calibrate {VGAM}R Documentation

Model Calibrations

Description

calibrate is a generic function used to produce calibrations from various model fitting functions. The function invokes particular `methods' which depend on the `class' of the first argument.

Usage

calibrate(object, ...)

Arguments

object An object for which a calibration is desired.
... Additional arguments affecting the calibration produced. Usually the most important argument in ... is newdata which, for calibrate, contains new response data, Y, say.

Details

Given a regression model with explanatory variables X and response Y, calibration involves estimating X from Y using the regression model. It can be loosely thought of as the opposite of predict (which takes an X and returns a Y.)

Value

In general, given a new response Y, the explanatory variables X are returned. However, for constrained ordination models such as CQO and CAO models, it is usually not possible to return X, so the latent variables are returned instead (they are linear combinations of the X). See the specific calibrate methods functions to see what they return.

Note

This function was not called predictx because of the inability of constrained ordination models to return X; they can only return the latent variable values (site scores) instead.

Author(s)

T. W. Yee

See Also

predict, calibrate.qrrvglm.

Examples

data(hspider)
hspider[,1:6] = scale(hspider[,1:6]) # Standardized environmental vars
set.seed(123)
p1 = cao(cbind(Pardlugu, Pardmont, Pardnigr, Pardpull, Zoraspin) ~
         WaterCon + BareSand + FallTwig + 
         CoveMoss + CoveHerb + ReflLux,
         family = poissonff, data = hspider, Rank = 1,
         df1.nl = c(Zoraspin=2, 1.9),
         Bestof = 3, Crow1positive = TRUE)

siteNos = 1:2  # Calibrate these sites
cp1 = calibrate(p1, new=data.frame(p1@y[siteNos,]), trace=TRUE)

## Not run: 
# Graphically compare the actual site scores with their calibrated values
persp(p1, main="Solid=actual, dashed=calibrated site scores",
      label=TRUE, col="blue", las=1)
abline(v=lv(p1)[siteNos], lty=1, col=1:length(siteNos)) # actual site scores
abline(v=cp1, lty=2, col=1:length(siteNos)) # calibrated values
## End(Not run)

[Package VGAM version 0.7-7 Index]