# Analogue and Weighted Averaging Methods for Palaeoecology

## Documentation for package ‘analogue’ version 0.18.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J L M N O P R S T V W

analogue-package | Analogue and weighted averaging methods for palaeoecology

## -- A --

abernethy | Abernethy Forest Pollen Sequence
analog | Analogue matching
analog.default | Analogue matching
analog.distance | Analogue matching
analogue | Analogue and weighted averaging methods for palaeoecology
as.data.frame.optima | Weighted averaging optima and tolerance ranges
as.data.frame.tolerance | Weighted averaging optima and tolerance ranges

## -- B --

bayesF | Bayes factors
Biome | North American Modern Pollen Database
bootstrap | Bootstrap estimation and errors
bootstrap.default | Bootstrap estimation and errors
bootstrap.mat | Bootstrap estimation and errors
bootstrap.wa | Bootstrap estimation and errors for WA models
bootstrapObject | Bootstrap object description

## -- C --

caterpillar | Caterpillar plot of species' WA optima and tolerance range.
caterpillarPlot | Caterpillar plot of species' WA optima and tolerance range.
caterpillarPlot.data.frame | Caterpillar plot of species' WA optima and tolerance range.
caterpillarPlot.default | Caterpillar plot of species' WA optima and tolerance range.
caterpillarPlot.wa | Caterpillar plot of species' WA optima and tolerance range.
ChiSquare | Prinicpal component regression transfer function models
chooseTaxa | Select taxa (variables) on basis of maximum abundance attained and number of occurrences.
chooseTaxa.default | Select taxa (variables) on basis of maximum abundance attained and number of occurrences.
Climate | North American Modern Pollen Database
cma | Close modern analogues
cma.analog | Close modern analogues
cma.default | Close modern analogues
cma.mat | Close modern analogues
cma.predict.mat | Close modern analogues
coef.pcr | Prinicpal component regression transfer function models
coef.wa | Weighted averaging transfer functions
compare | Compare proxies across two data sets
compare.default | Compare proxies across two data sets
crossval | Cross-validation of palaeoecological transfer function models
crossval.pcr | Cross-validation of palaeoecological transfer function models
crossval.wa | Cross-validation of palaeoecological transfer function models

## -- D --

densityplot | Lattice density plot for residual lengths
densityplot.residLen | Lattice density plot for residual lengths
deshrink | Deshrinking techniques for WA transfer functions
deshrinkPred | Deshrinking techniques for WA transfer functions
dissim | Extract dissimilarity coefficients from models
dissimilarities | Extract dissimilarity coefficients from models
dissimilarities.analog | Extract dissimilarity coefficients from models
dissimilarities.mat | Extract dissimilarity coefficients from models
distance | Flexibly calculate dissimilarity or distance measures
distance.default | Flexibly calculate dissimilarity or distance measures
distance.join | Flexibly calculate dissimilarity or distance measures
dotplot | Rank correlation between environmental and species dissimilarities.
dotplot.rankDC | Rank correlation between environmental and species dissimilarities.

## -- E --

eigenvals.pcr | Prinicpal component regression transfer function models
evenSample | Number of samples per gradient segments

## -- F --

fitted.bootstrap.mat | Bootstrap estimation and errors
fitted.logitreg | Fitted values for the training set from logistic regression models
fitted.mat | Modern Analogue Technique transfer function models
fitted.pcr | Prinicpal component regression transfer function models
fitted.prcurve | Predict new locations & fitted values on a principal curve
fitted.timetrack | Timetracks of change in species composition
fitted.wa | Weighted averaging transfer functions
fittedY | Squared residual length diagnostics
fuse | Fused dissimilarities
fuse.dist | Fused dissimilarities
fuse.matrix | Fused dissimilarities

## -- G --

getK | Extract and set the number of analogues
getK.bootstrap.mat | Extract and set the number of analogues
getK.default | Extract and set the number of analogues
getK.mat | Extract and set the number of analogues
getK.predict.mat | Extract and set the number of analogues
gradientDist | Positions of samples along a unit-length ordination gradient.
gradientDist.cca | Positions of samples along a unit-length ordination gradient.
gradientDist.default | Positions of samples along a unit-length ordination gradient.
gradientDist.prcurve | Positions of samples along a unit-length ordination gradient.

