MLRC: Palaeoenvironmental reconstruction using Maximum Likelihood...

In rioja: Analysis of Quaternary Science Data

Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces

Description

Functions for reconstructing (predicting) environmental values from biological assemblages using Maximum Likelihood response Surfaces.

Usage

MLRC(y, x, check.data=TRUE, lean=FALSE, n.cut=5, verbose=TRUE, ...)

MLRC.fit(y, x, n.cut=2, use.glm=FALSE, max.iter=50, lean=FALSE, verbose=FALSE, ...)

## S3 method for class 'MLRC'
 predict(object, newdata=NULL, sse=FALSE, nboot=100,
      match.data=TRUE, verbose=TRUE, ...)

## S3 method for class 'MLRC'
crossval(object, cv.method="loo", verbose=TRUE, ngroups=10,
      nboot=100, h.cutoff=0, h.dist=NULL, ...)

## S3 method for class 'MLRC'
performance(object, ...)

## S3 method for class 'MLRC'
print(x, ...)

## S3 method for class 'MLRC'
summary(object, full=FALSE, ...)

## S3 method for class 'MLRC'
plot(x, resid=FALSE, xval=FALSE, xlab="", ylab="", 
      ylim=NULL, xlim=NULL, add.ref=TRUE, add.smooth=FALSE, ...)

## S3 method for class 'MLRC'
residuals(object, cv=FALSE, ...)

## S3 method for class 'MLRC'
coef(object, ...)

## S3 method for class 'MLRC'
fitted(object, ...)

Arguments

y	a data frame or matrix of biological abundance data.
x, object	a vector of environmental values to be modelled or an object of class wa.
n.cut	cutoff value for number of occurrences. Species with fewer than n.cut occurrences will be excluded from the analysis.
use.glm	logical to use glm to fit responses rather than internal code. Defaults to FALSE.
newdata	new biological data to be predicted.
max.iter	maximum iterations of the logit regression algorithm.
check.data	logical to perform simple checks on the input data.
match.data	logical indicate the function will match two species datasets by their column names. You should only set this to FALSE if you are sure the column names match exactly.
lean	logical to exclude some output from the resulting models (used when cross-validating to speed calculations).
full	logical to show head and tail of output in summaries.
resid	logical to plot residuals instead of fitted values.
xval	logical to plot cross-validation estimates.
xlab, ylab, xlim, ylim	additional graphical arguments to plot.wa.
add.ref	add 1:1 line on plot.
add.smooth	add loess smooth to plot.
cv.method	cross-validation method, either "loo", "lgo", "bootstrap" or "h-block".
verbose	logical to show feedback during cross-validation.
nboot	number of bootstrap samples.
ngroups	number of groups in leave-group-out cross-validation, or a vector contain leave-out group menbership.
h.cutoff	cutoff for h-block cross-validation. Only training samples greater than h.cutoff from each test sample will be used.
h.dist	distance matrix for use in h-block cross-validation. Usually a matrix of geographical distances between samples.
sse	logical indicating that sample specific errors should be calculated.
cv	logical to indicate model or cross-validation residuals.
...	additional arguments.

Details

Function MLRC Maximim likelihood reconstruction using response curves.

Function predict predicts values of the environemntal variable for newdata or returns the fitted (predicted) values from the original modern dataset if newdata is NULL. Variables are matched between training and newdata by column name (if match.data is TRUE). Use compare.datasets to assess conformity of two species datasets and identify possible no-analogue samples.

MLRC has methods fitted and rediduals that return the fitted values (estimates) and residuals for the training set, performance, which returns summary performance statistics (see below), coef which returns the species coefficients, and print and summary to summarise the output. MLRC also has a plot method that produces scatter plots of predicted vs observed measurements for the training set.

Value

Function MLRC returns an object of class MLRC with the following named elements:

Function crossval also returns an object of class MLRC and adds the following named elements:

predicted	predicted values of each training set sample under cross-validation.
residuals.cv	prediction residuals.

If function predict is called with newdata=NULL it returns the fitted values of the original model, otherwise it returns a list with the following named elements:

fit	predicted values for newdata.

If sample specific errors were requested the list will also include:

fit.boot	mean of the bootstrap estimates of newdata.
v1	standard error of the bootstrap estimates for each new sample.
v2	root mean squared error for the training set samples, across all bootstram samples.
SEP	standard error of prediction, calculated as the square root of v1^2 + v2^2.

Function performance returns a matrix of performance statistics for the MLRC model. See performance, for a description of the summary.

Author(s)

Steve Juggins

References

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

Juggins, S. (1992) Diatoms in the Thames Estuary, England: Ecology, Palaeoecology, and Salinity Transfer Function. Bibliotheca Diatomologica, Band 25, 216pp.

Oksanen, J., Laara, E., Huttunen, P., & Merilainen, J. (1990) Maximum likelihood prediction of lake acidity based on sedimented diatoms. Journal of Vegetation Science, 1, 49-56.

ter Braak, C.J.F. & van Dam, H. (1989) Inferring pH from diatoms: a comparison of old and new calibration methods. Hydrobiologia, 178, 209-223.

See Also

WA, MAT, performance, and compare.datasets for diagnostics.

Examples

data(IK)
spec <- IK$spec / 100
SumSST <- IK$env$SumSST
core <- IK$core / 100

fit <- MLRC(spec, SumSST)
fit

#predict the core
pred <- predict(fit, core)

#plot predictions - depths are in rownames
depth <- as.numeric(rownames(core))
plot(depth, pred$fit[, 1], type="b")

## Not run: 
# this is slow!
# cross-validate model
fit.cv <- crossval(fit, cv.method="loo", verbose=5)

# predictions with sample specific errors
pred <- predict(fit, core, sse=TRUE, nboot=1000, verbose=5)

## End(Not run)

rioja documentation built on Sept. 26, 2024, 5:07 p.m.