surveillance (version 1.8-0)

hhh4_methods: Print, Summary and other Standard Methods for "hhh4" Objects

Description

Besides print and summary methods there are also some standard extraction methods defined for objects of class "hhh4" resulting from a call to hhh4.

Usage

## S3 method for class 'hhh4':
print(x, digits = max(3, getOption("digits") - 3), ...)
## S3 method for class 'hhh4':
summary(object, maxEV = FALSE, ...)
## S3 method for class 'hhh4':
coef(object, se = FALSE, reparamPsi = TRUE, 
     idx2Exp = NULL, amplitudeShift = FALSE, ...)
## S3 method for class 'hhh4':
fixef(object, ...)
## S3 method for class 'hhh4':
ranef(object, tomatrix = FALSE, ...)
## S3 method for class 'hhh4':
nobs(object, ...)
## S3 method for class 'hhh4':
logLik(object, ...)
## S3 method for class 'hhh4':
vcov(object, reparamPsi = TRUE, 
     idx2Exp = NULL, amplitudeShift = FALSE, ...)
## S3 method for class 'hhh4':
confint(object, parm, level = 0.95, 
        reparamPsi = TRUE, idx2Exp = NULL, amplitudeShift = FALSE, ...)

Arguments

x, object

an object of class "hhh4".

digits

the number of significant digits to use when printing

maxEV

logical indicating if the summary should contain the (range of the) dominant eigenvalue as a measure of the importance of the epidemic components. By default, the value is not calculated as this may take some seconds depending on the number of

...

For the print, summary, fixef and ranef methods: arguments passed to coef. For the remaining methods: unused (argument of the generic).

reparamPsi

logical. If TRUE (default), the overdispersion parameter from the negative binomial distribution is transformed from internal scale (-log) to standard scale, where zero corresponds to a Poisson distribution.

se

logical switch indicating if standard errors are required

idx2Exp

vector with integers idicating the parameters which should be returned on exp-scale.

amplitudeShift

logical switch indicating whether the parameters for sine/cosine terms modelling seasonal patterns (see addSeason2formula) should be transformed to an amplitude/shift formulation.

tomatrix

logical. If FALSE (default), the vector of all random effects is returned (as used internally). However, for random intercepts of type="car", the number of parameters is one less than the number of regions and the ind

parm

a vector of numbers or names, specifying which parameters are to be given confidence intervals. If missing, all parameters are considered.

level

the confidence level required.

Value

• The coef-method returns all estimated (regression) parameters from a hhh4 model as proposed by Paul and Held (2011). If the model includes random effects, those can be extracted with ranef, whereas fixef returns the fixed parameters.

  The nobs-method returns the number of observations used for model fitting. The logLik-method returns an object of class "logLik" with "df" and "nobs" attributes. For a random effects model, the value of the penalized log-likelihood at the MLE is returned, but degrees of freedom are not available (NA_real_). As a consequence, AIC and BIC are only well defined for models without random effects; otherwise these functions return NA_real_.

  The vcov-method returns the estimated variance-covariance matrix of the regression parameters. The estimated variance-covariance matrix of random effects is available as object$Sigma. The confint-method returns Wald-type confidence intervals (assuming asymptotic normality).

encoding

latin1

References

Paul, M. and Held, L. (2011) Predictive assessment of a non-linear random effects model for multivariate time series of infectious disease counts. Statistics in Medicine, 30, 1118--1136.

See Also

the plot-method for fitted hhh4 models.