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analogue (version 0.10-0)

Analogue and weighted averaging methods for palaeoecology

Description

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

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Version

Install

install.packages('analogue')

Monthly Downloads

936

Version

0.10-0

License

GPL-2

Maintainer

Gavin L Simpson

Last Published

January 3rd, 2013

Functions in analogue (0.10-0)

gradientDist

Positions of samples along a unit-length ordination gradient.
caterpillarPlot

Caterpillar plot of species' WA optima and tolerance range.
abernethy

Abernethy Forest Pollen Sequence
bayesF

Bayes factors
bootstrap

Bootstrap estimation and errors
Pollen

North American Modern Pollen Database
prcurve

Fits a principal curve to m-dimensional data
weightedCor

Weighted correlation test of WA reconstruction
hist.residLen

Histogram plot for residual lengths
logitreg

Logistic regression models for assessing analogues/non-analogues
getK

Extract and set the number of analogues
summary.bootstrap.mat

Summarise bootstrap resampling for MAT models
distance3

Flexibly calculate dissimilarity or distance measures
predict.mat

Predict method for Modern Analogue Technique models
optima

Weighted averaging optima and tolerance ranges
stdError

Standard error of MAT fitted and predicted values
summary.predict.mat

Summarise MAT model predictions
bootstrapObject

Bootstrap object description
plot.mcarlo

Plot Monte Carlo simulated dissimilarity distributions
predict.logitreg

Posterior probability of analogue-ness for fossil samples
residLen

Squared residual length diagnostics
panel.Loess

Loess smooths to stratigraphic diagrams
plot.dissimilarities

Plots the distribution of extracted dissimilarities
plot.minDC

Plot of minimum dissimilarity per sample
RMSEP

Root mean square error of prediction
analog

Analogue matching
timetrack

Timetracks of change in species composition
plot.logitreg

Produces plots of analogue logistic regression models
cma

Close modern analogues
summary.analog

Summarise analogue matching results
densityplot.residLen

Lattice density plot for residual lengths
dissimilarities

Extract dissimilarity coefficients from models
plot.mat

Plot diagnostics for a mat object
pcr

Prinicpal component regression transfer function models
distance

Flexibly calculate dissimilarity or distance measures
varExpl

Variance explained by ordination axes
analogue-package

Analogue methods for palaeoecology
swapdiat

SWAP sub-fossil diatom and pH training set
plot.wa

Plot diagnostics for a weighted averaging model
screeplot

Screeplots of model results
mcarlo

Monte Carlo simulation of dissimilarities
ImbrieKipp

Imbrie and Kipp foraminifera training set
join

Merge species data sets on common columns (species)
panel.Stratiplot

Panel function for stratigraphic diagrams
minDC

Extract minimum dissimilarities
deshrink

Deshrinking techniques for WA transfer functions
wa

Weighted averaging transfer functions
swappH

SWAP sub-fossil diatom and pH training set
bootstrap.wa

Bootstrap estimation and errors for WA models
mat

Modern Analogue Technique transfer function models
chooseTaxa

Select taxa (variables) on basis of maximum abundance attained and number of occurrences
tran

Common data transformations and standardizations
analogue-internal

Internal analogue Functions
reconPlot

Stratigraphic plots of palaeoenvironmental reconstructions
histogram.residLen

Lattice histogram plot for residual lengths
plot.residLen

Plot method for residual lengths
crossval

Cross-validation of palaeoecological transfer function models
summary.cma

Summarise the extraction of close modern analogues
summary.mat

Summarise Modern Analogue Technique models
splitSample

Select samples from along an environmental gradient
predict.wa

Predict from a weighted average model
Stratiplot

Palaeoecological stratigraphic diagrams
fuse

Fused dissimilarities
roc

ROC curve analysis
plot.prcurve

Plot a fitted principal curve in PCA space
rlgh

Round Loch of Glenhead Diatoms
plot.roc

Plot ROC curves and associated diagnostics
fitted.logitreg

Fitted values for the training set from logistic regression models
performance

Transfer function model performance statistics