| Analogue and weighted averaging methods for palaeoecology | analogue-package analogue |
| Abernethy Forest Pollen Sequence | abernethy |
| Analogue matching | analog analog.default analog.distance print.analog |
| Bayes factors | bayesF plot.bayesF print.bayesF |
| Bootstrap estimation and errors | bootstrap bootstrap.default bootstrap.mat fitted.bootstrap.mat print.bootstrap.mat print.fitted.bootstrap.mat print.residuals.bootstrap.mat resid.bootstrap.mat residuals.bootstrap.mat |
| Bootstrap estimation and errors for WA models | bootstrap.wa print.bootstrap.wa |
| Bootstrap object description | bootstrapObject |
| Caterpillar plot of species' WA optima and tolerance range. | caterpillar caterpillarPlot caterpillarPlot.data.frame caterpillarPlot.default caterpillarPlot.wa |
| Select taxa (variables) on basis of maximum abundance attained and number of occurrences. | chooseTaxa chooseTaxa.default |
| Close modern analogues | cma cma.analog cma.default cma.mat cma.predict.mat plot.cma print.cma |
| Compare proxies across two data sets | compare compare.default |
| Cross-validation of palaeoecological transfer function models | crossval crossval.pcr crossval.wa print.crossval |
| Lattice density plot for residual lengths | densityplot densityplot.residLen |
| Deshrinking techniques for WA transfer functions | deshrink deshrinkPred |
| Extract dissimilarity coefficients from models | dissim dissimilarities dissimilarities.analog dissimilarities.mat |
| Flexibly calculate dissimilarity or distance measures | distance distance.default distance.join oldDistance oldDistance.default oldDistance.join |
| Number of samples per gradient segments | evenSample |
| Fitted values for the training set from logistic regression models | fitted.logitreg |
| Fused dissimilarities | fuse fuse.dist fuse.matrix |
| Extract and set the number of analogues | getK getK.bootstrap.mat getK.default getK.mat getK.predict.mat setK<- setK<-.default setK<-.mat |
| Positions of samples along a unit-length ordination gradient. | gradientDist gradientDist.cca gradientDist.default gradientDist.prcurve |
| Histogram plot for residual lengths | hist.residLen |
| Lattice histogram plot for residual lengths | histogram histogram.residLen |
| Imbrie and Kipp foraminifera training set | ImbrieKipp Salinity SumSST V12.122 WinSST |
| Merge species data sets on common columns (species) | head.join join tail.join |
| Logistic regression models for assessing analogues/non-analogues | logitreg logitreg.analog logitreg.default print.logitreg print.summary.logitreg summary.logitreg |
| Modern Analogue Technique transfer function models | fitted.mat mat mat.default mat.formula print.fitted.mat print.mat print.residuals.mat resid.mat residuals.mat |
| Monte Carlo simulation of dissimilarities | mcarlo mcarlo.analog mcarlo.default mcarlo.mat print.mcarlo |
| Extract minimum dissimilarities | minDC minDC.analog minDC.default minDC.predict.mat minDC.wa print.minDC |
| Calculate Hill's N2 diversity measure | n2 n2.default |
| Weighted averaging optima and tolerance ranges | as.data.frame.optima as.data.frame.tolerance optima optima.default print.optima print.tolerance tolerance.default |
| Loess smooths to stratigraphic diagrams | panel.Loess |
| Panel function for stratigraphic diagrams | panel.Stratiplot |
| Prinicpal component regression transfer function models | ChiSquare coef.pcr eigenvals.pcr fitted.pcr Hellinger pcr pcr.default pcr.formula performance.pcr print.pcr residuals.pcr screeplot.pcr |
| Transfer function model performance statistics | performance performance.bootstrap.wa performance.crossval performance.predict.wa performance.wa print.performance |
| Plots the distribution of extracted dissimilarities | plot.dissimilarities |
| Plot distribution of samples along gradient | plot.evenSample |
| Produces plots of analogue logistic regression models | plot.logitreg |
| Plot diagnostics for a mat object | plot.mat |
| Plot Monte Carlo simulated dissimilarity distributions | plot.mcarlo |
| Plot of minimum dissimilarity per sample | plot.minDC |
| Plot a fitted principal curve in PCA space | lines.prcurve plot.prcurve |
| Plot method for residual lengths | plot.residLen |
| Plot ROC curves and associated diagnostics | plot.roc |
| Plot species responses along gradients or latent variables | plot.sppResponse |
| Plot diagnostics for a weighted averaging model | plot.wa |
| North American Modern Pollen Database | Biome Climate Location Pollen |
| Fits a principal curve to m-dimensional data | initCurve prcurve print.prcurve |
| Posterior probability of analogue-ness for fossil samples | predict.logitreg |
| Predict method for Modern Analogue Technique models | predict.mat print.predict.mat |
| Predicted values from a principal components regression | predict.pcr |
| Predict new locations & fitted values on a principal curve | fitted.prcurve predict.prcurve |
| Predict from a weighted average model | predict.wa print.predict.wa |
| Rank correlation between environmental and species dissimilarities. | dotplot dotplot.rankDC plot.rankDC print.rankDC rankDC |
| Stratigraphic plots of palaeoenvironmental reconstructions | reconPlot reconPlot.default reconPlot.predict.mat reconPlot.predict.wa |
| Squared residual length diagnostics | fittedY print.residLen residLen sqrlLinear sqrlUnimodal |
| Residuals of a principal curve fit. | resid.prcurve residuals.prcurve |
| Round Loch of Glenhead Diatoms | rlgh |
| Root mean square error of prediction | RMSEP RMSEP.bootstrap.mat RMSEP.bootstrap.wa RMSEP.default RMSEP.mat |
| ROC curve analysis | print.roc print.summary.roc roc roc.analog roc.default roc.mat summary.roc |
| 'scores' method for principal curve objects of class '"prcurve"'. | scores.prcurve |
| Screeplots of model results | screeplot.bootstrap.mat screeplot.mat |
| Smoother plugin function for use in fitting a principal curve | smoothGAM smoothSpline |
| Select samples from along an environmental gradient | splitSample |
| Species responses along gradients. | sppResponse sppResponse.prcurve |
| Standard error of MAT fitted and predicted values | stdError stdError.mat stdError.predict.mat |
| Palaeoecological stratigraphic diagrams | Stratiplot Stratiplot.default Stratiplot.formula Stratiplot.matrix |
| Summarise analogue matching results | print.summary.analog summary.analog |
| Summarise bootstrap resampling for MAT models | print.summary.bootstrap.mat summary.bootstrap.mat |
| Summarise the extraction of close modern analogues | print.summary.cma summary.cma |
| Summarise Modern Analogue Technique models | print.summary.mat summary.mat |
| Summarise MAT model predictions | print.summary.predict.mat summary.predict.mat |
| SWAP sub-fossil diatom and pH training set | swapdiat |
| SWAP sub-fossil diatom and pH training set | swappH |
| Timetracks of change in species composition | fitted.timetrack plot.timetrack points.timetrack predict.timetrack print.timetrack scores.timetrack timetrack |
| Morphological data for ten taxa of the genus Tortula | tortula |
| Common data transformations and standardizations | tran tran.default tran.formula |
| Variance explained by ordination axes | varExpl varExpl.cca varExpl.default varExpl.prcurve |
| Weighted averaging transfer functions | coef.wa fitted.wa print.wa residuals.wa wa wa.default wa.formula waFit |
| Weighted correlation test of WA reconstruction | plot.weightedCor print.weightedCor weightedCor weightedCor.default |
