Analogue Methods in Palaeoecology: Using the analogue Package

Palaeoecology is an important branch of ecology that uses the subfossil remains of organisms preserved in lake, ocean and bog sediments to inform on changes in ecosystems and the environment through time. The analogue package contains functions to perform modern analogue technique (MAT) transfer functions, which can be used to predict past changes in the environment, such as climate or lake-water pH from species data. A related technique is that of analogue matching, which is concerned with identifying modern sites that are floristically and faunistically similar to fossil samples. These techniques, and others, are increasingly being used to inform public policy on environmental pollution and conservation practices. These methods and other functionality in analogue are illustrated using the Surface Waters Acidification Project diatom:pH training set and diatom counts on samples of a sediment core from the Round Loch of Glenhead, Galloway, Scotland. The paper is aimed at palaeoecologists who are familiar with the techniques described but not with R.

• Publication year

  2007

• Venue

  Journal of Statistical Software

• Publication date

  2007-09-30

• Fields of study

  Computer Science, Environmental Science

• Identifiers
  DOI 10.18637/JSS.V022.I02
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Receiver operating characteristics curves and related decision measures: A tutorial

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  2005influential reference
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  2004influential reference
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  2004influential reference
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  2003influential reference
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  2000cited by this paper
• Matching diatom assemblages in lake sediment cores and modern surface sediment samples: the implications for lake conservation and restoration with special reference to acidified systems

  1997cited by this paper
• Bagging Predictors

  1996cited by this paper
• Non-linear methods for multivariate statistical calibration and their use in palaeoecology: a comparison of inverse (k-nearest neighbours, partial least squares and weighted averaging partial least squares) and classical approaches

  1995influential reference
• Applied Nonparametric Regression

  1994cited by this paper
• Assessing Test Accuracy and its Clinical Consequences: A Primer for Receiver Operating Characteristic Curve Analysis

  1993influential reference
• Assessing test accuracy and its clinical consequences: a primer for receiver operating characteristic curve analysis.

  1993cited by this paper
• The Surface Waters Acidification Project Palaeolimnology Programme: Modern Diatom / Lake-Water Chemistry Data-Set

  1991cited by this paper
• Diatoms and pH Reconstruction

  1990influential reference
• Monographs on statistics and applied probability

  1990cited by this paper
• ADAPTIVE CONTROL PROCESSES

  1990cited by this paper
• Acidification of lakes in Galloway, south west Scotland: a diatom and pollen study of the post-glacial history of the Round Loch of Glenhead

  1989cited by this paper
• Modern Analogues of Late-Quaternary Pollen Spectra from the Western Interior of North America

  1989cited by this paper
• Compositional dissimilarity as a robust measure of ecological distance

  1987influential reference
• Quantitative Interpretation of Fossil Pollen Spectra: Dissimilarity Coefficients and the Method of Modern Analogs

  1985influential reference
• Chapman and Hall

  1985cited by this paper
• Multidimensional scaling as a research tool in quaternary palynology: A review of theory and methods

  1980cited by this paper
• V. Adaptive Control Processes

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