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"), ...) ## S3 method for class 'bootstrap.wa': 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.
mat
, bootstrap
, wa
,
bootstrap.wa
.
## 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")