| modelAverage {secr} | R Documentation |
AIC- or AICc-weighted average of estimated ‘real’ or ‘beta’ parameters from multiple fitted secr models, and the tabulation of estimates.
## S3 method for class 'secr'
modelAverage(object, ..., realnames = NULL, betanames = NULL, newdata = NULL,
alpha = 0.05, dmax = 10, covar = FALSE, average = c("link", "real"),
criterion = c("AIC","AICc"), CImethod = c("Wald", "MATA"), chat = NULL)
## S3 method for class 'secrlist'
modelAverage(object, ..., realnames = NULL, betanames = NULL, newdata = NULL,
alpha = 0.05, dmax = 10, covar = FALSE, average = c("link", "real"),
criterion = c("AIC","AICc"), CImethod = c("Wald", "MATA"), chat = NULL)
object |
secr or secrlist object |
... |
other secr objects |
realnames |
character vector of real parameter names |
betanames |
character vector of beta parameter names |
newdata |
optional dataframe of values at which to evaluate models |
alpha |
alpha level for confidence intervals |
dmax |
numeric, the maximum AIC or AICc difference for inclusion in confidence set |
covar |
logical, if TRUE then return variance-covariance matrix |
average |
character string for scale on which to average real parameters |
criterion |
character, information criterion to use for model weights |
CImethod |
character, type of confidence interval (see Details) |
chat |
numeric optional variance inflation factor for quasi-AIC weights |
Models to be compared must have been fitted to the same data and use the
same likelihood method (full vs conditional). If realnames =
NULL and betanames = NULL then all real parameters will be
averaged; in this case all models must use the same real parameters. To
average beta parameters, specify betanames (this is ignored if a
value is provided for realnames). See predict.secr
for an explanation of the optional argument newdata;
newdata is ignored when averaging beta parameters.
Model-averaged estimates for parameter \theta are given by
\hat{\theta} = \sum\limits _k w_k \hat{\theta}_k
where the subscript k refers to a specific
model and the w_k are AIC or AICc weights (see
AIC.secr for details). Averaging of real parameters may be
done on the link scale before back-transformation
(average="link") or after back-transformation
(average="real").
Models for which dAIC > dmax (or dAICc > dmax) are given a
weight of zero and effectively are excluded from averaging.
Also,
\mbox{var} (\hat{\theta}) = \sum\limits _{k} { w_{k}
( \mbox{var}(\hat{\theta}_{k} | \beta _k) + \beta _k ^2)}
where \hat{\beta} _k = \hat{\theta}_k - \hat{\theta} and the variances are asymptotic estimates
from fitting each model k. This follows Burnham and Anderson
(2004) rather than Buckland et al. (1997).
Two methods are offered for confidence intervals. The default ‘Wald’
uses the above estimate of variance. The alternative ‘MATA’
(model-averaged tail area) avoids estimating a weighted variance and
is thought to provide better coverage at little cost in increased
interval length (Turek and Fletcher 2012). Turek and Fletcher (2012)
also found averaging with AIC weights (here criterion = 'AIC')
preferable to using AICc weights, even for small
samples. CImethod does not affect the reported standard errors.
If 'chat' is provided then quasi-AIC or quasi-AICc weights are used, depending on the value of 'criterion'.
For modelAverage, an array of model-averaged estimates, their
standard errors, and a 100(1-\alpha)% confidence
interval. The interval for real parameters is backtransformed from the
link scale. If there is only one row in newdata or beta
parameters are averaged or averaging is requested for only one parameter
then the array is collapsed to a matrix. If covar = TRUE then a
list is returned with separate components for the estimates and the
variance-covariance matrices.
modelAverage replaces the deprecated function model.average
whose name conflicted with a method in RMark.
Buckland S. T., Burnham K. P. and Augustin, N. H. (1997) Model selection: an integral part of inference. Biometrics 53, 603–618.
Burnham, K. P. and Anderson, D. R. (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Second edition. New York: Springer-Verlag.
Burnham, K. P. and Anderson, D. R. (2004) Multimodel inference - understanding AIC and BIC in model selection. Sociological Methods & Research 33, 261–304.
Turek, D. and Fletcher, D. (2012) Model-averaged Wald confidence intervals. Computational statistics and data analysis 56, 2809–2815.
modelAverage,
AIC.secr,
secr.fit,
collate
## Compare two models fitted previously
## secrdemo.0 is a null model
## secrdemo.b has a learned trap response
modelAverage(secrdemo.0, secrdemo.b)
modelAverage(secrdemo.0, secrdemo.b, betanames = c("D","g0","sigma"))
## In this case we find the difference was actually trivial...
## (subscripting of output is equivalent to setting fields = 1)