AICcmodavg (version 2.00)

confset: Computing Confidence Set for the Kullback-Leibler Best Model

Description

This function computes the confidence set on the best model given the data and model set. confset implements three different methods proposed by Burnham and Anderson (2002).

Usage

confset(cand.set, modnames = NULL, second.ord = TRUE, nobs = NULL,
        method = "raw", level = 0.95, delta = 6, c.hat = 1)

Arguments

cand.set

a list storing each of the models 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 NULL, the function uses the names in the cand.set list of candidate models. If no names appear in the list, generic names (e.g.,

second.ord

logical. If TRUE, the function returns the second-order Akaike information criterion (i.e., AICc).

nobs

this argument allows to specify a numeric value other than total sample size to compute the AICc (i.e., 'nobs' defaults to total number of observations). This is relevant only for mixed models or various models of 'unmarkedFit' classes where sample size

method

a character value, either as 'raw', 'ordinal', or 'ratio', indicating the method for determining the confidence set for the best model (see 'description' above for details).

level

the level of confidence (i.e., sum of model probabilities) used to determine the confidence set on the best model when using the 'raw' method. Note that the argument is not used for the other methods of determining the confidence set on the best model.

delta

the delta (Q)AIC(c) value associated with the cutoff point to determine the confidence set for the best model. Note that the argument is only used when method = 'ratio'.

c.hat

value of overdispersion parameter (i.e., variance inflation factor) such as that obtained from c_hat. Note that values of c.hat different from 1 are only appropriate for binomial GLM's with trials > 1 (i.e., success/trial or cbind(success, f

Value

• confset returns an object of class confset as a list with the following components, depending on which method is used:

  when method = 'raw':

• method
  identifies the method of determining the confidence set on the best model.
• level
  the confidence level used to determine the confidence set on the best model.
• table
  a reduced table with the models included in the confidence set.
• when method = 'ordinal':
• method
  identifies the method of determining the confidence set on the best model.
• substantial
  a reduced table with the models included in the confidence set for which delta (Q)AIC(c) <= 2.<="" description="">
• some
  a reduced table with the models included in the confidence set for which 2 < delta (Q)AIC(c) <= 7.<="" description="">
• little
  a reduced table with the models included in the confidence set for which 7 < delta (Q)AIC(c) <= 10.<="" description="">
• none
  a reduced table with the models included in the confidence set for which delta (Q)AIC(c) > 10.
• when method = 'ratio':
• method
  identifies the method of determining the confidence set on the best model.
• cutoff
  the cutoff value for the ratios used to determine the confidence set on the best model.
• delta
  the delta (Q)AIC(c) used to compute the cutoff value for ratios to determine the confidence set on the best model.
• table
  a reduced table with the models included in the confidence set.

Details

The first and simplest (method = 'raw'), relies on summing the Akaike weights (i.e., model probabilities) of the ranked models until we reach a given cutpoint (e.g., 0.95 for a 95 percent set).

The second method (method = 'ordinal') suggested is based on the classification of the models on an ordinal scale based on the delta (Q)AIC(c). The models are grouped in different classes based on their weight of support as determined by the delta (Q)AIC(c) values: substantial support (delta (Q)AIC(c) <= 2),="" some="" support="" (2="" <="" delta="" (q)aic(c)="" little="" (7="" no="" (delta=""> 10).

The third method (method = 'ratio') is based on identifying the ratios of model likelihoods (i.e., exp(-delta_(Q)AIC(c)/2) ) that exceed a cutpoint, similar to the building of profile likelihood intervals. An evidence ratio of each model relative to the top-ranked model is computed and the ratios exceeding the cutpoint determine which models are included in the confidence set. Note here that small cutoff points are suggested (e.g., 0.125, 0.050). The cutoff point is linked to delta (Q)AIC(c) by the following relationship: cutoff = exp(-1*delta_(Q)AIC(c)/2).

