provenance: Statistical Toolbox for Sedimentary Provenance Analysis
Version 1.7

Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov- Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances. Also included are tools to plot compositional data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.

AuthorPieter Vermeesch [aut, cre]
Date of publication2017-05-18 15:25:29 UTC
MaintainerPieter Vermeesch <p.vermeesch@ucl.ac.uk>
LicenseGPL-2
Version1.7
URL http://provenance.london-geochron.com
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("provenance")

Popular man pages

bray.diss: Bray-Curtis dissimilarity
diss: Calculate the dissimilarity matrix between two...
GPA: Generalised Procrustes Analysis of configurations
KS.diss: Kolmogorov-Smirnov dissimilarity
plot.ternary: Plot a ternary diagram
procrustes: Generalised Procrustes Analysis of provenance data
SH.diss: Sircombe and Hazelton distance
See all...

All man pages Function index File listing

Man pages

amalgamate: Group components of a composition
as.acomp: create an 'acomp' object
as.compositional: create a 'compositional' object
as.data.frame.compositional: create a 'data.frame' object
botev: Compute the optimal kernel bandwidth
bray.diss: Bray-Curtis dissimilarity
CLR: Centred logratio transformation
combine: Combine samples of distributional data
densities: A list of rock and mineral densities
diss: Calculate the dissimilarity matrix between two...
endmembers: Petrographic end-member compositions
get.f: Calculate the largest fraction that is likely to be missed
get.n: Calculate the number of grains required to achieve a desired...
get.p: Calculate the probability of missing a given population...
GPA: Generalised Procrustes Analysis of configurations
indscal: Individual Differences Scaling of provenance data
KDE: Create a kernel density estimate
KDEs: Generate an object of class 'KDEs'
KS.diss: Kolmogorov-Smirnov dissimilarity
Kuiper.diss: Kuiper dissimilarity
MDS: Multidimensional Scaling
minsorting: Assess settling equivalence of detrital components
Namib: An example dataset
PCA: Principal Component Analysis
plot.compositional: Plot a pie chart
plot.distributional: Plot continuous data as histograms or cumulative age...
plot.GPA: Plot a Procrustes configuration
plot.INDSCAL: Plot an INDSCAL group configuration and source weights
plot.KDE: Plot a kernel density estimate
plot.MDS: Plot an MDS configuration
plot.minsorting: Plot inferred grain size distributions
plot.PCA: Compositional biplot
plot.ternary: Plot a ternary diagram
procrustes: Generalised Procrustes Analysis of provenance data
provenance: Menu-based interface for 'provenance'
read.compositional: Read a .csv file with categorical data
read.densities: Read a .csv file with mineral and rock densities
read.distributional: Read a .csv file with continuous (detrital zircon) data
restore: Undo the effect of hydraulic sorting
SH.diss: Sircombe and Hazelton distance
subset.compositional: Get a subset of compositional data
subset.distributional: Get a subset of distributional data
summaryplot: Joint plot of several provenance datasets
ternary: Define a ternary composition

