summary.gllvm: Summarizing gllvm model fits

In gllvm: Generalized Linear Latent Variable Models

Summarizing gllvm model fits

Description

A summary of the fitted 'gllvm' object, including function call, distribution family and model parameters.

Usage

## S3 method for class 'gllvm'
summary(
  object,
  by = "all",
  digits = max(3L, getOption("digits") - 3L),
  signif.stars = getOption("show.signif.stars"),
  dispersion = FALSE,
  spp.intercepts = FALSE,
  row.intercepts = FALSE,
  Lvcoefs = FALSE,
  rotate = TRUE,
  type = NULL,
  ...
)

## S3 method for class 'summary.gllvm'
print(x, ...)

Arguments

object	an object of class 'gllvm'
by	By = "all" (default) will return a Wald statistics per predictor and LV if the ordination includes predictors, by = "terms" will return a multivariate Wald statistic per predictor (displayed at first LV), and by = "LV" will do the same but per dimension (displayed at first predictors).
digits	the number of significant digits to use when printing
signif.stars	If TRUE, significance stars are printed for each coefficient, defaults to TRUE
dispersion	option to return dispersion parameters, defaults to FALSE
spp.intercepts	option to return species intercepts, defaults to FALSE
row.intercepts	option to return row intercepts, defaults to FALSE
Lvcoefs	option to return species scores in the ordination, defaults to FALSE. Returns species optima for quadratic model.
rotate	defaults to TRUE. If TRUE rotates the output of the latent variables to principal direction, so that it coincides with the ordiplot results. If both unconstrained and constrained latent variables are included, predictor slopes are not rotated.
type	to match "type" in ordiplot.gllvm
...	not used.
x	a summary object

Details

Various options are available to include extra parameter estimates in the summary, which have been excluded by default, for readability.

Author(s)

Jenni Niku <[e-mail]>, Bert van der Veen

Examples

## Not run: 
## Load a dataset from the mvabund package
data(antTraits)
y <- as.matrix(antTraits$abund)
# Fit gllvm model
fit <- gllvm(y = y, family = poisson())
summary(fit)

## End(Not run)

gllvm documentation built on Sept. 18, 2023, 5:22 p.m.