## -- H --

head.join | Merge species data sets on common columns (species)
Hellinger | Prinicpal component regression transfer function models
hist.residLen | Histogram plot for residual lengths
histogram | Lattice histogram plot for residual lengths
histogram.residLen | Lattice histogram plot for residual lengths

## -- I --

ImbrieKipp | Imbrie and Kipp foraminifera training set
initCurve | Fits a principal curve to m-dimensional data

## -- J --

join | Merge species data sets on common columns (species)

## -- L --

lines.prcurve | Plot a fitted principal curve in PCA space
Location | North American Modern Pollen Database
logitreg | Logistic regression models for assessing analogues/non-analogues
logitreg.analog | Logistic regression models for assessing analogues/non-analogues
logitreg.default | Logistic regression models for assessing analogues/non-analogues

## -- M --

mat | Modern Analogue Technique transfer function models
mat.default | Modern Analogue Technique transfer function models
mat.formula | Modern Analogue Technique transfer function models
mcarlo | Monte Carlo simulation of dissimilarities
mcarlo.analog | Monte Carlo simulation of dissimilarities
mcarlo.default | Monte Carlo simulation of dissimilarities
mcarlo.mat | Monte Carlo simulation of dissimilarities
minDC | Extract minimum dissimilarities
minDC.analog | Extract minimum dissimilarities
minDC.default | Extract minimum dissimilarities
minDC.predict.mat | Extract minimum dissimilarities
minDC.wa | Extract minimum dissimilarities

## -- N --

n2 | Calculate Hill's N2 diversity measure
n2.default | Calculate Hill's N2 diversity measure

## -- O --

oldDistance | Flexibly calculate dissimilarity or distance measures
oldDistance.default | Flexibly calculate dissimilarity or distance measures
oldDistance.join | Flexibly calculate dissimilarity or distance measures
optima | Weighted averaging optima and tolerance ranges
optima.default | Weighted averaging optima and tolerance ranges

## -- P --

panel.Loess | Loess smooths to stratigraphic diagrams
panel.Stratiplot | Panel function for stratigraphic diagrams
pcr | Prinicpal component regression transfer function models
pcr.default | Prinicpal component regression transfer function models
pcr.formula | Prinicpal component regression transfer function models
performance | Transfer function model performance statistics
performance.bootstrap.wa | Transfer function model performance statistics
performance.crossval | Transfer function model performance statistics
performance.pcr | Prinicpal component regression transfer function models
performance.predict.wa | Transfer function model performance statistics
performance.wa | Transfer function model performance statistics
plot.bayesF | Bayes factors
plot.cma | Close modern analogues
plot.dissimilarities | Plots the distribution of extracted dissimilarities
plot.evenSample | Plot distribution of samples along gradient
plot.logitreg | Produces plots of analogue logistic regression models
plot.mat | Plot diagnostics for a mat object
plot.mcarlo | Plot Monte Carlo simulated dissimilarity distributions
plot.minDC | Plot of minimum dissimilarity per sample
plot.prcurve | Plot a fitted principal curve in PCA space
plot.rankDC | Rank correlation between environmental and species dissimilarities.
plot.residLen | Plot method for residual lengths
plot.roc | Plot ROC curves and associated diagnostics
plot.sppResponse | Plot species responses along gradients or latent variables
plot.timetrack | Timetracks of change in species composition
plot.wa | Plot diagnostics for a weighted averaging model
plot.weightedCor | Weighted correlation test of WA reconstruction
points.timetrack | Timetracks of change in species composition
Pollen | North American Modern Pollen Database
prcurve | Fits a principal curve to m-dimensional data
predict.logitreg | Posterior probability of analogue-ness for fossil samples
predict.mat | Predict method for Modern Analogue Technique models
predict.pcr | Predicted values from a principal components regression
predict.prcurve | Predict new locations & fitted values on a principal curve
predict.timetrack | Timetracks of change in species composition
predict.wa | Predict from a weighted average model
print.analog | Analogue matching
print.bayesF | Bayes factors
print.bootstrap.mat | Bootstrap estimation and errors
print.bootstrap.wa | Bootstrap estimation and errors for WA models
print.cma | Close modern analogues
print.crossval | Cross-validation of palaeoecological transfer function models
print.fitted.bootstrap.mat | Bootstrap estimation and errors
print.fitted.mat | Modern Analogue Technique transfer function models
print.logitreg | Logistic regression models for assessing analogues/non-analogues
print.mat | Modern Analogue Technique transfer function models
print.mcarlo | Monte Carlo simulation of dissimilarities
print.minDC | Extract minimum dissimilarities
print.optima | Weighted averaging optima and tolerance ranges
print.pcr | Prinicpal component regression transfer function models
print.performance | Transfer function model performance statistics
print.prcurve | Fits a principal curve to m-dimensional data
print.predict.mat | Predict method for Modern Analogue Technique models
print.predict.wa | Predict from a weighted average model
print.rankDC | Rank correlation between environmental and species dissimilarities.
print.residLen | Squared residual length diagnostics
print.residuals.bootstrap.mat | Bootstrap estimation and errors
print.residuals.mat | Modern Analogue Technique transfer function models
print.roc | ROC curve analysis
print.summary.analog | Summarise analogue matching results
print.summary.bootstrap.mat | Summarise bootstrap resampling for MAT models
print.summary.cma | Summarise the extraction of close modern analogues
print.summary.logitreg | Logistic regression models for assessing analogues/non-analogues
print.summary.mat | Summarise Modern Analogue Technique models
print.summary.predict.mat | Summarise MAT model predictions
print.summary.roc | ROC curve analysis
print.timetrack | Timetracks of change in species composition
print.tolerance | Weighted averaging optima and tolerance ranges
print.wa | Weighted averaging transfer functions
print.weightedCor | Weighted correlation test of WA reconstruction

