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analogue (version 0.14-0)

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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Install

install.packages('analogue')

Monthly Downloads

936

Version

0.14-0

License

GPL-2

Issues

7

Pull Requests

0

Stars

14

Forks

3

Maintainer

Gavin Simpson

Last Published

August 29th, 2014

Functions in analogue (0.14-0)

cma

Close modern analogues
join

Merge species data sets on common columns (species)
analog

Analogue matching
distance

Flexibly calculate dissimilarity or distance measures
RMSEP

Root mean square error of prediction
plot3d.prcurve-deprecated

Interactive 3D plot of a principal curve in principal coordinate space
mat

Modern Analogue Technique transfer function models
optima

Weighted averaging optima and tolerance ranges
Stratiplot

Palaeoecological stratigraphic diagrams
summary.mat

Summarise Modern Analogue Technique models
plot.logitreg

Produces plots of analogue logistic regression models
performance

Transfer function model performance statistics
analogue-internal

Internal analogue Functions
logitreg

Logistic regression models for assessing analogues/non-analogues
chooseTaxa

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

Abernethy Forest Pollen Sequence
roc

ROC curve analysis
weightedCor

Weighted correlation test of WA reconstruction
plot.evenSample

Plot distribution of samples along gradient
Plot3d

Interactive 3D plot of a principal curve in principal coordinate space
wa

Weighted averaging transfer functions
Pollen

North American Modern Pollen Database
plot.mat

Plot diagnostics for a mat object
scores.prcurve

scores method for principal curve objects of class "prcurve".
getK

Extract and set the number of analogues
histogram.residLen

Lattice histogram plot for residual lengths
evenSample

Number of samples per gradient segments
ImbrieKipp

Imbrie and Kipp foraminifera training set
densityplot.residLen

Lattice density plot for residual lengths
bootstrap.wa

Bootstrap estimation and errors for WA models
crossval

Cross-validation of palaeoecological transfer function models
summary.analog

Summarise analogue matching results
panel.Loess

Loess smooths to stratigraphic diagrams
bootstrap

Bootstrap estimation and errors
fuse

Fused dissimilarities
pcr

Prinicpal component regression transfer function models
gradientDist

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

Fits a principal curve to m-dimensional data
swappH

SWAP sub-fossil diatom and pH training set
deshrink

Deshrinking techniques for WA transfer functions
analogue-package

Analogue and weighted averaging methods for palaeoecology
summary.bootstrap.mat

Summarise bootstrap resampling for MAT models
panel.Stratiplot

Panel function for stratigraphic diagrams
bootstrapObject

Bootstrap object description
bayesF

Bayes factors
smoothers

Smoother plugin function for use in fitting a principal curve
plot.roc

Plot ROC curves and associated diagnostics
predict.prcurve

Predict news locations & fitted values on a principal curve
mcarlo

Monte Carlo simulation of dissimilarities
summary.predict.mat

Summarise MAT model predictions
plot.wa

Plot diagnostics for a weighted averaging model
predict.pcr

Predicted values from a principal components regression
rankDC

Rank correlation between environmental and species dissimilarities.
plot.minDC

Plot of minimum dissimilarity per sample
plot.prcurve

Plot a fitted principal curve in PCA space
predict.logitreg

Posterior probability of analogue-ness for fossil samples
plot.residLen

Plot method for residual lengths
stdError

Standard error of MAT fitted and predicted values
minDC

Extract minimum dissimilarities
predict.mat

Predict method for Modern Analogue Technique models
compare

Compare proxies across two data sets
residLen

Squared residual length diagnostics
residuals.prcurve

Residuals of a principal curve fit.
tran

Common data transformations and standardizations
plot.mcarlo

Plot Monte Carlo simulated dissimilarity distributions
hist.residLen

Histogram plot for residual lengths
sppResponse

Species responses along gradients.
swapdiat

SWAP sub-fossil diatom and pH training set
reconPlot

Stratigraphic plots of palaeoenvironmental reconstructions
screeplot

Screeplots of model results
timetrack

Timetracks of change in species composition
splitSample

Select samples from along an environmental gradient
n2

Calculate Hill's N2 diversity measure
rlgh

Round Loch of Glenhead Diatoms
dissimilarities

Extract dissimilarity coefficients from models
varExpl

Variance explained by ordination axes
predict.wa

Predict from a weighted average model
caterpillarPlot

Caterpillar plot of species' WA optima and tolerance range.
summary.cma

Summarise the extraction of close modern analogues
fitted.logitreg

Fitted values for the training set from logistic regression models
plot.dissimilarities

Plots the distribution of extracted dissimilarities