Extract standard information such as log-likelihood, AIC, coefficients, etc. from ADMB model fits
# S3 method for admb
AIC(object, ..., k = 2)# S3 method for admb
confint(object, parm, level = 0.95, method = "default",
type = "fixed", ...)
# S3 method for admb
print(x, verbose = FALSE, ...)
# S3 method for admb
summary(object, correlation = FALSE, symbolic.cor = FALSE,
...)
# S3 method for summary.admb
print(x, digits = max(3, getOption("digits") - 3),
symbolic.cor = x$symbolic.cor,
signif.stars = getOption("show.signif.stars"), ...)
# S3 method for admb
logLik(object, ...)
# S3 method for admb
coef(object, type = "fixed", ...)
# S3 method for admb
vcov(object, type = "fixed", ...)
stdEr(object, ...)
# S3 method for admb
stdEr(object, type = "fixed", ...)
# S3 method for admb
deviance(object, ...)
Extracts appropriate values: numeric (scalar) for AIC, type logLik for logLik, numeric vector of coefficients, numeric variance-covariance matrix of parameter estimates
an ADMB model fit (of class "admb")
other parameters (for S3 generic compatibility)
penalty value for AIC fits
(currently ignored: FIXME) select parameters
alpha level for confidence interval
(character): "default" or "quad", quadratic (Wald) intervals based on approximate standard errors; "profile", profile CIs (if profile was computed); "quantile", CIs based on quantiles of the MCMC-generated posterior density (if MCMC was computed); "HPDinterval", CIs based on highest posterior density (ditto)
which type of parameters to report. Character vector, including one or more of "fixed" or "par" (standard, fixed-effect parameters); "random" (random effect parameters); "rep" (report variables); "sdrpt" (sdreport variables); "extra" (report and sdreport); "all" (all of the above).
an ADMB model fit (of class "admb")
show messages
currently unused parameter
currently unused parameter
number of digits to display
show significance stars?
admbex <- system.file("doc","Reedfrog_runs.RData",package="R2admb")
load(admbex)
m1
coef(m1)
summary(m1)
coef(summary(m1)) ## returns just z-table
AIC(m1)
vcov(m1)
logLik(m1)
deviance(m1)
stdEr(m1)
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