Functions to extract various components of a fit
formula extracts the model formula.
family extracts the response family.
terms extracts the formula, with attributes describing the fixed-effect terms.
nobs returns the length of the response vector.
logLik extracts the log-likelihood (exact or approximated).
dev_resids returns a vector of squared (unscaled) deviance residuals (the summands in McCullagh and Nelder 1989, p. 34).
deviance returns the sum of squares of these (unscaled) deviance residuals, that is (consistently with stats::deviance) the unscaled deviance.
fitted extracts fitted values (see fitted.values).
response extracts the response (as a vector).
fixef extracts the fixed effects coefficients, β.
ranef extracts the predicted random effects, Lv (default since version 1.12.0), or optionally u (see random-effects for definitions). print.ranef controls their printing.
getDistMat returns a distance matrix for a geostatistical (Matérn etc.) random effect.
## S3 method for class 'HLfit' formula(x, which="hyper", ...) ## S3 method for class 'HLfit' family(object, ...) ## S3 method for class 'HLfit' terms(x, ...) ## S3 method for class 'HLfit' nobs(object, ...) ## S3 method for class 'HLfit' logLik(object, which, ...) ## S3 method for class 'HLfit' fitted(object, ...) ## S3 method for class 'HLfit' fixef(object, ...) ## S3 method for class 'HLfit' ranef(object, type = "correlated", ...) ## S3 method for class 'ranef' print(x, max.print = 40L, ...) ## S3 method for class 'HLfit' deviance(object, ...) ## getDistMat(object, scaled=FALSE, which = 1L) response(object,...) dev_resids(object,...)
object |
An object of class |
type |
For |
which |
For |
scaled |
If |
x |
For |
max.print |
Controls |
... |
Other arguments that may be needed by some method. |
With which="LogL_Lap", logLik() returns a Laplace approximation of log-likelihood based on the observed Hessian, rather than the expected Hessian. This is implemented only for the case family=Gamma(log), for demonstration purposes.
formula returns a formula, except a list of them from fitmv() output.
terms returns an object of class c("terms", "formula") which contains the terms representation of a symbolic model. See terms.object for its structure. terms(<fitmv() result>) returns a list of such terms.
Other return values are numeric (for logLik), vectors (most cases), matrices or dist objects (for getDistMat), or a family object (for family). ranef returns a list of vectors or matrices (the latter for random-coefficient terms).
McCullagh, P. and Nelder J. A. (1989) Generalized linear models. Second ed. Chapman & Hall: London.
Lee, Y., Nelder, J. A. (2001) Hierarchical generalised linear models: A synthesis of generalised linear models, random-effect models and structured dispersions. Biometrika 88, 987-1006.
Lee, Y., Nelder, J. A. and Pawitan, Y. (2006) Generalized linear models with random effects: unified analysis via h-likelihood. Chapman & Hall: London.
See residuals.HLfit to extract various residuals, residVar to extract residual variances or information about residual variance models, hatvalues to extract leverages, get_matrix to extract the model matrix and derived matrices, and vcov.HLfit to extract covariances matrices from a fit, get_RLRsim_args to extract arguments for (notably) tests of random effects in LMMs.
data("wafers")
m1 <- HLfit(y ~ X1+X2+(1|batch), resid.model = ~ 1,
data=wafers, method="ML")
fixef(m1)
ranef(m1)
data("blackcap")
fitobject <- fitme(migStatus ~ 1 + Matern(1|longitude+latitude),data=blackcap,
fixed=list(nu=4,rho=0.4,phi=0.05))
getDistMat(fitobject)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.