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analogue (version 0.3-3)

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

800

Version

0.3-3

License

GPL Version 2

Maintainer

Gavin L Simpson

Last Published

June 25th, 2025

Functions in analogue (0.3-3)

bayesF

Bayes factors
distance

Flexibly calculate dissimilarity or distance measures
dissimilarities

Extract dissimilarity coefficients from models
summary.cma

Summarising the extraction of close modern analogues
join

Merge species data sets on common columns (species)
bootstrap

Bootstrap estimation and errors
analogue-package

Analogue methods for palaeoecology
Screeplot

Screeplots of model results
predict.mat

Predict method for Modern Analogue Technique models
fitted.mat

Fitted values of a MAT model
analog

Analogue matching
cma

Close modern analogues
k

Extract and set the number of analogues
summary.bootstrap

Summarising bootstrap resampling for MAT models
summary.predict.mat

Summarising MAT model predictions
plot.cma

Draws stripcharts of close modern analogue results
plot.mcarlo

Plotting of Monte Carlo simulated dissimilarity distributions
analogue-internal

Internal analogue Functions
mcarlo

Monte Carlo simulation of dissimilarities
RMSEP

Root mean square error of prediction
plot.dissimilarities

Plots the distribution of extracted dissimilarities
reconPlot

Stratigraphic plots of palaeoenvironmental reconstructions
plot.roc

Plot ROC curves and associated diagnostics
residuals.bootstrap

Extract Bootstrapped Model Residuals
residuals.mat

Extract Model Residuals
mat

Modern Analogue Technique transfer function models
swapdiat

SWAP sub-fossil diatom and pH training set
summary.mat

Summarising Modern Analogue Technique models
plot.bayesF

Bayes factor plots
summary.analog

Summarising analogue matching results
roc

ROC curve analysis
rlgh

Round Loch of Glenhead Diatoms
plot.minDC

~~function to do ... ~~
plot.mat

Plot diagnostics for a mat object
minDC

Functions to extract and plot minimum dissimilarities
swappH

SWAP sub-fossil diatom and pH training set