scape: Simulate phylogenetic community structure across a landscape

In pez: Phylogenetics for the Environmental Sciences

Simulate phylogenetic community structure across a landscape

Description

scape simulates communities that are phylogenetically structured

Usage

scape(
  tree,
  scape.size = 10,
  g.center = 1,
  g.range = 1,
  g.repulse = 1,
  wd.all = 150,
  signal.center = TRUE,
  signal.range = TRUE,
  same.range = TRUE,
  repulse = TRUE,
  center.scale = 1,
  range.scale = 1,
  repulse.scale = 1,
  site.stoch.scale = 0.5,
  sd.center = 1,
  sd.range = 1,
  rho = NULL,
  th = 8
)

Arguments

tree	phylo object
scape.size	edge dimension of square landscape
g.center	strength of phylogenetic signal in species range centers
g.range	strength of phylogenetic signal in species range sizes
g.repulse	strength of phylogenetic repulsion
wd.all	niche width, larger values simulate broader range sizes
signal.center	simulate with phylosignal in range centers
signal.range	simulate with phylosignal in range size
same.range	make all range sizes equal
repulse	include phylogenetic repulsion in range centers
center.scale	adjust strength of phylogenetic attraction in range centers independent of g.center
range.scale	adjust strength of phylogenetic signal in range size independent of g.range
repulse.scale	adjust strength of phylogenetic repulsion independent of g.repulse
site.stoch.scale	adjust strength of random variation in species richness across sites
sd.center	sd in rnorm for the range centers, increase to get more variation in center values across species
sd.range	sd rnorm for the range sizes, increase to get more variation in range sizes across gradients
rho	Grafen branch adjustment of phylogenetic tree see corGrafen
th	probability threshold 10^-th above which species are considered present at a site

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 parameters g.center, g.range and g.repulse. 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; 0<g<1 represents stabilizing selection; and g>1 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 and range sizes g.range, can exhibit phylogenetic signal. Phylogenetic attraction is simulated in the g.center paramter, while repulsion in g.repulse. Both can be exhibited such that closly related species are generally found with similar range centers (phylogenetic attraction) but just not at the same site (phylogenetic repulsion). The function then returns probabilities of of each species across sites and the presence and absences of species based a supplied threshold, th, which can be increased to obtain more species at sites and thus increase average site species richness.

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.
X.joint	full probabilities of species at sites, used to construct cc
X1	probabilities of species along gradient 1
X2	probabilities of species along gradient 2
sppXs	full probabilities of each species as an array arranged in a scape.size-by-scape.size matrix
V.phylo	initial phylogenetic covariance matrix from tree
V.phylo.rho	phylogenetic covariance matrix from tree scaled by Grafen if rho is provided
V.center	scaled by g.center phylo covariance matrix used in the simulations
V.range	scaled by g.range phylo covariance matrix used in the simulations
V.repulse	scaled by g.repulse phylo covariance matrix used in the simulations
bspp1	species optima for gradient 1
bspp2	species optima for gradient 2
u	the env gradients values for the two gradients
wd	the denominator for species ranges

Author(s)

M.R. Helmus, cosmetic changes by Will Pearse

References

Helmus M.R. & Ives A.R. (2012). Phylogenetic diversity area curves. Ecology, 93, S31-S43.

See Also

eco.scape sim.phy sim.meta

Examples

#Create balanced tree with equal branch-lengths (signal in centers)
tree <- stree(8,type="balanced")
tree$edge.length <- rep(1, nrow(tree$edge))
tree$root <- 1
kk <- scape(tree, scape.size=100, g.center=100, g.range=1, g.repulse=1, wd.all=150,
    signal.center=TRUE, signal.range=FALSE, same.range=FALSE, repulse=FALSE,center.scale = 1,
    range.scale = 1, repulse.scale = 1, site.stoch.scale = 0, sd.center=3, sd.range=1,
    rho=NULL, th=20)

#Make some plots
par(mfrow=c(1,Ntip(tree)),mar=c(.1,.1,.1,.1))
for(j in seq_along(tree$tip.label))
    image(t(1 - kk$sppXs[,,j]/max(kk$sppXs[,,j])), xlab = "",
              ylab = "",main = "",axes=FALSE, col=grey.colors(10))

par(mfrow=c(2,1))
matplot((kk$X1), type = "l", xlab="gradient",ylab = "probability",
main = "Gradient 1",col=rainbow(dim(kk$X1)[2]),lty=1)
matplot((kk$X2), type = "l", xlab="gradient",ylab = "probability",
main = "Gradient 2",col=rainbow(dim(kk$X2)[2]),lty=1)

plot(x=seq_along(sites(kk$cc)),y = rowSums(comm(kk$cc)), main = "SR",type = "l")
cor(kk$X1)

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