analogue-package: Analogue and weighted averaging methods for palaeoecology
In analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Description Analogue methods Transfer function methods Utilities Documentation Author(s) References

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_methods: Analogue 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.

analogue documentation built on June 21, 2021, 1:08 a.m.