R: Analysis of Quaternary Science Data

# Analysis of Quaternary Science Data

## Documentation for package ‘rioja’ version 1.0-7

- DESCRIPTION file

## Help Pages

A B C D F H I L 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 | Constrained hierarchical clustering
bstick.chclust | Constrained hierarchical clustering

## -- C --

chclust | Constrained hierarchical clustering
coef.IKFA | Imbrie & Kipp Factor Analysis
coef.LWR | Weighted averaging (LWR) regression and calibration
coef.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
coef.MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
coef.MR | Multiple regression
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.LWR | Weighted averaging (LWR) regression and calibration
crossval.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
crossval.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
crossval.MR | Multiple regression
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.LWR | Weighted averaging (LWR) regression and calibration
fitted.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
fitted.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
fitted.MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
fitted.MR | Multiple regression
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

## -- L --

LWR | Weighted averaging (LWR) regression and calibration
LWR.fit | Weighted averaging (LWR) regression and calibration

## -- 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
MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
MLRC2.fit | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
MR | Multiple regression
MR.fit | Multiple regression

## -- 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.LWR | Weighted averaging (LWR) regression and calibration
performance.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
performance.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
performance.MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
performance.MR | Multiple regression
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.LWR | Weighted averaging (LWR) regression and calibration
plot.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
plot.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
plot.MR | Multiple regression
plot.randomPTF | Random transfer functions to calculate variable importance
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.LWR | Weighted averaging (LWR) regression and calibration
predict.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
predict.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
predict.MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
predict.MR | Multiple regression
predict.WA | Weighted averaging (WA) regression and calibration
predict.WAPLS | Weighted averaging partial least squares (WAPLS) regression and calibration
print.IKFA | Imbrie & Kipp Factor Analysis
print.LWR | Weighted averaging (LWR) regression and calibration
print.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
print.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
print.MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
print.MR | Multiple regression
print.randomPTF | Random transfer functions to calculate variable importance
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
randomPTF | Random transfer functions to calculate variable importance
residuals.IKFA | Imbrie & Kipp Factor Analysis
residuals.LWR | Weighted averaging (LWR) regression and calibration
residuals.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
residuals.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
residuals.MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
residuals.MR | Multiple regression
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.summ | Utility functions.
strat.plot | Plot a stratigraphic diagram
summary.IKFA | Imbrie & Kipp Factor Analysis
summary.LWR | Weighted averaging (LWR) regression and calibration
summary.MAT | Palaeoenvironmental reconstruction using the Modern Analogue Technique (MAT)
summary.MLRC | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
summary.MLRC2 | Palaeoenvironmental reconstruction using Maximum Likelihood Response Surfaces
summary.MR | Multiple regression
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