An R package for the analysis of Quaternary science data

Documentation for package ‘rioja’ version 0.5-5

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A B C D F H I M P R S W

-- --

rioja-package

Analysis of Quaternary Science Data

-- A --

aber	Abernethy Forest pollen data
addClustZone	Plot a stratigraphic diagram
addZone	Plot a stratigraphic diagram

-- B --

bstick.chclust

Constrained hierarchical clustering

-- C --

chclust	Constrained hierarchical clustering
coef.IKFA	Imbrie & Kipp Factor Analysis
coef.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
coef.WA	Weighted averaging (WA) regression and calibration
coef.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
communality	Imbrie & Kipp Factor Analysis
compare.datasets	Compare datasets for matching variables (species)
crossval	Palaeoecological transfer functions
crossval.default	Palaeoecological transfer functions
crossval.IKFA	Imbrie & Kipp Factor Analysis
crossval.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
crossval.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
crossval.WA	Weighted averaging (WA) regression and calibration
crossval.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration

-- D --

dot	Utility functions.
dot.data.frame	Utility functions.
dot.default	Utility functions.
dummy2factor	Utility functions.

-- F --

figCnvt	Graphic utilities.
fitted.IKFA	Imbrie & Kipp Factor Analysis
fitted.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
fitted.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
fitted.WA	Weighted averaging (WA) regression and calibration
fitted.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration

-- H --

Hill.N2	Utility functions.
hulls	Graphic utilities.

-- I --

IK	Imbrie and Kipp foraminifera data
IKFA	Imbrie & Kipp Factor Analysis
IKFA.fit	Imbrie & Kipp Factor Analysis
inkspot	Two-way ordered bubble plot of a species by sites data table
interp.dataset	Interpolate a dataset

-- M --

make.dummy	Utility functions.
MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
Merge	Merges two or more data frames on the basis of common column names.
MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
MLRC.fit	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces

-- P --

paldist	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
paldist2	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
performance	Palaeoecological transfer functions
performance.default	Palaeoecological transfer functions
performance.IKFA	Imbrie & Kipp Factor Analysis
performance.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
performance.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
performance.WA	Weighted averaging (WA) regression and calibration
performance.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
plot.chclust	Constrained hierarchical clustering
plot.compare.datasets	Compare datasets for matching variables (species)
plot.IKFA	Imbrie & Kipp Factor Analysis
plot.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
plot.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
plot.WA	Weighted averaging (WA) regression and calibration
plot.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
Ponds	Southeast England ponds and pools diatom and water chemistry dataset.
predict.IKFA	Imbrie & Kipp Factor Analysis
predict.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
predict.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
predict.WA	Weighted averaging (WA) regression and calibration
predict.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
print.C2	Imports results from a C2 model into R
print.IKFA	Imbrie & Kipp Factor Analysis
print.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
print.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
print.WA	Weighted averaging (WA) regression and calibration
print.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration

-- R --

rand.t.test	Palaeoecological transfer functions
rand.t.test.default	Palaeoecological transfer functions
rand.t.test.IKFA	Imbrie & Kipp Factor Analysis
rand.t.test.WA	Weighted averaging (WA) regression and calibration
rand.t.test.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
read.C2Model	Imports results from a C2 model into R
read.CEP	Reads and writes data in Cornell Ecology Program (CEP) format
read.Tilia	Read data in Tilia format
residuals.IKFA	Imbrie & Kipp Factor Analysis
residuals.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
residuals.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
residuals.WA	Weighted averaging (WA) regression and calibration
residuals.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
rioja	Analysis of Quaternary Science Data
RLGH	Diatom stratigraphic data from the Round Loch of Glenhead, Galloway, Southwest Scotland

-- S --

screeplot.IKFA	Imbrie & Kipp Factor Analysis
screeplot.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
screeplot.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
site.summ	Utility functions.
sp.plot	Plots species distributions along an environmental gradient
sp.plot.default	Plots species distributions along an environmental gradient
sp.plot.formula	Plots species distributions along an environmental gradient
sp.summ	Utility functions.
strat.plot	Plot a stratigraphic diagram
strat.plot.simple	Plot a simple stratigraphic diagram
summary.C2	Imports results from a C2 model into R
summary.IKFA	Imbrie & Kipp Factor Analysis
summary.MAT	Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
summary.MLRC	Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
summary.WA	Weighted averaging (WA) regression and calibration
summary.WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
SWAP	SWAP surface sediment diatom data and lake-water pH.

-- W --

WA	Weighted averaging (WA) regression and calibration
WA.fit	Weighted averaging (WA) regression and calibration
WAPLS	Weighted averaging partial least squares (WAPLS) regression and calibration
WAPLS.fit	Weighted averaging partial least squares (WAPLS) regression and calibration
write.CEP	Reads and writes data in Cornell Ecology Program (CEP) format
write.list.Excel	Utility functions.