VGAM (version 0.9-0)

huggins91: Huggins (1991) Capture-recapture Model Family Function (approximation only)

Description

Fits a Huggins (1991) capture-recapture model to a matrix of 0s and 1s: animals sampled on several occasions and individual animals caught at least once.

Usage

huggins91(link = "logit", parallel = TRUE,
          iprob = NULL, eim.not.oim = TRUE)

Arguments

link, parallel, iprob

See CommonVGAMffArguments for information. The parallel argument should generally be left alone since parallelism is assumed by Huggins (1991).

eim.not.oim

Logical. If TRUE use the EIM, else the OIM.

Value

• An object of class "vglmff" (see vglmff-class). The object is used by modelling functions such as vglm, and vgam.

Warning

This VGAM family function is experimental and does not work properly because the linear/additive predictor in the numerator and denominator must be the same. The parameter estimates of the Huggins (1991) model ought to be similar (probably in between, in some sense) to two models: Model 1 is where the capture history variable is included, Model 2 is where the capture history variable is not included. See the example below. A third model, called Model 3, allows for 'half' the capture history to be put in both numerator and denominator. This might be thought of as a compromise between Models 1 and 2, and may be useful as a crude approximation.

Under- or over-flow may occur if the data is ill-conditioned.

Details

This model operates on a response matrix of 0s and 1s. Each of at least two columns is an occasion where animals are potentially captured (e.g., a field trip), and each row is an individual animal. Capture is a 1, else a 0. Each row has at least one capture. It is well-known that animals are affected by capture, e.g., trap-shy or trap-happy. This VGAM family function attempts to allow the capture history to be modelled. This involves the use of the xij argument. Ignoring capture history effects would mean posbinomial could be used by aggregating over the sampling occasions.

Huggins (1991) suggests a model involving maximizing a conditional likelihood. The form of this is a numerator divided by a denominator, where the true model has part of the linear/additive predictor modelling capture history applying to the numerator only, so that part is set to zero in the denominator. The numerator of the conditional likelihood corresponds to a sequence of Bernoulli trials, with at least one success, for each animal.

Unfortunately the Huggins model is too difficult to fit in this package, and one can only use the same linear/additive predictor in the numerator as the denominator. Hence this VGAM family function does not implement the model properly.

The number of linear/additive predictors is twice the number of sampling occasions, i.e., $M = 2T$, say. The first two correspond to the first sampling occasion, the next two correspond to the second sampling occasion, etc. Even-numbered linear/additive predictors should correspond to what would happen if no capture had occurred (they belong to the denominator.) Odd-numbered linear/additive predictors correspond to what actually happened (they belong to the numerator.)

The fitted value for column $t$ is the $t$th numerator probability divided by the denominator.

References

Huggins, R. M. (1991) Some practical aspects of a conditional likelihood approach to capture experiments. Biometrics, 47, 725--732.

See Also

vglm.control for xij, dhuggins91, rhuggins91. posbinomial.

Examples

set.seed(123); nTimePts <- 5
hdata <- rhuggins91(n = 1000, nTimePts = nTimePts, pvars = 2)

# The truth: xcoeffs are c(-2, 1, 2) and capeffect = -1

# Model 1 is where capture history information is used
model1  <- vglm(cbind(y1, y2, y3, y4, y5) ~ x2 + Chistory,
               huggins91, data = hdata, trace  = TRUE,
               xij = list(Chistory ~ ch0 + zch0 +
                                     ch1 + zch1 + ch2 + zch2 +
                                     ch3 + zch3 + ch4 + zch4 - 1),
               form2 = ~ 1 + x2 + Chistory +
                          ch0 +  ch1 +  ch2 +  ch3 +  ch4 +
                         zch0 + zch1 + zch2 + zch3 + zch4)

coef(model1, matrix = TRUE) # Biased!!
summary(model1)
head(fitted(model1))
head(model.matrix(model1, type = "vlm"), 21)
head(hdata)

# Model 2 is where no capture history information is used
model2  <- vglm(cbind(y1, y2, y3, y4, y5) ~ x2,
               huggins91, data = hdata, trace  = TRUE)
coef(model2, matrix = TRUE) # Biased!!
summary(model2)

# Model 3 is where half the capture history is used in both
# the numerator and denominator
set.seed(123); nTimePts = 5
hdata2 <- rhuggins91(n = 1000, nTimePts = nTimePts, pvars = 2,
                    double.ch = TRUE)
head(hdata2)  # 2s have replaced the 1s in hdata
model3  <- vglm(cbind(y1, y2, y3, y4, y5) ~ x2 + Chistory,
               huggins91, data = hdata2, trace  = TRUE,
               xij = list(Chistory ~ ch0 + zch0 +
                                     ch1 + zch1 + ch2 + zch2 +
                                     ch3 + zch3 + ch4 + zch4 - 1),
               form2 = ~ 1 + x2 + Chistory +
                          ch0 +  ch1 +  ch2 +  ch3 +  ch4 +
                         zch0 + zch1 + zch2 + zch3 + zch4)
coef(model3, matrix = TRUE) # Biased!!