provenance: Statistical Toolbox for Sedimentary Provenance Analysis

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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 dissimilarity and Sircombe-Hazelton L2-norm. 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.

Author
Pieter Vermeesch [aut, cre]
Date of publication
2016-04-22 08:40:10
Maintainer
Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
License
GPL-2
Version
1.5

View on CRAN

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
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

Files in this package

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