twinstim_methods: Print, Summary and Extraction Methods for '"twinstim"'...

In surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Print, Summary and Extraction Methods for "twinstim" Objects

Description

Besides print and summary methods there are also some standard extraction methods defined for objects of class "twinstim": vcov, logLik, and nobs. This also enables the use of, e.g., confint and AIC. The model summary can be exported to LaTeX by the corresponding toLatex or xtable methods.

Usage

## S3 method for class 'twinstim'
print(x, digits = max(3, getOption("digits") - 3), ...)
## S3 method for class 'twinstim'
summary(object, test.iaf = FALSE,
        correlation = FALSE, symbolic.cor = FALSE, runtime = FALSE, ...)

## S3 method for class 'twinstim'
coeflist(x, ...)
## S3 method for class 'twinstim'
vcov(object, ...)
## S3 method for class 'twinstim'
logLik(object, ...)
## S3 method for class 'twinstim'
nobs(object, ...)

## S3 method for class 'summary.twinstim'
print(x,
      digits = max(3, getOption("digits") - 3), symbolic.cor = x$symbolic.cor,
      signif.stars = getOption("show.signif.stars"), ...)

## S3 method for class 'summary.twinstim'
toLatex(object,
        digits = max(3, getOption("digits") - 3), eps.Pvalue = 1e-4,
        align = "lrrrr", booktabs = getOption("xtable.booktabs", FALSE),
        withAIC = FALSE, ...)
## S3 method for class 'summary.twinstim'
xtable(x, caption = NULL, label = NULL,
      align = c("l", "r", "r", "r"), digits = 3,
      display = c("s", "f", "s", "s"), ...,
      ci.level = 0.95, ci.fmt = "%4.2f", ci.to = "--",
      eps.Pvalue = 1e-4)

Arguments

x, object	an object of class "twinstim" or "summary.twinstim", respectively.
digits	integer, used for number formatting with signif(). Minimum number of significant digits to be printed in values.
test.iaf	logical indicating if the simple Wald z- and p-values should be calculated for parameters of the interaction functions siaf and tiaf. Because it is often invalid or meaningless to do so, the default is FALSE.
correlation	logical. If TRUE, the correlation matrix of the estimated parameters is returned and printed.
symbolic.cor	logical. If TRUE, print the correlations in a symbolic form (see symnum) rather than as numbers.
runtime	logical. If TRUE, the summary additionally includes the time elapsed and the number of log-likelihood and score function evaluations during model fitting.
signif.stars	logical. If TRUE, “significance stars” are printed for each coefficient.
eps.Pvalue	passed to format.pval.
booktabs	logical indicating if the toprule, midrule and bottomrule commands from the LaTeX package booktabs should be used for horizontal lines rather than hline.
withAIC	logical indicating if the AIC and the log-likelihood of the model should be included below the table of coefficients in the LaTeX tabular.
caption, label, align, display	see xtable.
ci.level, ci.fmt, ci.to	the confidence intervals are calculated at level ci.level and printed using sprintf with format ci.fmt and separator ci.to.
...	For print.summary.twinstim, arguments passed to printCoefmat. For all other methods: unused (argument of the generic).

Details

The estimated coefficients and standard Wald-type confidence intervals can be extracted using the default coef and confint methods from package stats. Note, however, that there is the useful coeflist method to list the coefficients by model component.

The print and summary methods allow the compact or comprehensive representation of the fitting results, respectively. The former only prints the original function call, the estimated coefficients and the maximum log-likelihood value. The latter prints the whole coefficient matrix with standard errors, z- and p-values (see printCoefmat) – separately for the endemic and the epidemic component – and additionally the AIC, the achieved log-likelihood, the number of log-likelihood and score evaluations, and the runtime. They both append a big “WARNING”, if the optimization algorithm did not converge.

The toLatex method is essentially a translation of the printed summary table of coefficients to LaTeX code (using xtable). However, the xtable method does a different job in that it first converts coefficients to rate ratios (RR, i.e., the exp-transformation) and gives confidence intervals for those instead of standard errors and z-values. Intercepts and interaction function parameters are ignored by the xtable method.

Value

The print methods return their first argument, invisibly, as they always should. The vcov method returns the estimated variance-covariance matrix of the parameters, which is the inverse of object$fisherinfo (estimate of the expected Fisher information matrix). This "fisherinfo" is not always available (see twinstim), in which case object$fisherinfo.observed is used if available or an error is returned otherwise. The logLik and nobs methods return the maximum log-likelihood value of the model, and the number of events (excluding events of the prehistory), respectively.

The summary method returns a list containing some summary statistics of the model, which is nicely printed by the corresponding print method.

The toLatex method returns a character vector of class "Latex", each element containing one line of LaTeX code (see print.Latex). The xtable method returns an object of class "xtable". Note that the column name of the confidence interval, e.g. “95% CI”, contains the percent symbol that may need to be escaped when printing the "xtable" in the output format (see sanitize.text.function in print.xtable). This may also hold for row names.

Author(s)

Sebastian Meyer

Examples

# load a fit of the 'imdepi' data, see the example in ?twinstim
data("imdepifit")

# print method
imdepifit

# extract point estimates (in a single vector or listed by model component)
coef(imdepifit)
coeflist(imdepifit)

# variance-covariance matrix of endemic parameters
# (inverse of expected Fisher information)
unname(vcov(imdepifit)[1:4,1:4])

# the default confint() method may be used for Wald CI's
confint(imdepifit, parm="e.typeC", level=0.95)

# log-likelihood and AIC of the fitted model
logLik(imdepifit)
AIC(imdepifit)
nobs(imdepifit)

# produce a summary with parameter correlations and runtime information
(s <- summary(imdepifit, correlation=TRUE, symbolic.cor=TRUE, runtime=TRUE))

# create LaTeX code of coefficient table
toLatex(s, digits=2)

# or using the xtable-method (which produces rate ratios)
xtable(s)

surveillance documentation built on Nov. 4, 2024, 3 a.m.