Analogue and weighted averaging methods for palaeoecology


[Up] [Top]

Documentation for package ‘analogue’ version 0.6-23

Help Pages

A B C D F G H I J L M O P R S T V W

-- --

analogue-package Analogue methods for palaeoecology

-- A --

analog Analogue matching
analog.default Analogue matching
analogue Analogue methods for palaeoecology
as.data.frame.optima Weighted averaging optima and tolerance ranges
as.data.frame.tolerance Weighted averaging optima and tolerance ranges

-- B --

bayesF Bayes factors
Biome North American Modern Pollen Database
bootstrap Bootstrap estimation and errors
bootstrap.default Bootstrap estimation and errors
bootstrap.mat Bootstrap estimation and errors
bootstrap.wa Bootstrap estimation and errors for WA models
bootstrapObject Bootstrap object description

-- C --

Climate North American Modern Pollen Database
cma Close modern analogues
cma.analog Close modern analogues
cma.default Close modern analogues
coef.wa Weighted averaging transfer functions

-- D --

densityplot.residLen Lattice density plot for residual lengths
deshrink Deshrinking techniques for WA transfer functions
deshrinkPred Deshrinking techniques for WA transfer functions
dissim Extract dissimilarity coefficients from models
dissimilarities Extract dissimilarity coefficients from models
dissimilarities.analog Extract dissimilarity coefficients from models
distance Flexibly calculate dissimilarity or distance measures
distance.default Flexibly calculate dissimilarity or distance measures
distance.join Flexibly calculate dissimilarity or distance measures

-- F --

fitted.bootstrap.mat Bootstrap estimation and errors
fitted.mat Modern Analogue Technique transfer function models
fitted.wa Weighted averaging transfer functions
fittedY Squared residual length diagnostics
fuse Fused dissimilarities
fuse.dist Fused dissimilarities
fuse.matrix Fused dissimilarities

-- G --

getK Extract and set the number of analogues
getK.bootstrap.mat Extract and set the number of analogues
getK.default Extract and set the number of analogues
getK.mat Extract and set the number of analogues
getK.predict.mat Extract and set the number of analogues

-- H --

head.join Merge species data sets on common columns (species)
hist.residLen Histogram plot for residual lengths
histogram.residLen Lattice histogram plot for residual lengths

-- I --

ImbrieKipp Imbrie and Kipp foraminifera training set

-- J --

join Merge species data sets on common columns (species)

-- L --

Location North American Modern Pollen Database
logitreg Logistic regression models for assessing analogues/non-analogues
logitreg.analog Logistic regression models for assessing analogues/non-analogues
logitreg.default Logistic regression models for assessing analogues/non-analogues

-- M --

mat Modern Analogue Technique transfer function models
mat.default Modern Analogue Technique transfer function models
mat.formula Modern Analogue Technique transfer function models
mcarlo Monte Carlo simulation of dissimilarities
mcarlo.analog Monte Carlo simulation of dissimilarities
mcarlo.default Monte Carlo simulation of dissimilarities
mcarlo.mat Monte Carlo simulation of dissimilarities
minDC Extract minimum dissimilarities
minDC.analog Extract minimum dissimilarities
minDC.default Extract minimum dissimilarities
minDC.predict.mat Extract minimum dissimilarities
minDC.wa Extract minimum dissimilarities

-- O --

optima Weighted averaging optima and tolerance ranges
optima.default Weighted averaging optima and tolerance ranges

