modavgCustom {AICcmodavg}  R Documentation 
Compute Modelaveraged Parameter Estimate from Usersupplied Input Based on (Q)AIC(c)
Description
This function modelaverages the estimate of a parameter of interest among a set of candidate models, and computes the unconditional standard error and unconditional confidence intervals as described in Buckland et al. (1997) and Burnham and Anderson (2002).
Usage
modavgCustom(logL, K, modnames = NULL, estimate, se, second.ord = TRUE,
nobs = NULL, uncond.se = "revised", conf.level = 0.95,
c.hat = 1, useBIC = FALSE)
Arguments
logL 
a vector of loglikelihood values for the models in the candidate model set. 
K 
a vector containing the number of estimated parameters for each model in the candidate model set. 
modnames 
a character vector of model names to facilitate the identification of
each model in the model selection table. If 
estimate 
a vector of estimates for each of the models in the candidate model set. Estimates can be either beta estimates for a parameter of interest or a single prediction from each model. 
se 
a vector of standard errors for each of the estimates appearing in the

second.ord 
logical. If 
nobs 
the sample size required to compute the AICc, QAICc, BIC, or QBIC. 
uncond.se 
either, 
conf.level 
the confidence level ( 
c.hat 
value of overdispersion parameter (i.e., variance inflation factor) such
as that obtained from 
useBIC 
logical. If 
Details
modavgCustom
computes a modelaveraged estimate from the vector
of parameter estimates specified in estimate
. Estimates and
their associated standard errors must be specified in the same order as
the loglikelihood, number of estimated parameters, and model names.
Estimates provided may be for a parameter of interest (i.e., beta
estimates) or predictions from each model. This function is most useful
when model input is imported into R from other software (e.g., Program
MARK, PRESENCE) or for model classes that are not yet supported by the
other model averaging functions such as modavg
or
modavgPred
.
Value
modavgCustom
creates an object of class modavgCustom
with
the following components:
Mod.avg.table 
the model selection table 
Mod.avg.est 
the modelaveraged estimate 
Uncond.SE 
the unconditional standard error for the modelaveraged estimate 
Conf.level 
the confidence level used to compute the confidence interval 
Lower.CL 
the lower confidence limit 
Upper.CL 
the upper confidence limit 
Author(s)
Marc J. Mazerolle
References
Anderson, D. R. (2008) Modelbased Inference in the Life Sciences: a primer on evidence. Springer: New York.
Buckland, S. T., Burnham, K. P., Augustin, N. H. (1997) Model selection: an integral part of inference. Biometrics 53, 603–618.
Burnham, K. P., Anderson, D. R. (2002) Model Selection and Multimodel Inference: a practical informationtheoretic approach. Second edition. Springer: New York.
Dail, D., Madsen, L. (2011) Models for estimating abundance from repeated counts of an open population. Biometrics 67, 577–587.
Lebreton, J.D., Burnham, K. P., Clobert, J., Anderson, D. R. (1992) Modeling survival and testing biological hypotheses using marked animals: a unified approach with casestudies. Ecological Monographs 62, 67–118.
MacKenzie, D. I., Nichols, J. D., Lachman, G. B., Droege, S., Royle, J. A., Langtimm, C. A. (2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology 83, 2248–2255.
MacKenzie, D. I., Nichols, J. D., Hines, J. E., Knutson, M. G., Franklin, A. B. (2003) Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology 84, 2200–2207.
Royle, J. A. (2004) Nmixture models for estimating population size from spatially replicated counts. Biometrics 60, 108–115.
See Also
AICcCustom
, aictabCustom
,
bictabCustom
, modavg
,
modavgIC
, modavgShrink
,
modavgPred
Examples
## Not run:
##model averaging parameter estimate (natural average)
##vector with model LL's
LL < c(38.8876, 35.1783, 64.8970)
##vector with number of parameters
Ks < c(7, 9, 4)
##create a vector of names to trace back models in set
Modnames < c("Cm1", "Cm2", "Cm3")
##vector of beta estimates for a parameter of interest
model.ests < c(0.0478, 0.0480, 0.0478)
##vector of SE's of beta estimates for a parameter of interest
model.se.ests < c(0.0028, 0.0028, 0.0034)
##compute modelaveraged estimate and unconditional SE based on AICc
modavgCustom(logL = LL, K = Ks, modnames = Modnames,
estimate = model.ests, se = model.se.ests, nobs = 121)
##compute modelaveraged estimate and unconditional SE based on BIC
modavgCustom(logL = LL, K = Ks, modnames = Modnames,
estimate = model.ests, se = model.se.ests, nobs = 121,
useBIC = TRUE)
##modelaveraging with shrinkage based on AICc
##set up candidate models
data(min.trap)
Cand.mod < list( )
##global model
Cand.mod[[1]] < glm(Num_anura ~ Type + log.Perimeter,
family = poisson, offset = log(Effort),
data = min.trap)
Cand.mod[[2]] < glm(Num_anura ~ Type + Num_ranatra, family = poisson,
offset = log(Effort), data = min.trap)
Cand.mod[[3]] < glm(Num_anura ~ log.Perimeter + Num_ranatra,
family = poisson, offset = log(Effort), data = min.trap)
Model.names < c("Type + log.Perimeter", "Type + Num_ranatra",
"log.Perimeter + Num_ranatra")
##modelaveraged estimate with shrinkage (glm model type is already supported)
modavgShrink(cand.set = Cand.mod, modnames = Model.names,
parm = "log.Perimeter")
##equivalent manual version of modelaveraging with shrinkage
##this is especially useful when model classes are not supported
##extract vector of LL
LLs < sapply(Cand.mod, FUN = function(i) logLik(i)[1])
##extract vector of K
Ks < sapply(Cand.mod, FUN = function(i) attr(logLik(i), "df"))
##extract betas
betas < sapply(Cand.mod, FUN = function(i) coef(i)["log.Perimeter"])
##second model does not include log.Perimeter
betas[2] < 0
##extract SE's
ses < sapply(Cand.mod, FUN = function(i) sqrt(diag(vcov(i))["log.Perimeter"]))
ses[2] < 0
##modelaveraging with shrinkage based on AICc
modavgCustom(logL = LLs, K = Ks, modnames = Model.names,
nobs = nrow(min.trap), estimate = betas, se = ses)
##modelaveraging with shrinkage based on BIC
modavgCustom(logL = LLs, K = Ks, modnames = Model.names,
nobs = nrow(min.trap), estimate = betas, se = ses,
useBIC = TRUE)
## End(Not run)