phyloplot.gllvm: Plot phylogenetic random effects from gllvm

In gllvm: Generalized Linear Latent Variable Models

Plot phylogenetic random effects from gllvm

Description

Plots phylogenetic random effects with the phylogeny, and community effects

Usage

## S3 method for class '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.

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.

Author(s)

Bert van der Veen

References

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

Examples

## Not run: 
# 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)

## End(Not run)

gllvm documentation built on April 11, 2025, 6:12 p.m.