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analogue (version 0.4-0)

Analogue methods for palaeoecology

Description

Fits Modern Analogue Technique transfer function models for prediction of environmental data from species data. Also performs analogue matching, a related technique used in palaeo ecological restoration.

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Version

Install

install.packages('analogue')

Monthly Downloads

1,290

Version

0.4-0

License

GPL Version 2

Maintainer

Gavin L Simpson

Last Published

April 4th, 2025

Functions in analogue (0.4-0)

distance

Flexibly calculate dissimilarity or distance measures
cma

Close modern analogues
fitted.mat

Fitted values of a MAT model
dissimilarities

Extract dissimilarity coefficients from models
mat

Modern Analogue Technique transfer function models
analog

Analogue matching
predict.mat

Predict method for Modern Analogue Technique models
RMSEP

Root mean square error of prediction
plot.minDC

A plot of minimum dissimilarity per sample
plot.mat

Plot diagnostics for a mat object
summary.bootstrap.mat

Summarising bootstrap resampling for MAT models
reconPlot

Stratigraphic plots of palaeoenvironmental reconstructions
screeplot

Screeplots of model results
minDC

Functions to extract minimum dissimilarities
rlgh

Round Loch of Glenhead Diatoms
plot.cma

Draws stripcharts of close modern analogue results
plot.mcarlo

Plotting of Monte Carlo simulated dissimilarity distributions
swapdiat

SWAP sub-fossil diatom and pH training set
bootstrap

Bootstrap estimation and errors
plot.dissimilarities

Plots the distribution of extracted dissimilarities
summary.cma

Summarising the extraction of close modern analogues
bayesF

Bayes factors
plot.roc

Plot ROC curves and associated diagnostics
analogue-internal

Internal analogue Functions
swappH

SWAP sub-fossil diatom and pH training set
roc

ROC curve analysis
getK

Extract and set the number of analogues
summary.analog

Summarising analogue matching results
mcarlo

Monte Carlo simulation of dissimilarities
summary.predict.mat

Summarising MAT model predictions
residuals.mat

Extract Model Residuals
plot.bayesF

Bayes factor plots
residuals.bootstrap.mat

Extract Bootstrapped Model Residuals
join

Merge species data sets on common columns (species)
analogue-package

Analogue methods for palaeoecology
summary.mat

Summarising Modern Analogue Technique models