gllvm (version 2.0.5)

phyloplot.gllvm: Plot phylogenetic random effects from gllvm

Description

Plots phylogenetic random effects with the phylogeny, and community effects

Usage

# S3 method for gllvm
phyloplot(
  object,
  tree,
  comm.eff = TRUE,
  row.eff = FALSE,
  which.Xcoef = NULL,
  xlim = NULL,
  level = 0.95,
  col = c("#E69F00", "white", "#009E73"),
  col.sym = TRUE,
  tick.length = 2,
  mar.spec = c(3, 2, 0, 0),
  mar.phy = c(0, 2, 2, 0),
  mar.comm = c(3, 0.5, 2, 1.5),
  cex = 0.6,
  lwd = 1,
  col.edge = "black",
  pch = "x",
  heights = c(0.55, 0.35),
  widths = c(0.64, 0.1),
  phy.place = "top",
  ...
)

Arguments

object

an object of class 'gllvm'.

tree

an object of class ''

comm.eff

logical, defaults to TRUE. If present in the model, should community effects be plotted?

row.eff

logical, defaults to FALSE. If present in the model, should row effects (e.g., community responses to covariates) be included?

which.Xcoef

List of length 2 with names to subset the effects to plot. The first vector is for the species plot, the second for community effects.

xlim

vector of length two. Limits for the x-axis of the caterpillar plot. Defaults to NULL, in which case the limits are chosen based on the confidence intervals.

level

the confidence level. Scalar between 0 and 1.

col

vector of three colors (defaults to c("#E69F00","white","#009E73")) passed to colorRampPalette for species random effects.

col.sym

logical, defaults to TRUE. Then, the color scale of the species random effects plot is symmetrical (so that zero is nearly in the middle), so that both the lower and upper limit are determined by the largest absolute value. If FALSE, the lower and upper limits are determined by the smallest and largest values, respectively.

tick.length

numerical, defaults to 2. Length of ticks for the species-specific random effects plot.

mar.spec

vector of length 4, which defines the margins sizes for the species random effects plot. Defaults to c(3, 2, 0, 0).

mar.phy

vector of length 4, which defines the margins sizes for plotting the phylogeny. Defaults to c(0, 2, 2, 0).

mar.comm

vector of length 4, which defines the margins sizes for the caterpillar plot. Defaults to c(3, 0.5, 2, 1.5).

cex

the magnification to be used for text in the plot. Defaults to 0.6.

lwd

line thickness for the branches in the phylogeny and the confidence intervals in the caterpillar plot. Defaults to 1.

col.edge

character. Color of branches in the phylogeny.

pch

symbol used in the catter pillar plot. Defaults to "x".

heights

vector of length two. Relative row heights, defaults to c(0.55, 0.35).

widths

vector of length two. Relative column widths, defaults to c(0.64, 0.10).

phy.place

not (yet) in use.

...

additional not in use.

Author

Bert van der Veen

Details

Plots phylogenetically structured random effects together with the phylogeny, and with community-level effects (i.e., effects that are the same across species). If standard errors have been calculated for the model, the prediction intervals for species random effects are checked, and crossed out (i.e., displayed as white) if they cross zero.

References

van der Veen, B., O'Hara, R.B. (2024). Fast fitting of Fast fitting of phylogenetic mixed effects models. arXiv.

Examples

if (FALSE) {
# Load dataset
data(fungi)
Y <- fungi$Y
# Scale the predictor
X <- fungi$X
X[,"DBH.CM"] <- scale(X[, "DBH.CM"])
tree <- fungi$tree # the tree
colMat <- fungi$C # e.g., from ape::vcv(tree)
dist <- fungi$dist # e.g., from ape::cophenetic.phylo(tree)
order <- gllvm:::findOrder(covMat = colMat, distMat = dist, nn = 15,
                           order = order(dist[1:length(tree$tip.label), nrow(dist)],
                           decreasing = TRUE))$order
order <- tree$tip.label[order]
model <- gllvm(y = Y[,order], X = X,
                formula = ~(DBH.CM|1), beta0com = TRUE,
                family = "binomial", num.lv = 0, nn.colMat = 15,
                colMat = list(colMat[order,order], dist = dist[order,order]), 
                colMat.rho.struct = "term")
phyloplot(model, tree)
}