-- P --

panel.Loess Loess smooths to stratigraphic diagrams
panel.Stratiplot Panel function for stratigraphic diagrams
performance Transfer function model performance statistics
performance.bootstrap.wa Transfer function model performance statistics
performance.predict.wa Transfer function model performance statistics
performance.wa Transfer function model performance statistics
plot.bayesF Bayes factors
plot.cma Close modern analogues
plot.dissimilarities Plots the distribution of extracted dissimilarities
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.residLen Plot method for residual lengths
plot.roc Plot ROC curves and associated diagnostics
plot.wa Plot diagnostics for a weighted averaging model
Pollen North American Modern Pollen Database
predict.mat Predict method for Modern Analogue Technique models
predict.wa Predict from a weighted average model
print.analog Analogue matching
print.bayesF Bayes factors
print.bootstrap.mat Bootstrap estimation and errors
print.bootstrap.wa Bootstrap estimation and errors for WA models
print.cma Close modern analogues
print.fitted.bootstrap.mat Bootstrap estimation and errors
print.fitted.mat Modern Analogue Technique transfer function models
print.logitreg Logistic regression models for assessing analogues/non-analogues
print.mat Modern Analogue Technique transfer function models
print.mcarlo Monte Carlo simulation of dissimilarities
print.minDC Extract minimum dissimilarities
print.optima Weighted averaging optima and tolerance ranges
print.performance Transfer function model performance statistics
print.predict.mat Predict method for Modern Analogue Technique models
print.predict.wa Predict from a weighted average model
print.residLen Squared residual length diagnostics
print.residuals.bootstrap.mat Bootstrap estimation and errors
print.residuals.mat Modern Analogue Technique transfer function models
print.roc ROC curve analysis
print.summary.analog Summarise analogue matching results
print.summary.bootstrap.mat Summarise bootstrap resampling for MAT models
print.summary.cma Summarise the extraction of close modern analogues
print.summary.logitreg Logistic regression models for assessing analogues/non-analogues
print.summary.mat Summarise Modern Analogue Technique models
print.summary.predict.mat Summarise MAT model predictions
print.summary.roc ROC curve analysis
print.tolerance Weighted averaging optima and tolerance ranges
print.wa Weighted averaging transfer functions

-- R --

reconPlot Stratigraphic plots of palaeoenvironmental reconstructions
reconPlot.default Stratigraphic plots of palaeoenvironmental reconstructions
reconPlot.predict.mat Stratigraphic plots of palaeoenvironmental reconstructions
reconPlot.predict.wa Stratigraphic plots of palaeoenvironmental reconstructions
resid.bootstrap.mat Bootstrap estimation and errors
resid.mat Modern Analogue Technique transfer function models
residLen Squared residual length diagnostics
residuals.bootstrap.mat Bootstrap estimation and errors
residuals.mat Modern Analogue Technique transfer function models
residuals.wa Weighted averaging transfer functions
rlgh Round Loch of Glenhead Diatoms
RMSEP Root mean square error of prediction
RMSEP.bootstrap.mat Root mean square error of prediction
RMSEP.bootstrap.wa Root mean square error of prediction
RMSEP.default Root mean square error of prediction
RMSEP.mat Root mean square error of prediction
roc ROC curve analysis
roc.analog ROC curve analysis
roc.default ROC curve analysis
roc.mat ROC curve analysis

-- S --

Salinity Imbrie and Kipp foraminifera training set
screeplot.bootstrap.mat Screeplots of model results
screeplot.mat Screeplots of model results
setK<- Extract and set the number of analogues
setK<-.default Extract and set the number of analogues
setK<-.mat Extract and set the number of analogues
sqrlLinear Squared residual length diagnostics
sqrlUnimodal Squared residual length diagnostics
stdError Standard error of MAT fitted and predicted values
stdError.mat Standard error of MAT fitted and predicted values
stdError.predict.mat Standard error of MAT fitted and predicted values
Stratiplot Palaeoecological stratigraphic diagrams
Stratiplot.default Palaeoecological stratigraphic diagrams
Stratiplot.formula 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.logitreg Logistic regression models for assessing analogues/non-analogues
summary.mat Summarise Modern Analogue Technique models
summary.predict.mat Summarise MAT model predictions
summary.roc ROC curve analysis
SumSST Imbrie and Kipp foraminifera training set
swapdiat SWAP sub-fossil diatom and pH training set
swappH SWAP sub-fossil diatom and pH training set

-- T --

tail.join Merge species data sets on common columns (species)
tolerance Weighted averaging optima and tolerance ranges
tolerance.default Weighted averaging optima and tolerance ranges
tran Common data transformations and standardizations
tran.default Common data transformations and standardizations
tran.formula Common data transformations and standardizations

-- V --

V12.122 Imbrie and Kipp foraminifera training set

-- W --

wa Weighted averaging transfer functions
wa.default Weighted averaging transfer functions
wa.formula Weighted averaging transfer functions
WinSST Imbrie and Kipp foraminifera training set