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 |
| 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 |
| 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 |
| 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 |
| 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. |
| eigenvals.pcr | Prinicpal component regression transfer function models |
| evenSample | Number of samples per gradient segments |
| 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 news 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 |
| 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. |
| 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 |
| ImbrieKipp | Imbrie and Kipp foraminifera training set |
| initCurve | Fits a principal curve to m-dimensional data |
| join | Merge species data sets on common columns (species) |
| 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 |
| 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 |
| n2 | Calculate Hill's N2 diversity measure |
| n2.default | Calculate Hill's N2 diversity measure |
| 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 |
| 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 news 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |