analogue: Analogue and Weighted Averaging Methods for Palaeoecology

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

Author
Gavin L. Simpson [aut, cre], Jari Oksanen [aut]
Date of publication
2016-02-28 09:59:16
Maintainer
Gavin L. Simpson <ucfagls@gmail.com>
License
GPL-2
Version
0.17-0
URLs

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