R: Predict Method for a CQO fit

predictqrrvglm {VGAM} | R Documentation

## Predict Method for a CQO fit

### Description

Predicted values based on a constrained quadratic ordination (CQO) object.

### Usage

    predictqrrvglm(object, newdata=NULL,
                   type = c("link", "response", "latvar", "terms"),
                   se.fit = FALSE, deriv = 0, dispersion = NULL,
                   extra = object@extra, varI.latvar = FALSE, refResponse = NULL, ...)

### Arguments

`object` | Object of class inheriting from `"qrrvglm"`.
`newdata` | An optional data frame in which to look for variables with which to predict. If omitted, the fitted linear predictors are used.
`type, se.fit, dispersion, extra` | See `predictvglm`.
`deriv` | Derivative. Currently only 0 is handled.
`varI.latvar, refResponse` | Arguments passed into `Coef.qrrvglm`.
`...` | Currently undocumented.

### Details

Obtains predictions from a fitted CQO object. Currently there are lots of limitations of this function; it is unfinished.

### Value

See `predictvglm`.

### Note

This function is not robust and has not been checked fully.

### Author(s)

T. W. Yee

### References

Yee, T. W. (2004) A new technique for maximum-likelihood canonical Gaussian ordination. Ecological Monographs, 74, 685–701.

### See Also

`cqo`.

### Examples

    hspider[,1:6] <- scale(hspider[,1:6])  # Standardize the environmental vars
    set.seed(1234)
    # vvv p1 <- cqo(cbind(Alopacce, Alopcune, Alopfabr, Arctlute,
    # vvv                 Arctperi, Auloalbi, Pardlugu, Pardmont,
    # vvv                 Pardnigr, Pardpull, Trocterr, Zoraspin) ~
    # vvv       WaterCon + BareSand + FallTwig + CoveMoss + CoveHerb + ReflLux,
    # vvv       poissonff, data = hspider, Crow1positive = FALSE, I.tol = TRUE)
    # vvv sort(deviance(p1, history = TRUE))  # A history of all the iterations

    # vvv head(predict(p1))

    # The following should be all zeros
    # vvv max(abs(predict(p1, new = head(hspider)) - head(predict(p1))))
    # vvv max(abs(predict(p1, new = head(hspider), type = "res")-head(fitted(p1))))

[Package VGAM version 1.0-3 Index]