 1,
  sd.range = 1,
  K = 100,
  extinction = FALSE,
  rho = NULL
)

Arguments

tree	phylo object; must have branch lengths and be ultrametric
scape.size	edge dimension of square landscape
g.center	strength of phylogenetic signal in species range centers. See corBlomberg, 1=brownian,<1=rates of evol accelerate, >1=rates decelerate.
wd.all	niche width, larger values simulate broader range sizes
signal.center	simulate with phylosignal in range centers
center.scale	adjust strength of phylogenetic attraction in range centers independent of g.center
site.stoch.scale	adjust strength of random variation in species richness across sites
sd.center	sd in rnormrnorm for the range centers, increase to get more variation in center values across species
sd.range	sd in rnorm for the range sizes, increase to get more variation in range sizes across gradients
K	carrying capacity of a site in terms of maximum individuals that can be present. Currently a constant value. Used to scale the presence-absence matrix to include abundances.
extinction	TRUE/FALSE can species on the tree go extinct on the landscape? If the number of species present on the landscape should equal the number of tips on the tree, choose FALSE. See Details.
rho	Grafen branch adjustment of phylogenetic tree see corGrafen

Details

Simulates a landscape with species (i.e., tree tips) distributions dependent on a supplied phylogenetic tree. The amount and type of structure is determened by the signal parameter g.center. Parameters are based on an Ornstein-Uhlenbeck model of evolution with stabilizing selection. Values of g=1 indicate no stabilizing selection and correspond to the Brownian motion model of evolution; 01 corresponds to disruptive selection where phylogenetic signal for the supplied tree is amplified. See corBlomberg. Communities are simulated along two gradients where the positions along those gradients, g.center, can exhibit phylogenetic signal.

The function returns a landscape where the average range size is equivalent to the wd.all parameter - in the scape function, this parameter is not necessarily returned in the resulting landscape. To do this, the probability of presence (th) that returns the wd.all parameter is solved for. If there is no solution that can produce the wd.all given, the error "Error in uniroot(f, lower = 0, upper = max(X.), tol = 10^-200): f() values at end points not of opposite sign" will occur. This seems to mostly arise for extreme or unlikely parameter values (small species pools, low carrying capacities). Try adjusting parameter values first.

The extinction parameter specifies whether all of the species on the tree should be present in the final landscape. Some species will have probabilities of presence less than those required for presence. If extinctions is TRUE, these species will not be present. If FALSE, these species will be present in 1 site, that in which they have the highest probability of presence.

Value

cc	comparative.comm object with presence/absence results of simulations. The site names are the row.columns of the cells in the original grid cells that made up the data, and these co-ordinates are also given in the env slot of the object along with the environmental gradient information.
Y	presence/absence matrix
Yab	abundance matrix
index	spatial coordinates for X and Y (stacked columns)
X.joint	full probabilities of species at sites, used to construct Y
X1	probabilities of species along gradient 1
X2	probabilities of species along gradient 2
gradient1, gradient2	environmental gradient values
nichewd	average niche width of the assemblage
K	carrying capacity of each cell
environ	matrix depicting environmental values over the 2D landscape
sppXs	full probabilities of each species as an array arranged in a scape.size X scape.size matr ix
V.phylo	initial phylogenetic covariance matrix from tree, output of vcv.phylo(tree, corr=T)
V.phylo.rho	phylogenetic covariance matrix from tree scaled by Grafen if rho is provided, other wise just an output of vcv.phylo(tree, corr=T)
V.center	scaled (by g.center) phylo covariance matrix used in the simulations
bspp1	species optima for gradient 1
bspp2	pecies optima for gradient 2

Author(s)

Matt Helmus, Caroline Tucker, cosmetic edits by Will Pearse

See Also

scape sim.phy sim.meta

Examples

# Simulations
tree <- rcoal(64)

scape1 <- eco.scape(tree, scape.size=25, g.center=1,
    signal.center=FALSE, K=100, extinction=TRUE)
scape2 <- eco.scape(tree, scape.size=16, g.center=0.2,
    signal.center=TRUE, K=100, extinction=FALSE)
scape3 <- eco.scape(tree, scape.size=16, g.center=20,
    signal.center=TRUE, K=100, extinction=TRUE)

# Plotting distributions and landscape patterns
original_landscape <- scape1
abundmax <- original_landscape$K
PA_mat <- as.matrix(original_landscape$Y)
abund_mat <- original_landscape$Yab
site.size <- nrow(PA_mat)
species <- ncol(PA_mat)
mx <- original_landscape$gradient
env <- original_landscape$environ$env.gradient
par(mfrow=c(2,2), oma=c(0,0,2,0))
heatcol <- (colorRampPalette(c("yellow","red")))

image(matrix(env,sqrt(site.size),sqrt(site.size),byrow=TRUE),
    col=heatcol(max(env)),xaxt="n",yaxt="n",main="Env gradient")

image(matrix(rowSums(PA_mat),sqrt(site.size),sqrt(site.size),byrow=TRUE),
    col=heatcol(16),xaxt="n",yaxt="n",main="Species Richness")

hist(colSums(PA_mat),ylab="Number of species",xlab="Number of sites",
    main="Species Area Relationship",col="lightgrey")

hist(colSums(abund_mat),ylab="Number of species",xlab="Number of individuals",
    main="Species Abundance Relationship",col="lightgrey")
mtext("Env random, phy.signal=0.2, 32 species", outer=TRUE, side=3, cex=1.25)

pez documentation built on Sept. 1, 2022, 1:09 a.m.