Plot covariate coefficients and confidence intervals
Plots covariate coefficients and their confidence intervals.
## S3 method for class 'gllvm' coefplot( object, y.label = TRUE, which.Xcoef = NULL, order = TRUE, cex.ylab = 0.5, mfrow = NULL, mar = c(4, 6, 2, 1), xlim.list = NULL, ... )
object |
an object of class 'gllvm'. |
y.label |
logical, if |
which.Xcoef |
vector indicating which covariate coefficients will be plotted. Can be vector of covariate names or numbers. Default is |
order |
logical, whether or not coefficients are ordered, defaults to |
cex.ylab |
the magnification to be used for axis annotation relative to the current setting of cex. |
mfrow |
same as |
mar |
vector of length 4, which defines the margin sizes: |
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 |
... |
additional graphical arguments. |
Jenni Niku <jenni.m.e.niku@jyu.fi>, Francis K.C. Hui, Sara Taskinen
# Extract subset of the microbial data to be used as an example
data(microbialdata)
X <- microbialdata$Xenv
y <- microbialdata$Y[, order(colMeans(microbialdata$Y > 0),
decreasing = TRUE)[21:40]]
fit <- gllvm(y, X, formula = ~ pH + Phosp, family = poisson())
coefplot(fit)
## Not run:
## Load a dataset from the mvabund package
data(antTraits)
y <- as.matrix(antTraits$abund)
X <- as.matrix(antTraits$env)
# Fit model with environmental covariates
fit <- gllvm(y, X, formula = ~ Bare.ground + Shrub.cover,
family = poisson())
coefplot.gllvm(fit)
# Fit model with all environmental covariates
fitx <- gllvm(y, X, family = "negative.binomial")
coefplot(fitx, mfrow = c(3,2))
coefplot(fitx, which.Xcoef = 1:2)
# Fit gllvm model with environmental and trait covariates
TR <- antTraits$traits
fitT <- gllvm(y = y, X = X, TR = TR, family = "negative.binomial")
coefplot(fitT)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.