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      "name": "tortula",
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      "page": "analogue-package",
      "title": "Analogue and weighted averaging methods for palaeoecology",
      "topics": [
        "analogue-package",
        "analogue"
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    },
    {
      "page": "abernethy",
      "title": "Abernethy Forest Pollen Sequence",
      "topics": [
        "abernethy"
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    },
    {
      "page": "analog",
      "title": "Analogue matching",
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        "analog.default",
        "analog.distance",
        "print.analog"
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    },
    {
      "page": "bayesF",
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        "Bayes factors"
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        "plot.bayesF",
        "print.bayesF"
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        "bootstrap.default",
        "bootstrap.mat",
        "fitted.bootstrap.mat",
        "print.bootstrap.mat",
        "print.fitted.bootstrap.mat",
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        "residuals.bootstrap.mat"
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    },
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      "page": "bootstrap.wa",
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      "page": "bootstrapObject",
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    {
      "page": "caterpillarPlot",
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        "caterpillarPlot",
        "caterpillarPlot.data.frame",
        "caterpillarPlot.default",
        "caterpillarPlot.wa"
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    },
    {
      "page": "chooseTaxa",
      "title": "Select taxa (variables) on basis of maximum abundance attained and number of occurrences.",
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        "chooseTaxa",
        "chooseTaxa.default"
      ]
    },
    {
      "page": "cma",
      "title": "Close modern analogues",
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        "cma.analog",
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        "cma.mat",
        "cma.predict.mat",
        "plot.cma",
        "print.cma"
      ]
    },
    {
      "page": "compare",
      "title": "Compare proxies across two data sets",
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        "compare",
        "compare.default"
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    },
    {
      "page": "crossval",
      "title": "Cross-validation of palaeoecological transfer function models",
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        "crossval",
        "crossval.pcr",
        "crossval.wa",
        "print.crossval"
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    },
    {
      "page": "densityplot.residLen",
      "title": "Lattice density plot for residual lengths",
      "topics": [
        "densityplot",
        "densityplot.residLen"
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    },
    {
      "page": "deshrink",
      "title": "Deshrinking techniques for WA transfer functions",
      "topics": [
        "deshrink",
        "deshrinkPred"
      ]
    },
    {
      "page": "dissimilarities",
      "title": "Extract dissimilarity coefficients from models",
      "topics": [
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        "dissimilarities",
        "dissimilarities.analog",
        "dissimilarities.mat"
      ]
    },
    {
      "page": "distance",
      "title": "Flexibly calculate dissimilarity or distance measures",
      "concept": [
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        "dissimilarity coefficient",
        "similarity"
      ],
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        "distance",
        "distance.default",
        "distance.join",
        "oldDistance",
        "oldDistance.default",
        "oldDistance.join"
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    },
    {
      "page": "evenlySampled",
      "title": "Number of samples per gradient segments",
      "topics": [
        "evenSample"
      ]
    },
    {
      "page": "fitted.logitreg",
      "title": "Fitted values for the training set from logistic regression models",
      "topics": [
        "fitted.logitreg"
      ]
    },
    {
      "page": "fuse",
      "title": "Fused dissimilarities",
      "topics": [
        "fuse",
        "fuse.dist",
        "fuse.matrix"
      ]
    },
    {
      "page": "getK",
      "title": "Extract and set the number of analogues",
      "topics": [
        "getK",
        "getK.bootstrap.mat",
        "getK.default",
        "getK.mat",
        "getK.predict.mat",
        "setK<-",
        "setK<-.default",
        "setK<-.mat"
      ]
    },
    {
      "page": "gradientDist",
      "title": "Positions of samples along a unit-length ordination gradient.",
      "topics": [
        "gradientDist",
        "gradientDist.cca",
        "gradientDist.default",
        "gradientDist.prcurve"
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    },
    {
      "page": "hist.residLen",
      "title": "Histogram plot for residual lengths",
      "topics": [
        "hist.residLen"
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    },
    {
      "page": "histogram.residLen",
      "title": "Lattice histogram plot for residual lengths",
      "topics": [
        "histogram",
        "histogram.residLen"
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    },
    {
      "page": "ImbrieKipp",
      "title": "Imbrie and Kipp foraminifera training set",
      "topics": [
        "ImbrieKipp",
        "Salinity",
        "SumSST",
        "V12.122",
        "WinSST"
      ]
    },
    {
      "page": "join",
      "title": "Merge species data sets on common columns (species)",
      "topics": [
        "head.join",
        "join",
        "tail.join"
      ]
    },
    {
      "page": "logitreg",
      "title": "Logistic regression models for assessing analogues/non-analogues",
      "topics": [
        "logitreg",
        "logitreg.analog",
        "logitreg.default",
        "print.logitreg",
        "print.summary.logitreg",
        "summary.logitreg"
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    },
    {
      "page": "mat",
