| abernethy | Abernethy Forest Pollen Sequence |
| analog | Analogue matching |
| analogue-internal | Internal analogue Functions |
| analogue-package | Analogue and weighted averaging methods for palaeoecology |
| bayesF | Bayes factors |
| bootstrap | Bootstrap estimation and errors |
| bootstrapObject | Bootstrap object description |
| bootstrap.wa | Bootstrap estimation and errors for WA models |
| caterpillarPlot | Caterpillar plot of species' WA optima and tolerance range. |
| chooseTaxa | Select taxa (variables) on basis of maximum abundance... |
| cma | Close modern analogues |
| compare | Compare proxies across two data sets |
| crossval | Cross-validation of palaeoecological transfer function models |
| densityplot.residLen | Lattice density plot for residual lengths |
| deshrink | Deshrinking techniques for WA transfer functions |
| dissimilarities | Extract dissimilarity coefficients from models |
| distance | Flexibly calculate dissimilarity or distance measures |
| evenlySampled | Number of samples per gradient segments |
| fitted.logitreg | Fitted values for the training set from logistic regression... |
| fuse | Fused dissimilarities |
| getK | Extract and set the number of analogues |
| gradientDist | Positions of samples along a unit-length ordination gradient. |
| histogram.residLen | Lattice histogram plot for residual lengths |
| hist.residLen | Histogram plot for residual lengths |
| ImbrieKipp | Imbrie and Kipp foraminifera training set |
| join | Merge species data sets on common columns (species) |
| logitreg | Logistic regression models for assessing... |
| mat | Modern Analogue Technique transfer function models |
| mcarlo | Monte Carlo simulation of dissimilarities |
| minDC | Extract minimum dissimilarities |
| n2 | Calculate Hill's N2 diversity measure |
| optima | Weighted averaging optima and tolerance ranges |
| panel.Loess | Loess smooths to stratigraphic diagrams |
| panel.Stratiplot | Panel function for stratigraphic diagrams |
| pcr | Prinicpal component regression transfer function models |
| performance | Transfer function model performance statistics |
| 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.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.wa | Plot diagnostics for a weighted averaging model |
| 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 news locations & fitted values on a principal curve |
| predict.wa | Predict from a weighted average model |
| rankDC | Rank correlation between environmental and species... |
| reconPlot | Stratigraphic plots of palaeoenvironmental reconstructions |
| residLen | Squared residual length diagnostics |
| residuals.prcurve | Residuals of a principal curve fit. |
| rlgh | Round Loch of Glenhead Diatoms |
| RMSEP | Root mean square error of prediction |
| roc | ROC curve analysis |
| scores.prcurve | 'scores' method for principal curve objects of class... |
| screeplot | Screeplots of model results |
| smoothFuns | Smoother plugin function for use in fitting a principal curve |
| splitSample | Select samples from along an environmental gradient |
| sppResponse.prcurve | Species responses along gradients. |
| stdError | Standard error of MAT fitted and predicted values |
| Stratiplot | 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.mat | Summarise Modern Analogue Technique models |
| summary.predict.mat | Summarise MAT model predictions |
| swapdiat | SWAP sub-fossil diatom and pH training set |
| swappH | SWAP sub-fossil diatom and pH training set |
| timetrack | Timetracks of change in species composition |
| tortula | Morphological data for ten taxa of the genus Tortula |
| tran | Common data transformations and standardizations |
| varExpl | Variance explained by ordination axes |
| wa | Weighted averaging transfer functions |
| weightedCor | Weighted correlation test of WA reconstruction |
