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

Functions

abernethy Man page
analog Man page
analog.default Man page
analog.distance Man page
analogue Man page
analogue-package Man page
as.data.frame.optima Man page
as.data.frame.tolerance Man page
bayesF Man page
Biome Man page
bootstrap Man page
bootstrap.default Man page
bootstrap.mat Man page
bootstrapObject Man page
bootstrap.wa Man page
caterpillar Man page
caterpillarPlot Man page
caterpillarPlot.data.frame Man page
caterpillarPlot.default Man page
caterpillarPlot.wa Man page
ChiSquare Man page
chooseTaxa Man page
chooseTaxa.default Man page
class.deshrink Man page
Climate Man page
cma Man page
cma.analog Man page
cma.default Man page
cma.mat Man page
cma.predict.mat Man page
coef.pcr Man page
coef.wa Man page
ColSums Man page
compare Man page
compare.default Man page
crossval Man page
crossval.pcr Man page
crossval.wa Man page
cummean Man page
cumWmean Man page
densityplot Man page
densityplot.residLen Man page
deshrink Man page
deshrink.pred Man page
deshrinkPred Man page
dissim Man page
dissimilarities Man page
dissimilarities.analog Man page
dissimilarities.mat Man page
distance Man page
distance.default Man page
distance.join Man page
dotplot Man page
dotplot.rankDC Man page
eigenvals.pcr Man page
evenSample Man page
expand.deshrink Man page
fitted.bootstrap.mat Man page
fitted.logitreg Man page
fitted.mat Man page
fitted.pcr Man page
fitted.prcurve Man page
fitted.timetrack Man page
fitted.wa Man page
fittedY Man page
fixUpTol Man page
fuse Man page
fuse.dist Man page
fuse.matrix Man page
getK Man page
getK.bootstrap.mat Man page
getK.default Man page
getK.mat Man page
getK.predict.mat Man page
gradientDist Man page
gradientDist.cca Man page
gradientDist.default Man page
gradientDist.prcurve Man page
head.join Man page
Hellinger Man page
histogram Man page
histogram.residLen Man page
hist.residLen Man page
ImbrieKipp Man page
initCurve Man page
inv.deshrink Man page
join Man page
lines.prcurve Man page
Location Man page
logitreg Man page
logitreg.analog Man page
logitreg.default Man page
mat Man page
mat.default Man page
mat.formula Man page
maxBias Man page
mcarlo Man page
mcarlo.analog Man page
mcarlo.default Man page
mcarlo.mat Man page
minDC Man page
minDC.analog Man page
minDC.default Man page
minDC.predict.mat Man page
minDC.wa Man page
minDij Man page
n2 Man page
n2.default Man page
no.deshrink Man page
oldDistance Man page
oldDistance.default Man page
oldDistance.join Man page
optima Man page
optima.default Man page
panel.Loess Man page
panel.Stratiplot Man page
pcr Man page
pcr.default Man page
pcr.formula Man page
performance Man page
performance.bootstrap.wa Man page
performance.crossval Man page
performance.pcr Man page
performance.predict.wa Man page
performance.wa Man page
plot.bayesF Man page
plot.cma Man page
plot.dissimilarities Man page
plot.evenSample Man page
plot.logitreg Man page
plot.mat Man page
plot.mcarlo Man page
plot.minDC Man page
plot.prcurve Man page
plot.rankDC Man page
plot.residLen Man page
plot.roc Man page
plot.sppResponse Man page
plot.timetrack Man page
plot.wa Man page
plot.weightedCor Man page
points.timetrack Man page
Pollen Man page
prcurve Man page
predict.logitreg Man page
predict.mat Man page
predict.pcr Man page
predict.prcurve Man page
predict.timetrack Man page
predict.wa Man page
predWA Man page
predWAT Man page
print.analog Man page
print.bayesF Man page
print.bootstrap.mat Man page
print.bootstrap.wa Man page
print.bootstrap.wa Man page
print.cma Man page
print.crossval Man page
print.fitted.bootstrap.mat Man page
print.fitted.mat Man page
print.logitreg Man page
print.mat Man page
print.mcarlo Man page
print.minDC Man page
print.optima Man page
print.pcr Man page
print.performance Man page
print.prcurve Man page
print.predict.mat Man page
print.predict.wa Man page
print.rankDC Man page
print.residLen Man page
print.residuals.bootstrap.mat Man page
print.residuals.mat Man page
print.roc Man page
print.summary.analog Man page
print.summary.bootstrap Man page
print.summary.bootstrap.mat Man page
print.summary.cma Man page
print.summary.logitreg Man page
print.summary.mat Man page
print.summary.predict.mat Man page
print.summary.roc Man page
print.timetrack Man page
print.tolerance Man page
print.wa Man page
print.weightedCor Man page
rankDC Man page
rdaFit Man page
reconPlot Man page
reconPlot.default Man page
reconPlot.predict.mat Man page
reconPlot.predict.wa Man page
resid.bootstrap.mat Man page
residLen Man page
resid.mat Man page
resid.prcurve Man page
residuals.bootstrap.mat Man page
residuals.mat Man page
residuals.pcr Man page
residuals.prcurve Man page
residuals.wa Man page
rlgh Man page
RMSEP Man page
RMSEP.bootstrap.mat Man page
RMSEP.bootstrap.wa Man page
RMSEP.default Man page
RMSEP.mat Man page
roc Man page
roc.analog Man page
roc.default Man page
roc.mat Man page
RowSums Man page
Salinity Man page
scores.prcurve Man page
scores.rdaFit Man page
scores.timetrack Man page
Screeplot.bootstrap Man page
screeplot.bootstrap.mat Man page
screeplot.mat Man page
screeplot.pcr Man page
setK<- Man page
setK<-.default Man page
setK<-.mat Man page
.simpleCap Man page
smoothGAM Man page
smoothSpline Man page
splitSample Man page
sppN2 Man page
sppResponse Man page
sppResponse.prcurve Man page
sqrlLinear Man page
sqrlUnimodal Man page
stdError Man page
stdError.mat Man page
stdError.predict.mat Man page
Stratiplot Man page
Stratiplot.default Man page
Stratiplot.formula Man page
Stratiplot.matrix Man page
summary.analog Man page
summary.bootstrap Man page
summary.bootstrap.mat Man page
summary.cma Man page
summary.logitreg Man page
summary.mat Man page
summary.predict.mat Man page
summary.roc Man page
SumSST Man page
swapdiat Man page
swappH Man page
tail.join Man page
timetrack Man page
tolerance.default Man page
tran Man page
tran.default Man page
tran.formula Man page
V12.122 Man page
varExpl Man page
varExpl.cca Man page
varExpl.default Man page
varExpl.prcurve Man page
wa Man page
wa.default Man page
waFit Man page
wa.formula Man page
WApred Man page
WATpred Man page
w.avg Man page
weightedCor Man page
weightedCor.default Man page
WinSST Man page
wmean Man page
w.tol Man page

Files

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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