References

Burnham, K. P., Anderson, D. R. (2002) Model Selection and Multimodel Inference: a practical information-theoretic approach. Second edition. Springer: New York.

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.

See Also

AICc, aictab, c_hat, evidence, importance, modavg, modavgShrink, modavgPred

Examples

##anuran larvae example from Mazerolle (2006)
data(min.trap)
##assign "UPLAND" as the reference level as in Mazerolle (2006)          
min.trap$Type <- relevel(min.trap$Type, ref = "UPLAND") 

##set up candidate models          
Cand.mod <- list()
##global model          
Cand.mod[[1]] <- glm(Num_anura ~ Type + log.Perimeter + Num_ranatra,
                     family = poisson, offset = log(Effort),
                     data = min.trap) 
Cand.mod[[2]] <- glm(Num_anura ~ Type + log.Perimeter, family = poisson,
                     offset = log(Effort), data = min.trap) 
Cand.mod[[3]] <- glm(Num_anura ~ Type + Num_ranatra, family = poisson,
                     offset = log(Effort), data = min.trap) 
Cand.mod[[4]] <- glm(Num_anura ~ Type, family = poisson,
                     offset = log(Effort), data = min.trap) 
Cand.mod[[5]] <- glm(Num_anura ~ log.Perimeter + Num_ranatra,
                     family = poisson, offset = log(Effort),
                     data = min.trap) 
Cand.mod[[6]] <- glm(Num_anura ~ log.Perimeter, family = poisson,
                     offset = log(Effort), data = min.trap) 
Cand.mod[[7]] <- glm(Num_anura ~ Num_ranatra, family = poisson,
                     offset = log(Effort), data = min.trap) 
Cand.mod[[8]] <- glm(Num_anura ~ 1, family = poisson,
                     offset = log(Effort), data = min.trap) 
          
##check c-hat for global model
c_hat(Cand.mod[[1]]) #uses Pearson's chi-square/df
##note the very low overdispersion: in this case, the analysis could be
##conducted without correcting for c-hat as its value is reasonably close
##to 1  

##assign names to each model
Modnames <- c("type + logperim + invertpred", "type + logperim",
              "type + invertpred", "type", "logperim + invertpred",
              "logperim", "invertpred", "intercept only") 

##compute confidence set based on 'raw' method
confset(cand.set = Cand.mod, modnames = Modnames, second.ord = TRUE,
        method = "raw")  



##example with linear mixed model
require(nlme)

##set up candidate model list for Orthodont data set shown in Pinheiro
##and Bates (2000:  Mixed-effect models in S and S-PLUS. Springer Verlag:
##New York.)
Cand.models <- list()
Cand.models[[1]] <- lme(distance ~ age, random = ~age | Subject,
                        data = Orthodont, method = "ML")
Cand.models[[2]] <- lme(distance ~ age + Sex, data = Orthodont,
                        random = ~ 1 | Subject, method = "ML")
Cand.models[[3]] <- lme(distance ~ 1, data = Orthodont,
                        random = ~ 1 | Subject, method = "ML")

##create a vector of model names
Modnames <- paste("mod", 1:length(Cand.models), sep = "")

##compute confidence set based on 'raw' method
confset(cand.set = Cand.models, modnames = Modnames, second.ord = TRUE,
        method = "raw")
##round to 4 digits after decimal point
print(confset(cand.set = Cand.models, modnames = Modnames,
              second.ord = TRUE, method = "raw"), digits = 4)

confset(cand.set = Cand.models, modnames = Modnames, second.ord = TRUE,
        level = 0.9, method = "raw")

##compute confidence set based on 'ordinal' method
confset(cand.set = Cand.models, modnames = Modnames, second.ord = TRUE,
        method = "ordinal")

##compute confidence set based on 'ratio' method
confset(cand.set = Cand.models, modnames = Modnames, second.ord = TRUE,
        method = "ratio", delta = 4)

confset(cand.set = Cand.models, modnames = Modnames, second.ord = TRUE,
        method = "ratio", delta = 8)