analogue: Analogue and Weighted Averaging Methods for Palaeoecology
Version 0.17-0

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

Browse man pages Browse package API and functions Browse package files

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
URL https://github.com/gavinsimpson/analogue
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("analogue")

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

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

Files

inst
inst/TODO
inst/COPYING
inst/CITATION
inst/NEWS
inst/THANKS
inst/ChangeLog
inst/doc
inst/doc/analogue_methods.Rnw
inst/doc/analogue_methods.pdf
inst/doc/analogue_methods.R
inst/ONEWS.Rd
tests
tests/Examples
tests/Examples/analogue-Ex.Rout.save
tests/testthat
tests/testthat/test-new-distance.R
tests/testthat/test-analog.R
tests/testthat/test-tran.R
tests/test-all.R
src
src/distx.c
src/wastats.c
src/distxy.c
NAMESPACE
data
data/swapdiat.rda
data/rlgh.rda
data/Pollen.rda
data/Location.rda
data/Climate.rda
data/swappH.rda
data/Biome.rda
data/abernethy.rda
data/ImbrieKipp.rda
data/V12.122.rda
data/WinSST.rda
data/SumSST.rda
data/Salinity.rda
R
R/fitted.prcurve.R
R/points.timetrack.R
R/mat.R
R/predict.logitreg.R
R/coef.pcr.R
R/deshrinkPred.R
R/summary.cma.R
R/summary.mat.R
R/crossval.R
R/fuse.dist.R
R/tail.join.R
R/summary.predict.mat.R
R/summary.analog.R
R/densityplot.residLen.R
R/screeplot.pcr.R
R/bootstrap.R
R/summary.roc.R
R/cma.R
R/plot.dissimilarities.R
R/minDC.R
R/print.wa.R
R/print.residLen.R
R/timetrack.R
R/crossval.pcr.R
R/performance.crossval.R
R/logitreg.analog.R
R/panel.Loess.R
R/getK.R
R/summary.logitreg.R
R/minDC.wa.R
R/residuals.pcr.R
R/predict.mat.R
R/deshrink.R
R/performance.wa.R
R/rankDC.R
R/fitted.logitreg.R
R/residuals.wa.R
R/chooseTaxa.R
R/fuse.R
R/print.roc.R
R/scores.prcurve.R
R/lines.prcurve.R
R/reconPlot.predict.wa.R
R/crossval.wa.R
R/fitPCR.R
R/plot.roc.R
R/new-distance.R
R/plot.bayesF.R
R/logitreg.R
R/plot.logitreg.R
R/performance.pcr.R
R/plot.wa.R
R/initCurve.R
R/plot.mat.R
R/predict.timetrack.R
R/hist.residLen.R
R/plot.mcarlo.R
R/summary.bootstrap.mat.R
R/screeplot.R
R/smoothSpline.R
R/tolerance.R
R/stdError.R
R/smoothGAM.R
R/tran.R
R/print.bootstrap.wa.R
R/plot.gradientDist.R
R/waFit.R
R/residuals.bootstrap.mat.R
R/RMSEP.bootstrap.wa.R
R/histogram.residLen.R
R/evenSample.R
R/predict.pcr.R
R/varExpl.R
R/RMSEP.R
R/print.predict.wa.R
R/wa.formula.R
R/plot.rankDC.R
R/Stratiplot.formula.R
R/Stratiplot.R
R/prcurve.R
R/plot.prcurve.R
R/internal.R
R/eigenvals.pcr.R
R/sppResponse.R
R/rdaFit.R
R/fitted.wa.R
R/ccaFit.R
R/caterpillarPlot.R
R/coef.wa.R
R/wa.R
R/join.R
R/fitted.mat.R
R/as.data.frame.optima.R
R/residuals.prcurve.R
R/plot.sppResponse.R
R/head.join.R
R/splitSample.R
R/fixUpTol.R
R/dotplot.rankDC.R
R/weightedCor.R
R/predict.wa.R
R/fuse.matrix.R
R/bootstrap.wa.R
R/plot.timetrack.R
R/fitted.timetrack.R
R/plot.cma.R
R/performance.bootstrap.wa.R
R/predict.prcurve.R
R/residLen.R
R/print.performance.R
R/reconPlot.R
R/performance.predict.wa.R
R/plot.residLen.R
R/compare.R
R/gradientDist.R
R/scores.timetrack.R
R/roc.R
R/panel.Stratiplot.R
R/sppResponse.prcurve.R
R/n2.R
R/residuals.mat.R
R/dissimilarities.R
R/fitted.pcr.R
R/Stratiplot.matrix.R
R/pcr.R
R/zzz.R
R/performance.R
R/optima.R
R/print.summary.roc.R
R/plot.evenSample.R
R/distance.R
R/mcarlo.R
R/analog.R
R/bayesF.R
vignettes
vignettes/analogue_methods.Rnw
vignettes/Z.cls
vignettes/analogue_refs.bib
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/panel.Loess.Rd
man/evenlySampled.Rd
man/plot.evenSample.Rd
man/swappH.Rd
man/Pollen.Rd
man/bootstrap.Rd
man/gradientDist.Rd
man/plot.mcarlo.Rd
man/rlgh.Rd
man/n2.Rd
man/plot.wa.Rd
man/screeplot.Rd
man/rankDC.Rd
man/predict.logitreg.Rd
man/predict.pcr.Rd
man/residLen.Rd
man/fitted.logitreg.Rd
man/prcurve.Rd
man/abernethy.Rd
man/predict.wa.Rd
man/smoothFuns.Rd
man/performance.Rd
man/plot.minDC.Rd
man/mcarlo.Rd
man/densityplot.residLen.Rd
man/predict.prcurve.Rd
man/plot.roc.Rd
man/mat.Rd
man/pcr.Rd
man/distance.Rd
man/plot.mat.Rd
man/panel.Stratiplot.Rd
man/plot.dissimilarities.Rd
man/RMSEP.Rd
man/analogue-internal.Rd
man/fuse.Rd
man/hist.residLen.Rd
man/tran.Rd
man/histogram.residLen.Rd
man/summary.predict.mat.Rd
man/dissimilarities.Rd
man/plot.prcurve.Rd
man/wa.Rd
man/timetrack.Rd
man/summary.analog.Rd
man/residuals.prcurve.Rd
man/ImbrieKipp.Rd
man/logitreg.Rd
man/varExpl.Rd
man/summary.bootstrap.mat.Rd
man/deshrink.Rd
man/summary.cma.Rd
man/optima.Rd
man/compare.Rd
man/bayesF.Rd
man/plot.residLen.Rd
man/join.Rd
man/scores.prcurve.Rd
man/sppResponse.prcurve.Rd
man/weightedCor.Rd
man/reconPlot.Rd
man/roc.Rd
man/caterpillarPlot.Rd
man/getK.Rd
man/minDC.Rd
man/bootstrap.wa.Rd
man/bootstrapObject.Rd
man/cma.Rd
man/crossval.Rd
man/plot.sppResponse.Rd
man/swapdiat.Rd
man/Stratiplot.Rd
man/summary.mat.Rd
man/chooseTaxa.Rd
man/splitSample.Rd
man/plot.logitreg.Rd
man/analog.Rd
man/analogue-package.Rd
man/predict.mat.Rd
man/stdError.Rd
analogue documentation built on May 19, 2017, 10:14 p.m.