      "title": "Modern Analogue Technique transfer function models",
      "topics": [
        "fitted.mat",
        "mat",
        "mat.default",
        "mat.formula",
        "print.fitted.mat",
        "print.mat",
        "print.residuals.mat",
        "resid.mat",
        "residuals.mat"
      ]
    },
    {
      "page": "mcarlo",
      "title": "Monte Carlo simulation of dissimilarities",
      "topics": [
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        "mcarlo.analog",
        "mcarlo.default",
        "mcarlo.mat",
        "print.mcarlo"
      ]
    },
    {
      "page": "minDC",
      "title": "Extract minimum dissimilarities",
      "topics": [
        "minDC",
        "minDC.analog",
        "minDC.default",
        "minDC.predict.mat",
        "minDC.wa",
        "print.minDC"
      ]
    },
    {
      "page": "n2",
      "title": "Calculate Hill's N2 diversity measure",
      "topics": [
        "n2",
        "n2.default"
      ]
    },
    {
      "page": "optima",
      "title": "Weighted averaging optima and tolerance ranges",
      "topics": [
        "as.data.frame.optima",
        "as.data.frame.tolerance",
        "optima",
        "optima.default",
        "print.optima",
        "print.tolerance",
        "tolerance.default"
      ]
    },
    {
      "page": "panel.Loess",
      "title": "Loess smooths to stratigraphic diagrams",
      "topics": [
        "panel.Loess"
      ]
    },
    {
      "page": "panel.Stratiplot",
      "title": "Panel function for stratigraphic diagrams",
      "topics": [
        "panel.Stratiplot"
      ]
    },
    {
      "page": "pcr",
      "title": "Prinicpal component regression transfer function models",
      "topics": [
        "ChiSquare",
        "coef.pcr",
        "eigenvals.pcr",
        "fitted.pcr",
        "Hellinger",
        "pcr",
        "pcr.default",
        "pcr.formula",
        "performance.pcr",
        "print.pcr",
        "residuals.pcr",
        "screeplot.pcr"
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    },
    {
      "page": "performance",
      "title": "Transfer function model performance statistics",
      "topics": [
        "performance",
        "performance.bootstrap.wa",
        "performance.crossval",
        "performance.predict.wa",
        "performance.wa",
        "print.performance"
      ]
    },
    {
      "page": "plot.dissimilarities",
      "title": "Plots the distribution of extracted dissimilarities",
      "topics": [
        "plot.dissimilarities"
      ]
    },
    {
      "page": "plot.evenSample",
      "title": "Plot distribution of samples along gradient",
      "topics": [
        "plot.evenSample"
      ]
    },
    {
      "page": "plot.logitreg",
      "title": "Produces plots of analogue logistic regression models",
      "topics": [
        "plot.logitreg"
      ]
    },
    {
      "page": "plot.mat",
      "title": "Plot diagnostics for a mat object",
      "topics": [
        "plot.mat"
      ]
    },
    {
      "page": "plot.mcarlo",
      "title": "Plot Monte Carlo simulated dissimilarity distributions",
      "topics": [
        "plot.mcarlo"
      ]
    },
    {
      "page": "plot.minDC",
      "title": "Plot of minimum dissimilarity per sample",
      "topics": [
        "plot.minDC"
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    },
    {
      "page": "plot.prcurve",
      "title": "Plot a fitted principal curve in PCA space",
      "topics": [
        "lines.prcurve",
        "plot.prcurve"
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    },
    {
      "page": "plot.residLen",
      "title": "Plot method for residual lengths",
      "topics": [
        "plot.residLen"
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    },
    {
      "page": "plot.roc",
      "title": "Plot ROC curves and associated diagnostics",
      "concept": [
        "ROC",
        "likelihood ratios"
      ],
      "topics": [
        "plot.roc"
      ]
    },
    {
      "page": "plot.sppResponse",
      "title": "Plot species responses along gradients or latent variables",
      "topics": [
        "plot.sppResponse"
      ]
    },
    {
      "page": "plot.wa",
      "title": "Plot diagnostics for a weighted averaging model",
      "topics": [
        "plot.wa"
      ]
    },
    {
      "page": "Pollen",
      "title": "North American Modern Pollen Database",
      "topics": [
        "Biome",
        "Climate",
        "Location",
        "Pollen"
      ]
    },
    {
      "page": "prcurve",
      "title": "Fits a principal curve to m-dimensional data",
      "topics": [
        "initCurve",
        "prcurve",
        "print.prcurve"
      ]
    },
    {
      "page": "predict.logitreg",
      "title": "Posterior probability of analogue-ness for fossil samples",
      "topics": [
        "predict.logitreg"
      ]
    },
    {
      "page": "predict.mat",
      "title": "Predict method for Modern Analogue Technique models",
      "topics": [
        "predict.mat",
        "print.predict.mat"
      ]
    },
    {
      "page": "predict.pcr",
      "title": "Predicted values from a principal components regression",
      "topics": [
        "predict.pcr"
      ]
    },
    {
      "page": "predict.prcurve",
      "title": "Predict new locations & fitted values on a principal curve",
      "topics": [
        "fitted.prcurve",
        "predict.prcurve"
      ]
    },
    {
      "page": "predict.wa",
      "title": "Predict from a weighted average model",
      "topics": [
        "predict.wa",
        "print.predict.wa"
      ]
    },
    {
      "page": "rankDC",
      "title": "Rank correlation between environmental and species dissimilarities.",
      "topics": [
        "dotplot",
        "dotplot.rankDC",
        "plot.rankDC",
        "print.rankDC",
        "rankDC"
      ]
    },
    {
      "page": "reconPlot",
      "title": "Stratigraphic plots of palaeoenvironmental reconstructions",
      "topics": [
        "reconPlot",
        "reconPlot.default",
        "reconPlot.predict.mat",
        "reconPlot.predict.wa"
      ]
    },
    {
      "page": "residLen",
      "title": "Squared residual length diagnostics",
      "topics": [
        "fittedY",
        "print.residLen",
        "residLen",
        "sqrlLinear",
        "sqrlUnimodal"
      ]
    },
    {
      "page": "residuals.prcurve",
      "title": "Residuals of a principal curve fit.",
      "topics": [
        "resid.prcurve",
        "residuals.prcurve"
      ]
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