Analogue and Weighted Averaging Methods for Palaeoecology

Documentation for package ‘analogue’ version 0.18.1

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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