| RMSEP {analogue} | R Documentation |
Calculates or extracts the RMSEP from transfer function models.
RMSEP(object, ...)
## S3 method for class 'mat':
RMSEP(object, k, weighted = FALSE,
...)
## S3 method for class 'bootstrap.mat':
RMSEP(object, type = c("birks1990", "standard"),
...)
object |
An R object. |
k |
numeric; the number of analogues to use in calculating the
RMSEP. May be missing. If missing, k is extracted from the
model using getK. |
weighted |
logical; Return the RMSEP for the weighted or unweighted model? The default is for an unweighted model. |
type |
The type of RMSEP to return/calculate. See Details, below. |
... |
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 deviation 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.
The RMSEP for objects of class "mat" is a leave-one-out
cross-validated RMSEP, and is calculated as for type =
"standard".
A numeric vector of length 1 that is the RMSEP of object.
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") ## Leave-one-out RMSEP for the MAT model RMSEP(swap.mat) ## 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")