RMSEP {analogue}R Documentation

Root mean square error of prediction

Description

Calculates or extracts the RMSEP from transfer function models.

Usage

RMSEP(object, ...)

## S3 method for class 'bootstrap':
RMSEP(object, type = c("birks1990", "standard"),
          ...)

Arguments

object An object. Currently only objects of class "bootstrap".
type The type of RMSEP to return/calculate.
... Arguments passed to other methods.

Details

There are two forms of RMSEP in common usage. Within palaeoecology, the RMSEP of Birks et al. (1990) is most familiar:

RMSEP = sqrt(s[1]^2 + s[2]^2)

where where s[1] is the standard error of the out-of-bag (OOB) residuals and s[2] is the mean bias or the mean of the OOB residuals.

In the wider statistical literature, the following form of RMSEP is more commonly used:

RMSEP = sqrt(mean((y[i] - yhat[i])^2))

where y[i] are the observed values and hat{y_i} the transfer function predictions/fitted values.

The first form of RMSEP is returned by default or if type = "birks1990" is supplied. The latter form is returned if type = "standard" is supplied.

Value

A numeric vector of length 1 that is the RMSEP of object.

Note

RMSEP is a generic function. Currently it can only be used with objects of class "bootstrap". Further methods are planned.

Author(s)

Gavin L. Simpson

References

Birks, H.J.B., Line, J.M., Juggins, S., Stevenson, A.C. and ter Braak, C.J.F. (1990). Diatoms and pH reconstruction. Philosophical Transactions of the Royal Society of London; Series B, 327; 263–278.

See Also

bootstrap

Examples

## continue the RLGH and SWAP example from ?join
example(join)

## fit the MAT model using the squared chord distance measure
swap.mat <- mat(swapdiat, swappH, method = "SQchord")

## bootstrap training set
swap.boot <- bootstrap(swap.mat, n.boot = 100)
swap.boot

## extract the Birks et al (1990) RMSEP
RMSEP(swap.boot)

## Calculate the alternative formulation
RMSEP(swap.boot, type = "standard")

[Package analogue version 0.3-3 Index]