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provenance (version 0.6)

Statistical Toolbox for Sedimentary Provenance Analysis

Description

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.

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Version

Install

install.packages('provenance')

Monthly Downloads

207

Version

0.6

License

GPL-2

Maintainer

Pieter Vermeesch

Last Published

September 21st, 2015

Functions in provenance (0.6)

as.data.frame.compositional

create a data.frame object
plot.minsorting

Plot inferred grain size distributions
plot.ternary

Plot a ternary diagram
get.n

Calculate the number of grains required to achieve a desired level of sampling resolution
KDE

Create a kernel density estimate
subset.distributional

Get a subset of distributional data
Namib

An example dataset
provenance

library(provenance)
plot.KDE

#' Plot a kernel density estimate
read.densities

Read a .csv file with mineral and rock densities
CLR

Centred logratio transformation
plot.MDS

Plot an MDS configuration
plot.PCA

Compositional biplot
endmembers

Petrographic end-member compositions
as.acomp

create an acomp object
subset.compositional

Get a subset of compositional data
KDEs

Generate an object of class KDEs
bray.diss

Bray-Curtis dissimilarity
botev

Compute the optimal kernel bandwidth
get.f

Calculate the largest fraction that is likely to be missed
PCA

Principal Component Analysis
ternary

Define a ternary composition
as.compositional

create a compositional object
plot.GPA

Plot a Procrustes configuration
SH.diss

Sircombe and Hazelton distance
get.p

Calculate the probability of missing a given population fraction
plot.distributional

Plot continuous data as histograms or cumulative age distributions
indscal

Individual Differences Scaling of provenance data
procrustes

Generalised Procrustes Analysis (GPA)
plot.compositional

Plot a pie chart
plot.INDSCAL

Plot an INDSCAL group configuration and source weights
MDS

Multidimensional Scaling
amalgamate

Group components of a composition
read.distributional

Read a .csv file with continuous (detrital zircon) data
read.compositional

Read a .csv file with categorical data
KS.diss

Kolmogorov-Smirnov dissimilarity
summaryplot

Joint plot of several provenance datasets
diss

Calculate the dissimilarity matrix between two distributional or compositional datasets
restore

Undo the effect of hydraulic sorting
densities

A list of rock and mineral densities
minsorting

Assess settling equivalence of detrital components