gllvm (version 2.0.5)

coefplot.gllvm: Plot covariate coefficients and confidence intervals

Description

Plots covariate coefficients and their confidence intervals.

Usage

# S3 method for gllvm
coefplot(
  object,
  y.label = TRUE,
  which.Xcoef = NULL,
  order = TRUE,
  cex.ylab = 0.5,
  cex.xlab = 1.3,
  mfrow = NULL,
  mar = c(4, 6, 2, 1),
  xlim.list = NULL,
  ind.spp = NULL,
  ...
)

Arguments

object

an object of class 'gllvm'.

y.label

logical, if TRUE (default) colnames of y with respect to coefficients are added to plot.

which.Xcoef

vector indicating which covariate coefficients will be plotted. Can be vector of covariate names or numbers. Default is NULL when all covariate coefficients are plotted.

order

logical, whether or not coefficients are ordered, defaults to TRUE.

cex.ylab

the magnification to be used for axis annotation relative to the current setting of cex.

cex.xlab

the magnification to be used for axis annotation.

mfrow

same as mfrow in par. If NULL (default) it is determined automatically.

mar

vector of length 4, which defines the margin sizes: c(bottom, left, top, right). Defaults to c(4,5,2,1).

xlim.list

list of vectors with length of two to define the intervals for an x axis in each covariate plot. Defaults to NULL when the interval is defined by the range of point estimates and confidence intervals

ind.spp

vector of species indices to construct the caterpillar plot for

...

additional graphical arguments.

Author

Jenni Niku <[e-mail]>, Francis K.C. Hui, Sara Taskinen, Bert van der Veen

Examples

# Extract subset of the microbial data to be used as an example
data(microbialdata)
X <- microbialdata$Xenv
y <- microbialdata$Y[, order(colMeans(microbialdata$Y > 0), 
                     decreasing = TRUE)[21:40]]
fit <- gllvm(y, X, formula = ~ pH + Phosp, family = poisson())
coefplot(fit)
if (FALSE) {
# Fit  gllvm model with environmental covariances and reduced rank
fitRR <- gllvm(y = y, X = X, num.RR = 2, family = "negative.binomial")
coefplot(fitRR, mfrow=c(2,3))
}