Analogue and Weighted Averaging Methods for Palaeoecology

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 |

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