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analogue

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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.

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Install

install.packages('analogue')

Monthly Downloads

1,136

Version

0.17-0

License

GPL-2

Issues

7

Pull Requests

0

Stars

14

Forks

3

Maintainer

Gavin Simpson

Last Published

February 28th, 2016

Functions in analogue (0.17-0)

abernethy

Abernethy Forest Pollen Sequence
Pollen

North American Modern Pollen Database
getK

Extract and set the number of analogues
predict.pcr

Predicted values from a principal components regression
RMSEP

Root mean square error of prediction
Stratiplot

Palaeoecological stratigraphic diagrams
performance

Transfer function model performance statistics
ImbrieKipp

Imbrie and Kipp foraminifera training set
analog

Analogue matching
chooseTaxa

Select taxa (variables) on basis of maximum abundance attained and number of occurrences.
densityplot.residLen

Lattice density plot for residual lengths
evenSample

Number of samples per gradient segments
caterpillarPlot

Caterpillar plot of species' WA optima and tolerance range.
mcarlo

Monte Carlo simulation of dissimilarities
pcr

Prinicpal component regression transfer function models
compare

Compare proxies across two data sets
panel.Loess

Loess smooths to stratigraphic diagrams
plot.mcarlo

Plot Monte Carlo simulated dissimilarity distributions
residLen

Squared residual length diagnostics
predict.logitreg

Posterior probability of analogue-ness for fossil samples
hist.residLen

Histogram plot for residual lengths
bootstrapObject

Bootstrap object description
bootstrap

Bootstrap estimation and errors
n2

Calculate Hill's N2 diversity measure
analogue-package

Analogue and weighted averaging methods for palaeoecology
rankDC

Rank correlation between environmental and species dissimilarities.
plot.sppResponse

Plot species responses along gradients or latent variables
plot.logitreg

Produces plots of analogue logistic regression models
plot.residLen

Plot method for residual lengths
screeplot

Screeplots of model results
cma

Close modern analogues
plot.prcurve

Plot a fitted principal curve in PCA space
analogue-internal

Internal analogue Functions
bootstrap.wa

Bootstrap estimation and errors for WA models
mat

Modern Analogue Technique transfer function models
predict.prcurve

Predict news locations \& fitted values on a principal curve
dissimilarities

Extract dissimilarity coefficients from models
optima

Weighted averaging optima and tolerance ranges
plot.evenSample

Plot distribution of samples along gradient
join

Merge species data sets on common columns (species)
plot.roc

Plot ROC curves and associated diagnostics
prcurve

Fits a principal curve to m-dimensional data
deshrink

Deshrinking techniques for WA transfer functions
summary.cma

Summarise the extraction of close modern analogues
histogram.residLen

Lattice histogram plot for residual lengths
panel.Stratiplot

Panel function for stratigraphic diagrams
predict.wa

Predict from a weighted average model
distance

Flexibly calculate dissimilarity or distance measures
reconPlot

Stratigraphic plots of palaeoenvironmental reconstructions
rlgh

Round Loch of Glenhead Diatoms
logitreg

Logistic regression models for assessing analogues/non-analogues
swappH

SWAP sub-fossil diatom and pH training set
summary.mat

Summarise Modern Analogue Technique models
minDC

Extract minimum dissimilarities
fuse

Fused dissimilarities
fitted.logitreg

Fitted values for the training set from logistic regression models
splitSample

Select samples from along an environmental gradient
bayesF

Bayes factors
gradientDist

Positions of samples along a unit-length ordination gradient.
varExpl

Variance explained by ordination axes
plot.minDC

Plot of minimum dissimilarity per sample
stdError

Standard error of MAT fitted and predicted values
timetrack

Timetracks of change in species composition
summary.predict.mat

Summarise MAT model predictions
plot.mat

Plot diagnostics for a mat object
summary.bootstrap.mat

Summarise bootstrap resampling for MAT models
swapdiat

SWAP sub-fossil diatom and pH training set
plot.dissimilarities

Plots the distribution of extracted dissimilarities
roc

ROC curve analysis
residuals.prcurve

Residuals of a principal curve fit.
wa

Weighted averaging transfer functions
predict.mat

Predict method for Modern Analogue Technique models
smoothers

Smoother plugin function for use in fitting a principal curve
plot.wa

Plot diagnostics for a weighted averaging model
scores.prcurve

scores method for principal curve objects of class "prcurve".
tran

Common data transformations and standardizations
sppResponse

Species responses along gradients.
weightedCor

Weighted correlation test of WA reconstruction
summary.analog

Summarise analogue matching results
crossval

Cross-validation of palaeoecological transfer function models