notExp2 {mgcv}R Documentation

Alternative to log parameterization for variance components


notLog2 and notExp2 are alternatives to log and exp or notLog and notExp for re-parameterization of variance parameters. They are used by the pdTens and pdIdnot classes which in turn implement smooths for gamm.

The functions are typically used to ensure that smoothing parameters are positive, but the notExp2 is not monotonic: rather it cycles between `effective zero' and `effective infinity' as its argument changes. The notLog2 is the inverse function of the notExp2 only over an interval centered on zero.

Parameterizations using these functions ensure that estimated smoothing parameters remain positive, but also help to ensure that the likelihood is never indefinite: once a working parameter pushes a smoothing parameter below `effetive zero' or above `effective infinity' the cyclic nature of the notExp2 causes the likelihood to decrease, where otherwise it might simply have flattened.

This parameterization is really just a numerical trick, in order to get lme to fit gamm models, without failing due to indefiniteness. Note in particular that asymptoticresults on the likelihood/REML criterion are not invalidated by the trick, unless parameter estimates end up close to the effective zero or effective infinity: but if this is the case then the asymptotics would also have been invalid for a conventional monotonic parameterization.

This reparameterization was made necessary by some modifications to the underlying optimization method in lme introduced in nlme 3.1-62. It is possible that future releases will return to the notExp parameterization.

Note that you can reset `effective zero' and `effective infinity': see below.





x Argument array of real numbers (notExp) or positive real numbers (notLog).
d the range of notExp2 runs from exp(-d) to exp(d). To change the range used by gamm reset using options.
b determines the period of the cycle of notExp2.


An array of function values evaluated at the supplied argument values.


Simon N. Wood


See Also

pdTens, pdIdnot, gamm


## Illustrate the notExp2 function:
x <- seq(-50,50,length=1000)
op <- par(mfrow=c(2,2))
lines(x,log(exp(x)),col=2) # redundancy intended
x <- x/4
lines(x,log(exp(x)),col=2) # redundancy intended

[Package mgcv version 1.3-23 Index]