analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.

AuthorGavin L. Simpson [aut, cre], Jari Oksanen [aut]
Date of publication2016-02-28 09:59:16
MaintainerGavin L. Simpson <ucfagls@gmail.com>
LicenseGPL-2
Version0.17-0
https://github.com/gavinsimpson/analogue

View on CRAN

Man pages

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

tran: Common data transformations and standardizations

varExpl: Variance explained by ordination axes

wa: Weighted averaging transfer functions

weightedCor: Weighted correlation test of WA reconstruction

Files in this package

analogue
analogue/inst
analogue/inst/TODO
analogue/inst/COPYING
analogue/inst/CITATION
analogue/inst/NEWS
analogue/inst/THANKS
analogue/inst/ChangeLog
analogue/inst/doc
analogue/inst/doc/analogue_methods.Rnw
analogue/inst/doc/analogue_methods.pdf
analogue/inst/doc/analogue_methods.R
analogue/inst/ONEWS.Rd
analogue/tests
analogue/tests/Examples
analogue/tests/Examples/analogue-Ex.Rout.save
analogue/tests/testthat
analogue/tests/testthat/test-new-distance.R
analogue/tests/testthat/test-analog.R
analogue/tests/testthat/test-tran.R
analogue/tests/test-all.R
analogue/src
analogue/src/distx.c
analogue/src/wastats.c
analogue/src/distxy.c
analogue/NAMESPACE
analogue/data
analogue/data/swapdiat.rda
analogue/data/rlgh.rda
analogue/data/Pollen.rda
analogue/data/Location.rda
analogue/data/Climate.rda
analogue/data/swappH.rda
analogue/data/Biome.rda
analogue/data/abernethy.rda
analogue/data/ImbrieKipp.rda
analogue/data/V12.122.rda
analogue/data/WinSST.rda
analogue/data/SumSST.rda
analogue/data/Salinity.rda
analogue/R
analogue/R/fitted.prcurve.R analogue/R/points.timetrack.R analogue/R/mat.R analogue/R/predict.logitreg.R analogue/R/coef.pcr.R analogue/R/deshrinkPred.R analogue/R/summary.cma.R analogue/R/summary.mat.R analogue/R/crossval.R analogue/R/fuse.dist.R analogue/R/tail.join.R analogue/R/summary.predict.mat.R analogue/R/summary.analog.R analogue/R/densityplot.residLen.R analogue/R/screeplot.pcr.R analogue/R/bootstrap.R analogue/R/summary.roc.R analogue/R/cma.R analogue/R/plot.dissimilarities.R analogue/R/minDC.R analogue/R/print.wa.R analogue/R/print.residLen.R analogue/R/timetrack.R analogue/R/crossval.pcr.R analogue/R/performance.crossval.R analogue/R/logitreg.analog.R analogue/R/panel.Loess.R analogue/R/getK.R analogue/R/summary.logitreg.R analogue/R/minDC.wa.R analogue/R/residuals.pcr.R analogue/R/predict.mat.R analogue/R/deshrink.R analogue/R/performance.wa.R analogue/R/rankDC.R analogue/R/fitted.logitreg.R analogue/R/residuals.wa.R analogue/R/chooseTaxa.R analogue/R/fuse.R analogue/R/print.roc.R analogue/R/scores.prcurve.R analogue/R/lines.prcurve.R analogue/R/reconPlot.predict.wa.R analogue/R/crossval.wa.R analogue/R/fitPCR.R analogue/R/plot.roc.R analogue/R/new-distance.R analogue/R/plot.bayesF.R analogue/R/logitreg.R analogue/R/plot.logitreg.R analogue/R/performance.pcr.R analogue/R/plot.wa.R analogue/R/initCurve.R analogue/R/plot.mat.R analogue/R/predict.timetrack.R analogue/R/hist.residLen.R analogue/R/plot.mcarlo.R analogue/R/summary.bootstrap.mat.R analogue/R/screeplot.R analogue/R/smoothSpline.R analogue/R/tolerance.R analogue/R/stdError.R analogue/R/smoothGAM.R analogue/R/tran.R analogue/R/print.bootstrap.wa.R analogue/R/plot.gradientDist.R analogue/R/waFit.R analogue/R/residuals.bootstrap.mat.R analogue/R/RMSEP.bootstrap.wa.R analogue/R/histogram.residLen.R analogue/R/evenSample.R analogue/R/predict.pcr.R analogue/R/varExpl.R analogue/R/RMSEP.R analogue/R/print.predict.wa.R analogue/R/wa.formula.R analogue/R/plot.rankDC.R analogue/R/Stratiplot.formula.R analogue/R/Stratiplot.R analogue/R/prcurve.R analogue/R/plot.prcurve.R analogue/R/internal.R analogue/R/eigenvals.pcr.R