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analogue

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

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Version

Install

install.packages('analogue')

Monthly Downloads

1,129

Version

0.17-7

License

GPL-2

Issues

8

Pull Requests

0

Stars

14

Forks

3

Maintainer

Gavin Simpson

Last Published

September 21st, 2024

Functions in analogue (0.17-7)

ImbrieKipp

Imbrie and Kipp foraminifera training set
analogue-internal

Internal analogue Functions
Pollen

North American Modern Pollen Database
bayesF

Bayes factors
bootstrap

Bootstrap estimation and errors
RMSEP

Root mean square error of prediction
bootstrap.wa

Bootstrap estimation and errors for WA models
analogue-package

Analogue and weighted averaging methods for palaeoecology
deshrink

Deshrinking techniques for WA transfer functions
abernethy

Abernethy Forest Pollen Sequence
Stratiplot

Palaeoecological stratigraphic diagrams
dissimilarities

Extract dissimilarity coefficients from models
fitted.logitreg

Fitted values for the training set from logistic regression models
analog

Analogue matching
distance

Flexibly calculate dissimilarity or distance measures
bootstrapObject

Bootstrap object description
join

Merge species data sets on common columns (species)
cma

Close modern analogues
compare

Compare proxies across two data sets
evenSample

Number of samples per gradient segments
fuse

Fused dissimilarities
plot.evenSample

Plot distribution of samples along gradient
plot.logitreg

Produces plots of analogue logistic regression models
panel.Stratiplot

Panel function for stratigraphic diagrams
pcr

Prinicpal component regression transfer function models
logitreg

Logistic regression models for assessing analogues/non-analogues
optima

Weighted averaging optima and tolerance ranges
plot.minDC

Plot of minimum dissimilarity per sample
plot.prcurve

Plot a fitted principal curve in PCA space
minDC

Extract minimum dissimilarities
predict.prcurve

Predict new locations & fitted values on a principal curve
predict.wa

Predict from a weighted average model
caterpillarPlot

Caterpillar plot of species' WA optima and tolerance range.
panel.Loess

Loess smooths to stratigraphic diagrams
predict.mat

Predict method for Modern Analogue Technique models
rlgh

Round Loch of Glenhead Diatoms
n2

Calculate Hill's N2 diversity measure
plot.residLen

Plot method for residual lengths
chooseTaxa

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

ROC curve analysis
getK

Extract and set the number of analogues
rankDC

Rank correlation between environmental and species dissimilarities.
gradientDist

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

Stratigraphic plots of palaeoenvironmental reconstructions
scores.prcurve

scores method for principal curve objects of class "prcurve".
predict.pcr

Predicted values from a principal components regression
swappH

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

Summarise analogue matching results
crossval

Cross-validation of palaeoecological transfer function models
summary.bootstrap.mat

Summarise bootstrap resampling for MAT models
screeplot

Screeplots of model results
plot.roc

Plot ROC curves and associated diagnostics
densityplot.residLen

Lattice density plot for residual lengths
prcurve

Fits a principal curve to m-dimensional data
predict.logitreg

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

Histogram plot for residual lengths
mat

Modern Analogue Technique transfer function models
histogram.residLen

Lattice histogram plot for residual lengths
summary.predict.mat

Summarise MAT model predictions
performance

Transfer function model performance statistics
mcarlo

Monte Carlo simulation of dissimilarities
plot.dissimilarities

Plots the distribution of extracted dissimilarities
swapdiat

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

Plot diagnostics for a mat object
plot.sppResponse

Plot species responses along gradients or latent variables
timetrack

Timetracks of change in species composition
tortula

Morphological data for ten taxa of the genus Tortula
plot.mcarlo

Plot Monte Carlo simulated dissimilarity distributions
plot.wa

Plot diagnostics for a weighted averaging model
residLen

Squared residual length diagnostics
sppResponse

Species responses along gradients.
stdError

Standard error of MAT fitted and predicted values
tran

Common data transformations and standardizations
residuals.prcurve

Residuals of a principal curve fit.
varExpl

Variance explained by ordination axes
smoothers

Smoother plugin function for use in fitting a principal curve
splitSample

Select samples from along an environmental gradient
wa

Weighted averaging transfer functions
summary.cma

Summarise the extraction of close modern analogues
summary.mat

Summarise Modern Analogue Technique models
weightedCor

Weighted correlation test of WA reconstruction