Print, Summary and Extraction Methods for
summary methods there
are also some standard extraction methods defined for objects of class
also enables the use of, e.g.,
AIC. The model
summary can be exported to LaTeX
by the corresponding
# S3 method for twinstim print(x, digits = max(3, getOption("digits") - 3), ...) # S3 method for twinstim summary(object, test.iaf = FALSE, correlation = FALSE, symbolic.cor = FALSE, runtime = FALSE, ...) # S3 method for twinstim coeflist(x, ...) # S3 method for twinstim vcov(object, ...) # S3 method for twinstim logLik(object, ...) # S3 method for twinstim nobs(object, ...) # S3 method for summary.twinstim print(x, digits = max(3, getOption("digits") - 3), symbolic.cor = x$symbolic.cor, signif.stars = getOption("show.signif.stars"), ...) # S3 method for 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 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)
- x, object
an object of class
integer, used for number formatting with
signif(). Minimum number of significant digits to be printed in values.
logical indicating if the simple Wald z- and p-values should be calculated for parameters of the interaction functions
tiaf. Because it is often invalid or meaningless to do so, the default is
TRUE, the correlation matrix of the estimated parameters is returned and printed.
TRUE, print the correlations in a symbolic form (see
symnum) rather than as numbers.
TRUE, the summary additionally includes the time elapsed and the number of log-likelihood and score function evaluations during model fitting.
TRUE, “significance stars” are printed for each coefficient.
logical indicating if the
bottomrulecommands from the LaTeX package booktabs should be used for horizontal lines rather than
logical indicating if the AIC and the log-likelihood of the model should be included below the table of coefficients in the LaTeX tabular.
the confidence intervals are calculated at level
ci.leveland printed using
print.summary.twinstim, arguments passed to
For all other methods: unused (argument of the generic).
The estimated coefficients and standard Wald-type confidence intervals
can be extracted using the default
confint methods from package stats.
Note, however, that there is the useful
coeflist method to
list the coefficients by model component.
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
-- 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.
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
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
twinstim), in which case
object$fisherinfo.observed is used if available or an error is
nobs methods return the maximum
log-likelihood value of the model, and the number of events (excluding
events of the prehistory), respectively.
summary method returns a list containing some summary
statistics of the model, which is nicely printed by the corresponding
toLatex method returns a character vector of class
"Latex", each element containing one line of LaTeX code (see
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
print.xtable). This may also hold for row names.
# 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) .opt <- options(xtable.comment = FALSE) # or using the xtable-method (which produces rate ratios) xtable(s) options(.opt)