polf {VGAM} | R Documentation

## Poisson-Ordinal Link Function

### Description

Computes the Poisson-ordinal transformation, including its inverse and the first two derivatives.

### Usage

    polf(theta, cutpoint = NULL,
         inverse = FALSE, deriv = 0, short = TRUE, tag = FALSE)

### Arguments

`theta` | Numeric or character. See below for further details.
`cutpoint` | The cutpoints should be non-negative integers. If `polf()` is used as the link function in `cumulative` then one should choose `reverse = TRUE, parallel = TRUE`.
`inverse, deriv, short, tag` | Details at `Links`.

### Details

The Poisson-ordinal link function (POLF) can be applied to a parameter lying in the unit interval. Its purpose is to link cumulative probabilities associated with an ordinal response coming from an underlying Poisson distribution. If the cutpoint is zero then a complementary log-log link is used.

See `Links` for general information about VGAM link functions.

### Value

See Yee (2012) for details.

### Warning

Prediction may not work on `vglm` or `vgam` etc. objects if this link function is used.

### Note

Numerical values of `theta` too close to 0 or 1 or out of range result in large positive or negative values, or maybe 0 depending on the arguments. Although measures have been taken to handle cases where `theta` is too close to 1 or 0, numerical instabilities may still arise.

In terms of the threshold approach with cumulative probabilities for an ordinal response this link function corresponds to the Poisson distribution (see `poissonff`) that has been recorded as an ordinal response using known cutpoints.

### Author(s)

Thomas W. Yee

### References

Yee, T. W. (2012) Ordinal ordination with normalizing link functions for count data, (in preparation).

### See Also

`Links`, `ordpoisson`, `poissonff`, `nbolf`, `golf`, `cumulative`.

### Examples

    ## Not run:
    polf("p", cutpoint = 2, short = FALSE)
    polf("p", cutpoint = 2, tag = TRUE)

    p <- seq(0.01, 0.99, by = 0.01)
    y <- polf(p, cutpoint = 2)
    y. <- polf(p, cutpoint = 2, deriv = 1)
    max(abs(polf(y, cutpoint = 2, inv = TRUE) - p))  # Should be 0

    #\ dontrun{ par(mfrow = c(2, 1), las = 1)
    #plot(p, y, type = "l", col = "blue", main = "polf()")
    #abline(h = 0, v = 0.5, col = "orange", lty = "dashed")
    #
    #plot(p, y., type = "l", col = "blue",
    #     main = "(Reciprocal of) first POLF derivative")
    #}

    # Rutherford and Geiger data
    ruge <- data.frame(yy = rep(0:14,
          times = c(57,203,383,525,532,408,273,139,45,27,10,4,0,1,1)))
    with(ruge, length(yy))  # 2608 1/8-minute intervals
    cutpoint <- 5
    ruge <- transform(ruge, yy01 = ifelse(yy <= cutpoint, 0, 1))
    fit <- vglm(yy01 ~ 1, binomialff(link = polf(cutpoint = cutpoint)), ruge)
    coef(fit, matrix = TRUE)
    exp(coef(fit))

    # Another example
    pdata <- data.frame(x2 = sort(runif(nn <- 1000)))
    pdata <- transform(pdata, x3 = runif(nn))
    pdata <- transform(pdata, mymu = exp( 3 + 1 * x2 - 2 * x3))
    pdata <- transform(pdata, y1 = rpois(nn, lambda = mymu))
    cutpoints <- c(-Inf, 10, 20, Inf)
    pdata <- transform(pdata, cuty = Cut(y1, breaks = cutpoints))
    #\ dontrun{ with(pdata, plot(x2, x3, col = cuty, pch = as.character(cuty))) }
    with(pdata, table(cuty) / sum(table(cuty)))
    fit <- vglm(cuty ~ x2 + x3, data = pdata, trace = TRUE,
                cumulative(reverse = TRUE,
                           parallel = TRUE,
                           link = polf(cutpoint = cutpoints[2:3]),
                           multiple.responses = TRUE))
    head(depvar(fit))
    head(fitted(fit))
    head(predict(fit))
    coef(fit)
    coef(fit, matrix = TRUE)
    constraints(fit)
    fit@misc$earg

    ## End(Not run)

[Package VGAM version 1.0-4 Index]