R: Positive Binomial Distribution Family Function

posbinomial {VGAM} | R Documentation

## Positive Binomial Distribution Family Function

### Description

Fits a positive binomial distribution.

### Usage

    posbinomial(link = "logitlink", multiple.responses = FALSE, parallel = FALSE,
                omit.constant = FALSE, p.small = 1e-4, no.warning = FALSE,
                zero = NULL)

### Arguments

`link, multiple.responses, parallel, zero` | Details at `CommonVGAMffArguments`.
`omit.constant` | Logical. If `TRUE` then the constant (`lchoose(size, size * yprop)` is omitted from the `loglikelihood` calculation. If the model is to be compared using `AIC()` or `BIC()` (see `AICvlm` or `BICvlm`) to the likes of `posbernoulli.tb` etc. then it is important to set `omit.constant = TRUE` because all models then will not have any normalizing constants in the likelihood function. Hence they become comparable. This is because the M_0 Otis et al. (1978) model coincides with `posbinomial()`. See below for an example. Also see `posbernoulli.t` regarding estimating the population size (`N.hat` and `SE.N.hat`) if the number of trials is the same for all observations.
`p.small, no.warning` | See `posbernoulli.t`.

### Details

The positive binomial distribution is the ordinary binomial distribution but with the probability of zero being zero. Thus the other probabilities are scaled up (i.e., divided by 1-P(Y=0)). The fitted values are the ordinary binomial distribution fitted values, i.e., the usual mean.

In the capture–recapture literature this model is called the M_0 if it is an intercept-only model. Otherwise it is called the M_h when there are covariates. It arises from a sum of a sequence of τ-Bernoulli random variates subject to at least one success (capture). Here, each animal has the same probability of capture or recapture, regardless of the τ sampling occasions. Independence between animals and between sampling occasions etc. is assumed.

### Value

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

### Warning

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

### Note

The input for this family function is the same as `binomialff`.

If `multiple.responses = TRUE` then each column of the matrix response should be a count (the number of successes), and the `weights` argument should be a matrix of the same dimension as the response containing the number of trials. If `multiple.responses = FALSE` then the response input should be the same as `binomialff`.

Yet to be done: a `quasi.posbinomial()` which estimates a dispersion parameter.

### Author(s)

Thomas W. Yee

### References

Otis, D. L. et al. (1978). Statistical inference from capture data on closed animal populations, Wildlife Monographs, 62, 3–135.

Patil, G. P. (1962). Maximum likelihood estimation for generalised power series distributions and its application to a truncated binomial distribution. Biometrika, 49, 227–237.

Pearson, K. (1913). A Monograph on Albinism in Man. Drapers Company Research Memoirs.

### See Also

`posbernoulli.b`, `posbernoulli.t`, `posbernoulli.tb`, `gtbinomial`, `binomialff`, `AICvlm`, `BICvlm`, `simulate.vlm`.

### Examples

    # Number of albinotic children in families with 5 kids (from Patil, 1962) ,,,,
    albinos <- data.frame(y = c(rep(1, 25), rep(2, 23), rep(3, 10), 4, 5),
                          n = rep(5, 60))
    fit1 <- vglm(cbind(y, n-y) ~ 1, posbinomial, albinos, trace = TRUE)
    summary(fit1)
    Coef(fit1)  # = MLE of p = 0.3088
    head(fitted(fit1))
    sqrt(vcov(fit1, untransform = TRUE))  # SE = 0.0322

    # Fit a M_0 model (Otis et al. 1978) to the deermice data ,,,,,,,,,,,,,,,,,,,,,,,
    M.0 <- vglm(cbind(    y1 + y2 + y3 + y4 + y5 + y6,
                      6 - y1 - y2 - y3 - y4 - y5 - y6) ~ 1, trace = TRUE,
                posbinomial(omit.constant = TRUE), data = deermice)
    coef(M.0, matrix = TRUE)
    Coef(M.0)
    constraints(M.0, matrix = TRUE)
    summary(M.0)
    c(   N.hat = M.0@extra$N.hat,     # Since tau = 6, i.e., 6 Bernoulli trials per
      SE.N.hat = M.0@extra$SE.N.hat)  # observation is the same for each observation

    # Compare it to the M_b using AIC and BIC
    M.b <- vglm(cbind(y1, y2, y3, y4, y5, y6) ~ 1, trace = TRUE,
                posbernoulli.b, data = deermice)
    sort(c(M.0 = AIC(M.0), M.b = AIC(M.b)))  # Okay since omit.constant = TRUE
    sort(c(M.0 = BIC(M.0), M.b = BIC(M.b)))  # Okay since omit.constant = TRUE

[Package VGAM version 1.1-3 Index]