RMSEP {analogue} | R Documentation |
Calculates or extracts the RMSEP from transfer function models.
RMSEP(object, ...) ## S3 method for class 'bootstrap': RMSEP(object, type = c("birks1990", "standard"), ...)
object |
An object. Currently only objects of class
"bootstrap" . |
type |
The type of RMSEP to return/calculate. |
... |
Arguments passed to other methods. |
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.
A numeric vector of length 1 that is the RMSEP of object
.
RMSEP
is a generic function. Currently it can only be used with
objects of class "bootstrap"
. Further methods are planned.
Gavin L. Simpson
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.
## 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")