morph {mcmc} R Documentation

## Variable Transformation

### Description

Utility functions for variable transformation.

### Usage

```morph(b, r, p, center)
morph.identity()
```

### Arguments

 `b` Positive real number. May be missing. `r` Non-negative real number. May be missing. If `p` is specified, `r` defaults to 0. `p` Real number strictly greater than 2. May be missing. If `r` is specified, `p` defaults to 3. `center` Real scalar or vector. May be missing. If `center` is a vector it should be the same length of the state of the Markov chain, `center` defaults to 0

### Details

The `morph` function facilitates using variable transformations by providing functions to (using X for the original random variable with the pdf f.X, and Y for the transformed random variable with the pdf f.Y):

• Calculate the log unnormalized probability density for Y induced by the transformation.

• Transform an arbitrary function of X to a function of Y.

• Transform values of X to values of Y.

• Transform values of Y to values of X (the inverse transformation).

for a select few transformations.

`morph.identity` implements the identity transformation, Y=X.

The parameters `r`, `p`, `b` and `center` specify the transformation function. In all cases, `center` gives the center of the transformation, which is the value c in the equation

Y = f(X - c).

If no parameters are specified, the identity transformation, Y=X, is used.

The parameters `r`, `p` and `b` specify a function g, which is a monotonically increasing bijection from the non-negative reals to the non-negative reals. Then

f(X) = g(|X|) * X / |X|

where |X| represents the Euclidean norm of the vector X. The inverse function is given by

f^{-1}(Y) = g^{-1}(|Y|) * Y / |Y|.

The parameters `r` and `p` are used to define the function

g1(x) = x + (x-r)^p * I(x > r)

where I(•) is the indicator function. We require that `r` is non-negative and `p` is strictly greater than 2. The parameter `b` is used to define the function

g2(x) = (exp(b * x) - exp(1) / 3) * I(x > 1 / b) + (x^3 * b^3 exp(1) / 6 + x * b * exp(1) / 2) * I(x <= 1 / b).

We require that b is positive.

The parameters `r`, `p` and `b` specify f^{-1} in the following manner:

• If one or both of `r` and `p` is specified, and `b` is not specified, then

f^{-1}(X) = g1(|X|) * X / |X|.

If only `r` is specified, `p = 3` is used. If only `p` is specified, `r = 0` is used.

• If only `b` is specified, then

f^{-1}(X) = g2(|X|) * X / |X|.

• If one or both of `r` and `p` is specified, and `b` is also specified, then

f^{-1}(X) = g2(g1(|X|)) * X / |X|.

### Value

a list containing the functions

• `outfun(f)`, a function that operates on functions. `outfun(f)` returns the function ```function(state, ...) f(inverse(state), ...)```.

• `inverse`, the inverse transformation function.

• `transform`, the transformation function.

• `lud`, a function that operates on functions. As input, `lud` takes a function that calculates a log unnormalized probability density, and returns a function that calculates the log unnormalized density by transforming a random variable using the `transform` function. ```lud(f) = function(state, ...) f(inverse(state), ...) + log.jacobian(state)```, where `log.jacobian` represents the function that calculate the log Jacobian of the transformation. `log.jacobian` is not returned.

### Warning

The equations for the returned `transform` function (see below) do not have a general analytical solution when `p` is not equal to 3. This implementation uses numerical approximation to calculate `transform` when `p` is not equal to 3. If computation speed is a factor, it is advisable to use `p=3`. This is not a factor when using `morph.metrop`, as `transform` is only called once during setup, and not at all while running the Markov chain.

`morph.metrop`

### Examples

```
# use an exponential transformation, centered at 100.
b1 <- morph(b=1, center=100)
# original log unnormalized density is from a t distribution with 3
# degrees of freedom, centered at 100.
lud.transformed <- b1\$lud(function(x) dt(x - 100, df=3, log=TRUE))
d.transformed <- Vectorize(function(x) exp(lud.transformed(x)))
## Not run:
curve(d.transformed, from=-3, to=3, ylab="Induced Density")

## End(Not run)
```

[Package mcmc version 0.9-6 Index]