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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.

Links

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Install

install.packages('analogue')

Monthly Downloads

1,136

Version

0.17-3

License

GPL-2

Issues

7

Pull Requests

0

Stars

14

Forks

3

Maintainer

Gavin Simpson

Last Published

May 11th, 2019

Functions in analogue (0.17-3)

RMSEP

Root mean square error of prediction
optima

Weighted averaging optima and tolerance ranges
bootstrap

Bootstrap estimation and errors
deshrink

Deshrinking techniques for WA transfer functions
bayesF

Bayes factors
dissimilarities

Extract dissimilarity coefficients from models
hist.residLen

Histogram plot for residual lengths
panel.Loess

Loess smooths to stratigraphic diagrams
plot.evenSample

Plot distribution of samples along gradient
histogram.residLen

Lattice histogram plot for residual lengths
plot.logitreg

Produces plots of analogue logistic regression models
minDC

Extract minimum dissimilarities
rankDC

Rank correlation between environmental and species dissimilarities.
n2

Calculate Hill's N2 diversity measure
bootstrap.wa

Bootstrap estimation and errors for WA models
reconPlot

Stratigraphic plots of palaeoenvironmental reconstructions
scores.prcurve

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

Screeplots of model results
plot.residLen

Plot method for residual lengths
wa

Weighted averaging transfer functions
bootstrapObject

Bootstrap object description
distance

Flexibly calculate dissimilarity or distance measures
evenSample

Number of samples per gradient segments
performance

Transfer function model performance statistics
weightedCor

Weighted correlation test of WA reconstruction
plot.dissimilarities

Plots the distribution of extracted dissimilarities
abernethy

Abernethy Forest Pollen Sequence
predict.mat

Predict method for Modern Analogue Technique models
predict.pcr

Predicted values from a principal components regression
analog

Analogue matching
caterpillarPlot

Caterpillar plot of species' WA optima and tolerance range.
summary.analog

Summarise analogue matching results
ImbrieKipp

Imbrie and Kipp foraminifera training set
summary.bootstrap.mat

Summarise bootstrap resampling for MAT models
summary.predict.mat

Summarise MAT model predictions
swapdiat

SWAP sub-fossil diatom and pH training set
chooseTaxa

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

North American Modern Pollen Database
plot.roc

Plot ROC curves and associated diagnostics
residLen

Squared residual length diagnostics
residuals.prcurve

Residuals of a principal curve fit.
fitted.logitreg

Fitted values for the training set from logistic regression models
cma

Close modern analogues
rlgh

Round Loch of Glenhead Diatoms
compare

Compare proxies across two data sets
analogue-package

Analogue and weighted averaging methods for palaeoecology
analogue-internal

Internal analogue Functions
getK

Extract and set the number of analogues
gradientDist

Positions of samples along a unit-length ordination gradient.
plot.minDC

Plot of minimum dissimilarity per sample
roc

ROC curve analysis
crossval

Cross-validation of palaeoecological transfer function models
fuse

Fused dissimilarities
densityplot.residLen

Lattice density plot for residual lengths
plot.prcurve

Plot a fitted principal curve in PCA space
predict.prcurve

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

Predict from a weighted average model
panel.Stratiplot

Panel function for stratigraphic diagrams
swappH

SWAP sub-fossil diatom and pH training set
timetrack

Timetracks of change in species composition
join

Merge species data sets on common columns (species)
smoothers

Smoother plugin function for use in fitting a principal curve
pcr

Prinicpal component regression transfer function models
logitreg

Logistic regression models for assessing analogues/non-analogues
mat

Modern Analogue Technique transfer function models
splitSample

Select samples from along an environmental gradient
mcarlo

Monte Carlo simulation of dissimilarities
plot.mat

Plot diagnostics for a mat object
tran

Common data transformations and standardizations
plot.mcarlo

Plot Monte Carlo simulated dissimilarity distributions
varExpl

Variance explained by ordination axes
prcurve

Fits a principal curve to m-dimensional data
sppResponse

Species responses along gradients.
predict.logitreg

Posterior probability of analogue-ness for fossil samples
plot.sppResponse

Plot species responses along gradients or latent variables
stdError

Standard error of MAT fitted and predicted values
plot.wa

Plot diagnostics for a weighted averaging model
summary.cma

Summarise the extraction of close modern analogues
summary.mat

Summarise Modern Analogue Technique models
Stratiplot

Palaeoecological stratigraphic diagrams