# provenance: Statistical Toolbox for Sedimentary Provenance Analysis

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

## Man pages

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