## -- R --

rankDC | Rank correlation between environmental and species dissimilarities.
reconPlot | Stratigraphic plots of palaeoenvironmental reconstructions
reconPlot.default | Stratigraphic plots of palaeoenvironmental reconstructions
reconPlot.predict.mat | Stratigraphic plots of palaeoenvironmental reconstructions
reconPlot.predict.wa | Stratigraphic plots of palaeoenvironmental reconstructions
resid.bootstrap.mat | Bootstrap estimation and errors
resid.mat | Modern Analogue Technique transfer function models
resid.prcurve | Residuals of a principal curve fit.
residLen | Squared residual length diagnostics
residuals.bootstrap.mat | Bootstrap estimation and errors
residuals.mat | Modern Analogue Technique transfer function models
residuals.pcr | Prinicpal component regression transfer function models
residuals.prcurve | Residuals of a principal curve fit.
residuals.wa | Weighted averaging transfer functions
rlgh | Round Loch of Glenhead Diatoms
RMSEP | Root mean square error of prediction
RMSEP.bootstrap.mat | Root mean square error of prediction
RMSEP.bootstrap.wa | Root mean square error of prediction
RMSEP.default | Root mean square error of prediction
RMSEP.mat | Root mean square error of prediction
roc | ROC curve analysis
roc.analog | ROC curve analysis
roc.default | ROC curve analysis
roc.mat | ROC curve analysis

## -- S --

Salinity | Imbrie and Kipp foraminifera training set
scores.prcurve | 'scores' method for principal curve objects of class '"prcurve"'.
scores.timetrack | Timetracks of change in species composition
screeplot.bootstrap.mat | Screeplots of model results
screeplot.mat | Screeplots of model results
screeplot.pcr | Prinicpal component regression transfer function models
setK<- | Extract and set the number of analogues
setK<-.default | Extract and set the number of analogues
setK<-.mat | Extract and set the number of analogues
smoothGAM | Smoother plugin function for use in fitting a principal curve
smoothSpline | Smoother plugin function for use in fitting a principal curve
splitSample | Select samples from along an environmental gradient
sppResponse | Species responses along gradients.
sppResponse.prcurve | Species responses along gradients.
sqrlLinear | Squared residual length diagnostics
sqrlUnimodal | Squared residual length diagnostics
stdError | Standard error of MAT fitted and predicted values
stdError.mat | Standard error of MAT fitted and predicted values
stdError.predict.mat | Standard error of MAT fitted and predicted values
Stratiplot | Palaeoecological stratigraphic diagrams
Stratiplot.default | Palaeoecological stratigraphic diagrams
Stratiplot.formula | Palaeoecological stratigraphic diagrams
Stratiplot.matrix | Palaeoecological stratigraphic diagrams
summary.analog | Summarise analogue matching results
summary.bootstrap.mat | Summarise bootstrap resampling for MAT models
summary.cma | Summarise the extraction of close modern analogues
summary.logitreg | Logistic regression models for assessing analogues/non-analogues
summary.mat | Summarise Modern Analogue Technique models
summary.predict.mat | Summarise MAT model predictions
summary.roc | ROC curve analysis
SumSST | Imbrie and Kipp foraminifera training set
swapdiat | SWAP sub-fossil diatom and pH training set
swappH | SWAP sub-fossil diatom and pH training set

## -- T --

tail.join | Merge species data sets on common columns (species)
timetrack | Timetracks of change in species composition
tolerance.default | Weighted averaging optima and tolerance ranges
tortula | Morphological data for ten taxa of the genus Tortula
tran | Common data transformations and standardizations
tran.default | Common data transformations and standardizations
tran.formula | Common data transformations and standardizations

## -- V --

V12.122 | Imbrie and Kipp foraminifera training set
varExpl | Variance explained by ordination axes
varExpl.cca | Variance explained by ordination axes
varExpl.default | Variance explained by ordination axes
varExpl.prcurve | Variance explained by ordination axes

## -- W --

wa | Weighted averaging transfer functions
wa.default | Weighted averaging transfer functions
wa.formula | Weighted averaging transfer functions
waFit | Weighted averaging transfer functions
weightedCor | Weighted correlation test of WA reconstruction
weightedCor.default | Weighted correlation test of WA reconstruction
WinSST | Imbrie and Kipp foraminifera training set