Man pages for gavinsimpson/analogue
Analogue and Weighted Averaging Methods for Palaeoecology

abernethyAbernethy Forest Pollen Sequence
analogAnalogue matching
analogue-internalInternal analogue Functions
analogue-packageAnalogue and weighted averaging methods for palaeoecology
bayesFBayes factors
bootstrapBootstrap estimation and errors
bootstrapObjectBootstrap object description
bootstrap.waBootstrap estimation and errors for WA models
caterpillarPlotCaterpillar plot of species' WA optima and tolerance range.
chooseTaxaSelect taxa (variables) on basis of maximum abundance...
cmaClose modern analogues
compareCompare proxies across two data sets
crossvalCross-validation of palaeoecological transfer function models
densityplot.residLenLattice density plot for residual lengths
deshrinkDeshrinking techniques for WA transfer functions
dissimilaritiesExtract dissimilarity coefficients from models
distanceFlexibly calculate dissimilarity or distance measures
evenlySampledNumber of samples per gradient segments
fitted.logitregFitted values for the training set from logistic regression...
fuseFused dissimilarities
getKExtract and set the number of analogues
gradientDistPositions of samples along a unit-length ordination gradient.
histogram.residLenLattice histogram plot for residual lengths
hist.residLenHistogram plot for residual lengths
ImbrieKippImbrie and Kipp foraminifera training set
joinMerge species data sets on common columns (species)
logitregLogistic regression models for assessing...
matModern Analogue Technique transfer function models
mcarloMonte Carlo simulation of dissimilarities
minDCExtract minimum dissimilarities
n2Calculate Hill's N2 diversity measure
optimaWeighted averaging optima and tolerance ranges
panel.LoessLoess smooths to stratigraphic diagrams
panel.StratiplotPanel function for stratigraphic diagrams
pcrPrinicpal component regression transfer function models
performanceTransfer function model performance statistics
plot.dissimilaritiesPlots the distribution of extracted dissimilarities
plot.evenSamplePlot distribution of samples along gradient
plot.logitregProduces plots of analogue logistic regression models
plot.matPlot diagnostics for a mat object
plot.mcarloPlot Monte Carlo simulated dissimilarity distributions
plot.minDCPlot of minimum dissimilarity per sample
plot.prcurvePlot a fitted principal curve in PCA space
plot.residLenPlot method for residual lengths
plot.rocPlot ROC curves and associated diagnostics
plot.sppResponsePlot species responses along gradients or latent variables
plot.waPlot diagnostics for a weighted averaging model
PollenNorth American Modern Pollen Database
prcurveFits a principal curve to m-dimensional data
predict.logitregPosterior probability of analogue-ness for fossil samples
predict.matPredict method for Modern Analogue Technique models
predict.pcrPredicted values from a principal components regression
predict.prcurvePredict news locations & fitted values on a principal curve
predict.waPredict from a weighted average model
rankDCRank correlation between environmental and species...
reconPlotStratigraphic plots of palaeoenvironmental reconstructions
residLenSquared residual length diagnostics
residuals.prcurveResiduals of a principal curve fit.
rlghRound Loch of Glenhead Diatoms
RMSEPRoot mean square error of prediction
rocROC curve analysis
scores.prcurve'scores' method for principal curve objects of class...
screeplotScreeplots of model results
smoothFunsSmoother plugin function for use in fitting a principal curve
splitSampleSelect samples from along an environmental gradient
sppResponse.prcurveSpecies responses along gradients.
stdErrorStandard error of MAT fitted and predicted values
StratiplotPalaeoecological stratigraphic diagrams
summary.analogSummarise analogue matching results
summary.bootstrap.matSummarise bootstrap resampling for MAT models
summary.cmaSummarise the extraction of close modern analogues
summary.matSummarise Modern Analogue Technique models
summary.predict.matSummarise MAT model predictions
swapdiatSWAP sub-fossil diatom and pH training set
swappHSWAP sub-fossil diatom and pH training set
timetrackTimetracks of change in species composition
tortulaMorphological data for ten taxa of the genus Tortula
tranCommon data transformations and standardizations
varExplVariance explained by ordination axes
waWeighted averaging transfer functions
weightedCorWeighted correlation test of WA reconstruction
gavinsimpson/analogue documentation built on Oct. 12, 2018, 9:13 a.m.