Analogue and Weighted Averaging Methods for Palaeoecology

Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.


Released version

CRAN version

Build status

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What is analogue?

analogue is an R package for use with palaeoecological data. Originally, analogue was intended as an R implementation of analogue methods such as analogue matching, ROC curves, and MAT transfer function models, and the computation of dissimilarity coefficients. Since then the scope of the package has grown to include a number of other methods applicable to data routinely encountered in palaeoecology and palaeolimnology.

Features

  • Transfer functions
    • MAT
    • Weighted Averaging with monotonic, inverse, and classical deshrinking, with and without tolerance down-weighting
    • Principal Component Regression (using ecologically-relevant transformations)
    • Cross-validation (Bootstrapping, leave-one-out, k-fold)
    • Analogue statistics
  • Analogue matching
  • Dissimilarity coefficients
    • Chord, Bray-Curtis, Gower's Generalised coefficient, Manhattan, ...
  • Dissimilarity decisions thresholds
    • ROC curves
    • Monte Carlo resampling
    • Logistic regression
  • Stratigraphic diagrams
  • Principal curves

Bugs, feature requests

Bug reports and feature requests should be filed as issues.

Licence

analogue is released under the GNU General Public Licence Version 2.

Links

News

analogue News

Version 1.17-1

  • prcurve modified to use package princurve version >= 2.0.2.

  • join() had a serious bug that caused the columns to be labelled incorrectly when a type = "left"join was used, if the columns weren't in the same order in the data frames to be merged. Issue #16

  • Stratiplot() gained argument labelValues, which allows for custom labelling of variables in a plot. A vector of expressions can be supplied for fancy labelling such as that required for isotopes, equations, sub/superscripts, greek characters, etc.

  • The Climate data set had incorrectly-named columns and was missing some variables. The NAMPD is now updated to version 1.7-3 and the name and missing data issues have been fixed. Reported by Simon Goring in Issue #17.

Version 1.17-0

  • Stratiplot() now draws a plot on the current device and returns a "trellis" object invisibly. This fixes #13 and prevents a blank page being drawn in devices such as pdf().

  • Stratiplot() now handles a matrix as argument x via an S3 method for class "matrix".

  • tran() add a "none" transformation which just returns its input. This is useful if you are writing code and comparing transformations and need to temporarily turn them off.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("analogue")

0.17-1 by Gavin L. Simpson, 6 months ago


https://github.com/gavinsimpson/analogue


Report a bug at https://github.com/gavinsimpson/analogue/issues


Browse source code at https://github.com/cran/analogue


Authors: Gavin L. Simpson [aut, cre] , Jari Oksanen [aut]


Documentation:   PDF Manual  


Task views: Analysis of Ecological and Environmental Data


GPL-2 license


Imports mgcv, MASS, stats, graphics, grid, brglm, princurve, lattice

Depends on vegan

Suggests testthat


Imported by IntClust, neotoma.

Depended on by analogueExtra.


See at CRAN