analogue/R/sppResponse.R analogue/R/rdaFit.R analogue/R/fitted.wa.R analogue/R/ccaFit.R analogue/R/caterpillarPlot.R analogue/R/coef.wa.R analogue/R/wa.R analogue/R/join.R analogue/R/fitted.mat.R analogue/R/as.data.frame.optima.R analogue/R/residuals.prcurve.R analogue/R/plot.sppResponse.R analogue/R/head.join.R analogue/R/splitSample.R analogue/R/fixUpTol.R analogue/R/dotplot.rankDC.R analogue/R/weightedCor.R analogue/R/predict.wa.R analogue/R/fuse.matrix.R analogue/R/bootstrap.wa.R analogue/R/plot.timetrack.R analogue/R/fitted.timetrack.R analogue/R/plot.cma.R analogue/R/performance.bootstrap.wa.R analogue/R/predict.prcurve.R analogue/R/residLen.R analogue/R/print.performance.R analogue/R/reconPlot.R analogue/R/performance.predict.wa.R analogue/R/plot.residLen.R analogue/R/compare.R analogue/R/gradientDist.R analogue/R/scores.timetrack.R analogue/R/roc.R analogue/R/panel.Stratiplot.R analogue/R/sppResponse.prcurve.R analogue/R/n2.R analogue/R/residuals.mat.R analogue/R/dissimilarities.R analogue/R/fitted.pcr.R analogue/R/Stratiplot.matrix.R analogue/R/pcr.R analogue/R/zzz.R analogue/R/performance.R analogue/R/optima.R analogue/R/print.summary.roc.R analogue/R/plot.evenSample.R analogue/R/distance.R analogue/R/mcarlo.R analogue/R/analog.R analogue/R/bayesF.R
analogue/vignettes
analogue/vignettes/analogue_methods.Rnw
analogue/vignettes/Z.cls
analogue/vignettes/analogue_refs.bib
analogue/README.md
analogue/MD5
analogue/build
analogue/build/vignette.rds
analogue/DESCRIPTION
analogue/man
analogue/man/panel.Loess.Rd analogue/man/evenlySampled.Rd analogue/man/plot.evenSample.Rd analogue/man/swappH.Rd analogue/man/Pollen.Rd analogue/man/bootstrap.Rd analogue/man/gradientDist.Rd analogue/man/plot.mcarlo.Rd analogue/man/rlgh.Rd analogue/man/n2.Rd analogue/man/plot.wa.Rd analogue/man/screeplot.Rd analogue/man/rankDC.Rd analogue/man/predict.logitreg.Rd analogue/man/predict.pcr.Rd analogue/man/residLen.Rd analogue/man/fitted.logitreg.Rd analogue/man/prcurve.Rd analogue/man/abernethy.Rd analogue/man/predict.wa.Rd analogue/man/smoothFuns.Rd analogue/man/performance.Rd analogue/man/plot.minDC.Rd analogue/man/mcarlo.Rd analogue/man/densityplot.residLen.Rd analogue/man/predict.prcurve.Rd analogue/man/plot.roc.Rd analogue/man/mat.Rd analogue/man/pcr.Rd analogue/man/distance.Rd analogue/man/plot.mat.Rd analogue/man/panel.Stratiplot.Rd analogue/man/plot.dissimilarities.Rd analogue/man/RMSEP.Rd analogue/man/analogue-internal.Rd analogue/man/fuse.Rd analogue/man/hist.residLen.Rd analogue/man/tran.Rd analogue/man/histogram.residLen.Rd analogue/man/summary.predict.mat.Rd analogue/man/dissimilarities.Rd analogue/man/plot.prcurve.Rd analogue/man/wa.Rd analogue/man/timetrack.Rd analogue/man/summary.analog.Rd analogue/man/residuals.prcurve.Rd analogue/man/ImbrieKipp.Rd analogue/man/logitreg.Rd analogue/man/varExpl.Rd analogue/man/summary.bootstrap.mat.Rd analogue/man/deshrink.Rd analogue/man/summary.cma.Rd analogue/man/optima.Rd analogue/man/compare.Rd analogue/man/bayesF.Rd analogue/man/plot.residLen.Rd analogue/man/join.Rd analogue/man/scores.prcurve.Rd analogue/man/sppResponse.prcurve.Rd analogue/man/weightedCor.Rd analogue/man/reconPlot.Rd analogue/man/roc.Rd analogue/man/caterpillarPlot.Rd analogue/man/getK.Rd analogue/man/minDC.Rd analogue/man/bootstrap.wa.Rd analogue/man/bootstrapObject.Rd analogue/man/cma.Rd analogue/man/crossval.Rd analogue/man/plot.sppResponse.Rd analogue/man/swapdiat.Rd analogue/man/Stratiplot.Rd analogue/man/summary.mat.Rd analogue/man/chooseTaxa.Rd analogue/man/splitSample.Rd analogue/man/plot.logitreg.Rd analogue/man/analog.Rd analogue/man/analogue-package.Rd analogue/man/predict.mat.Rd analogue/man/stdError.Rd

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