Functions

Abramson Source code
CLR Man page Source code
GPA Man page Source code
KDE Man page Source code
KDEs Man page Source code
KS.diss Man page Source code
Kuiper.diss Man page Source code
MDS Man page Source code
MDS.compositional Man page Source code
MDS.diss Man page Source code
MDS.distributional Man page Source code
Namib Man page
PCA Man page Source code
Rf Source code
SH.diss Man page Source code
_PACKAGE Man page
adapt.f Source code
amalgamate Man page Source code
amalgamate.SRDcorrected Man page Source code
amalgamate.compositional Man page Source code
amalgamate.default Man page Source code
annotation Source code
annotation.KDEs Source code
annotation.compositional Source code
annotation.default Source code
annotation.distributional Source code
appendList Source code
as.acomp Man page Source code
as.compositional Man page Source code
as.compositional.matrix Source code
as.data.frame.compositional Man page Source code
botev Man page Source code
bray.diss Man page Source code
checkdiss Source code
combine Man page Source code
commonbandwidth Source code
correct Source code
dct1d Source code
densities Man page
diss Man page Source code
diss.compositional Man page Source code
diss.distributional Man page Source code
emptyplot Source code
endmembers Man page
fixedpoint Source code
get.data.names Source code
get.densities Source code
get.f Man page Source code
get.n Man page Source code
get.p Man page Source code
getG Source code
getSS Source code
getc2 Source code
getdisslist Source code
gui.3way Source code
gui.SRD Source code
gui.amalgamate.components Source code
gui.combine.samples Source code
gui.get.dataset Source code
gui.get.datasets Source code
gui.get.kdes Source code
gui.help Source code
gui.load.densities Source code
gui.mds Source code
gui.minsorting Source code
gui.open.compositional Source code
gui.open.distributional Source code
gui.plot.multiple Source code
gui.plot.single Source code
gui.samplesize Source code
gui.save.plots Source code
gui.subset.components Source code
gui.subset.samples Source code
indscal Man page Source code
initConf Source code
initWeights Source code
lines.ternary Source code
minsorting Man page Source code
names.KDEs Source code
names.compositional Source code
names.distributional Source code
names.ternary Source code
ndim Source code
normDissN Source code
pilotdensity Source code
plot.GPA Man page Source code
plot.INDSCAL Man page Source code
plot.KDE Man page Source code
plot.KDEs Source code
plot.MDS Man page Source code
plot.PCA Man page Source code
plot.compositional Man page Source code
plot.distributional Man page Source code
plot.minsorting Man page Source code
plot.ternary Man page Source code
plotlines Source code
plotpath Source code
procfit Source code
procrustes Man page Source code
provenance Man page Man page Source code
provenance-package Man page Man page
read.compositional Man page Source code
read.densities Man page Source code
read.distributional Man page Source code
repList Source code
restore Man page Source code
restore.composition Source code
saveplot Source code
setmM Source code
sig2.con Source code
smacofIndDiff Source code
spp Source code
subset.compositional Man page Source code
subset.distributional Man page Source code
sumList Source code
sumcols Source code
sumlabels Source code
summaryplot Man page Source code
ternary Man page Source code
ternaryclosure Source code
torgerson Source code
tr Source code
xyz2xy Source code

Files

inst
inst/Trace.csv
inst/PT.csv
inst/CITATION
inst/DZ.csv
inst/endmembers.csv
inst/DZerr.csv
inst/Major.csv
inst/densities.csv
inst/PTHM.csv
inst/HM.csv
NAMESPACE
data
data/densities.rda
data/endmembers.rda
data/Namib.rda
R
R/botev.R
R/provenance.R
R/plot.R
R/indscal.R
R/minsorting.R
R/documentation.R
R/kde.R
R/srd.R
R/toolbox.R
R/gui.R
R/sircombe.R
MD5
DESCRIPTION
man
man/minsorting.Rd
man/provenance.Rd
man/ternary.Rd
man/Namib.Rd
man/combine.Rd
man/subset.distributional.Rd
man/KDEs.Rd
man/as.acomp.Rd
man/as.data.frame.compositional.Rd
man/plot.GPA.Rd
man/plot.MDS.Rd
man/plot.minsorting.Rd
man/bray.diss.Rd
man/SH.diss.Rd
man/Kuiper.diss.Rd
man/plot.compositional.Rd
man/get.p.Rd
man/CLR.Rd
man/diss.Rd
man/plot.ternary.Rd
man/densities.Rd
man/endmembers.Rd
man/indscal.Rd
man/botev.Rd
man/amalgamate.Rd
man/KDE.Rd
man/read.compositional.Rd
man/summaryplot.Rd
man/GPA.Rd
man/get.n.Rd
man/plot.PCA.Rd
man/read.densities.Rd
man/as.compositional.Rd
man/PCA.Rd
man/plot.distributional.Rd
man/plot.INDSCAL.Rd
man/get.f.Rd
man/restore.Rd
man/procrustes.Rd
man/MDS.Rd
man/read.distributional.Rd
man/KS.diss.Rd
man/subset.compositional.Rd
man/plot.KDE.Rd
provenance documentation built on May 19, 2017, 6:11 p.m.

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