rioja-package {rioja}

Analysis of Quaternary Science Data

Description

rioja: An R package for the analysis of Quaternary science data. Contains functions for constrained clustering, transfer functions, and plotting stratigraphic data.

Details

The rioja package contains a number of tools for analysing and visualising (bio)stratigraphic data and for developing palaeoecological transfer functions from a dataset of modern species counts and environmental measurements. Resulting models can be cross-validated using the crossval function, which allows internal cross-validation using leave-one-out, leave-n-out, bootstrapping or h-block cross-validation.

Index of help topics:

IK                      Imbrie and Kipp foraminifera data
IKFA                    Imbrie & Kipp Factor Analysis
LWR                     Weighted averaging (LWR) regression and
                        calibration
MAT                     Palaeoenvironmental reconstruction using the
                        Modern Analogue Technique (MAT)
MLRC                    Palaeoenvironmental reconstruction using
                        Maximum Likelihood Response Surfaces
MLRC2                   Palaeoenvironmental reconstruction using
                        Maximum Likelihood Response Surfaces
MR                      Multiple regression
Merge                   Merges two or more data frames on the basis of
                        common column names.
Ponds                   Southeast England ponds and pools diatom and
                        water chemistry dataset.
RLGH                    Diatom stratigraphic data from the Round Loch
                        of Glenhead, Galloway, Southwest Scotland
SWAP                    SWAP surface sediment diatom data and
                        lake-water pH.
WA                      Weighted averaging (WA) regression and
                        calibration
WAPLS                   Weighted averaging partial least squares
                        (WAPLS) regression and calibration
aber                    Abernethy Forest pollen data
chclust                 Constrained hierarchical clustering
compare.datasets        Compare datasets for matching variables
                        (species)
hulls                   Graphic utilities.
inkspot                 Two-way ordered bubble plot of a species by
                        sites data table
interp.dataset          Interpolate a dataset
make.dummy              Utility functions.
performance             Palaeoecological transfer functions
randomPTF               Random transfer functions to calculate variable
                        importance
rioja-package           Analysis of Quaternary Science Data
strat.plot              Plot a stratigraphic diagram

Author(s)

Steve Juggins

Maintainer: Steve Juggins <[e-mail]>