analogue is a package for quantitative palaeoecology with a focus on analogue methods, transfer functions, and data handling and display.
analogue provides functions for analogue matching and the modern
analogue technique (MAT) via analog and
mat. A wide range of dissimilarity coefficients are
available via the distance function.
Additional analysis of modern and no-analogue problems is facilitated
via a range of functions implementing many methods from the
literature. In particular, the receiver operating characteric (ROC)
curves method of Gavin et al (2003) is available in roc
and a related method employing direct logistic regression modelling
(Simpson & Birks, 2012) is available in logitreg.
Several approaches to fitting transfer function models are provided by analogue:
wa: Simple and tolerance-downweighted weighted averaging with classical, inverse, and monotonic spline deshrinking.
mat: The modern analogue technique (MAT).
pcr: Principal components regression with ecologically meaningful transformations
A range of functions for working with and exploring training sets and palaeoenvironmental reconstructions is also included in analogue. These include
crossval leave-one-out, repeated k-fold, and bootstrap cross-validation methods.
compare compare properties of taxa or other proxies across modern and fossil data sets.
evenSample are training set samples evenly distributed along the gradient of interest?
splitSample splits a gradient into a set of bins or chunks and samples evenly from within each chunk to create a representative test set for cross-validation.
timetrack overlays a fossil or secondary data set on to an (constrained) ordination of a modern or reference data set.
weightedCor implements the weighted correlation test of a Weighted Averaging reconstruction as proposed by Telford & Birks (2011).
analogue provides a range of utilities for working with palaeo data.
tran a range of transformations applicable to or commonly used with palaeo data.
Stratiplot draws stratigraphic diagrams using the Lattice package.
join merging of modern/training set and fossil data sets.
chooseTaxa selects taxa that meet certain abundance and occurrence criteria.
A full tutorial and worked example for the main features of analogue matching and MAT is avilable in the vignette
analogue_methodsAnalogue Methods in Palaeoecology
Gavin L. Simpson, Jari Oksanen
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Gavin, D.G., Oswald, W.W., Wahl, E.R. and Williams, J.W. (2003) A statistical approach to evaluating distance metrics and analog assignments for pollen records. Quaternary Research 60, 356--367.
Simpson, G.L. & Birks H.J.B. (2012) Statistical Learning in Palaeolimnology. In Birks, H.J.B, Lotter, A.F. Juggins S., and Smol, J.P. (Eds) Tracking Environmental Change Using Lake Sediments, Volume 5: Data Handling and Numerical Techniques. Springer, Dordrecht.
Telford R.J. and Birks, H.J.B. (2011) A novel method for assessing the statistical significance of quantitative reconstructions inferred from biotic assemblages. Quanternary Science Reviews 30:1272-1278.