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compositions (version 1.30-1)

Compositional Data Analysis

Description

The package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by Aitchison and Pawlowsky-Glahn.

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Version

Install

install.packages('compositions')

Monthly Downloads

30,396

Version

1.30-1

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

April 12th, 2013

Functions in compositions (1.30-1)

Coxite

Compositions, depths and porosities of 25 specimens of coxite
arrows3D

arrows in 3D, based on package rgl
Bayesite

Permeabilities of bayesite
Skulls

Measurement of skulls
gsi.diagExtract

Internal functions: Get the diagonal of a matrix
ellipses

Draw ellipses
geometricmean

The geometric mean
Boxite

Compositions and depth of 25 specimens of boxite
DiagnosticProb

Diagnostic probabilities
Hydrochem

Hydrochemical composition data set of Llobregat river basin water (NE Spain)
Glacial

Compositions and total pebble counts of 92 glacial tills
Yatquat

Yatquat fruit evaluation
Sediments

Proportions of sand, silt and clay in sediments specimens
SkyeAFM

AFM compositions of 23 aphyric Skye lavas
gsi.textpanel

Internal function: A panel displaying a label only
alr

Additive log ratio transform
apt

Additive planar transform
gsi.drop

Internal functions: A conditional drop
gsiinternal

Environment containing the the old gsi functions
ClamEast

Color-size compositions of 20 clam colonies from East Bay
acomp

Aitchison compositions
SimulatedAmounts

Simulated amount datasets
gsi.varwithlosts

Internal function: computes variance of compositional data set with missing/zero values
gsi.addclass

Internal function: give a derived subclass to an object
Firework

Firework mixtures
gsireset3D

Internal functions of the compositions package
gsi.add

Internal functions: Parallel operations of single and multiple datasets
endmemberCoordinates

Recast amounts as mixtures of end-members
aplus

Amounts analysed in log-scale
gsi.simshape

Internal function: Reshape an object to the shape type of another
axis3D

Drawing a 3D coordiante system to a plot, based on package rgl
colorsForOutliers

Create a color/char palette or for groups of outliers
jura

The jura dataset
PogoJump

Honk Kong Pogo-Jumps Championship
ClamWest

Color-size compositions of 20 clam colonies from West Bay
ShiftOperators

Shifts of machine operators
CompLinModCoReg

Compositional Linear Model of Coregionalisation
barplot.acomp

Bar charts of amounts
SerumProtein

Serum Protein compositions of blood samples
ArcticLake

Artic lake sediment samples of different water depth
lines

Draws connected lines from point to point.
is.acomp

Check for compositional data type
ilrBase

The canonical basis in the clr plane used for ilr and ipt transforms.
cor.acomp

Correlations of amounts and compositions
gsicall

Internal functions of the compositions package
ClusterFinder1

Heuristics to find subpopulations of outliers
idt

Isometric default transform
ilt

Isometric log transform
IsMahalanobisOutlier

Checking for outliers
balance

Compute balances for a compositional dataset.
AnimalVegetation

Animal and vegetation measurement
WhiteCells

White-cell composition of 30 blood samples by two different methods
outlierclassifier

Detect and classify compositional outliers.
coloredBiplot

A biplot providing somewhat easier access to details of the plot.
fitdirichlet

Fitting a Dirichlet distribution
biplot3D

Three-dimensional biplots, based on package rgl
gsi.recode

Internal function: Recode missings with IEEE number and vice versa
princomp.rcomp

Principal component analysis for real compositions
gausstest

Classical Gauss Test
lrvgram

vgram2lrvgram
mean.acomp

Mean amounts and mean compositions
plot.acomp

Ternary diagrams
ConfRadius

Helper to compute confidence ellipsoids
plotmissingsummary

Plot a Missing Summary
princomp.rplus

Principal component analysis for real amounts
gsi.mapin01

Internal functions: Storing integers as reals
gsiinternal3

Internal functions of the compositions package
vcovAcomp

Variance covariance matrix of parameters in compositional regression
Hongite

Compositions of 25 specimens of hongite
Blood23

Blood samples
acomparith

Power transform in the simplex
gsi2.invperm

Internal function: Invert a permutation
missing.compositions

The policy of treatment of missing values in the "compositions" package
as.data.frame

Convert "compositions" classes to data frames
scale

Normalizing datasets by centering and scaling
groupparts

Group amounts of parts
gsiinternal1

Internal functions of the compositions package
fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model
ccomp

Count compositions
powerofpsdmatrix

power transform of a matrix
rmultarithm

vectorial arithmetic for datasets in a classical vector scale
replot

Modify parameters of compositional plots.
clr2ilr

Convert between clr and ilr, and between cpt and ipt.
compositions-package

library(compositions)
plot3Dacomp

3D-plot of compositional data
Activity31

Activity patterns of a statistician for 20 days
HotellingsTsq

Hotellings T square distribution
rlnorm

The multivariate lognormal distribution
norm

Vector space norm
cdt

Centered default transform
gsiCoorInfo

Internal functions of the compositions package
gof

Compositional Goodness of fit test
gsiinternal2

Internal functions of the compositions package
gsi.margin

Internal function: Compute a desired compositional margin
CoDaDendrogram

Dendrogram representation of acomp or rcomp objects
gsi.isSingleRow

Internal function: Can something be considered as a single multivariate data item?
rnorm

Normal distributions on special spaces
pwlrPlot

Plots of pairwise logratio against a covariable.
oneOrDataset

Treating single compositions as one-row datasets
binary

Treating binary and g-adic numbers
Read standard data files

Reads a data file in a geoeas format
segments

Draws straight lines from point to point.
clo

Closure of a composition
missingProjector

Returns a projector the the observed space in case of missings.
logratioVariogram

Empirical variograms for compositions
kingTetrahedron

Ploting composition into rotable tetrahedron
perturbe

Perturbation of compositions
qqnorm

Normal quantile plots for compositions and amounts
gsi.eps

Internal variable: Negligible differences
HouseholdExp

Household Expenditures
meanrow

The arithmetic mean of rows or columns
normalize

Normalize vectors to norm 1
princomp.acomp

Principal component analysis for Aitchison compositions
acompmargin

Marginal compositions in Aitchison Compositions
robustnessInCompositions

Handling robustness issues and outliers in compositions.
matmult

inner product for matrices and vectors
pairwiseplot

Creates a paneled plot like pairs for two different datasets.
var.acomp

Variances and covariances of amounts and compositions
getdetectionlimit

Gets the detection limit stored in the data set
gsi.diagGenerate

Internal functions: Generate a diagonal matrix
boxplot

Displaying compositions and amounts with box-plots
rpois

Simulate count compositions without overdispersion
ilr

Isometric log ratio transform
Kongite

Compositions of 25 specimens of kongite
ratioLoadings

Loadings of relations of two amounts
outliersInCompositions

Analysing outliers in compositions.
iit

Isometric identity transform
gsi.plain

Internal function: Convert to plain vector or matrix
missingsummary

Classify and summarize missing values in a dataset
compOKriging

Compositional Ordinary Kriging
gsigetBalStruct

An Auxiliary functions to compute user-defined ilr and ipt transforms.
Supervisor

Proportions of supervisor's statements assigned to different categories
ccompgof

Compositional Goodness of fit test
gsi.eq

Internal function: Checking equality of IEEE special numbers
gsi.getD

Interal function: Get number of samples and number of parts in a compositional object
plot3Daplus

3D-plot of positive data
gsi.expandrcomp

Internal function: Scaling rcomp
princomp.rmult

Principal component analysis for real data
gsiplotmargin

Internal functions of the compositions package
mvar

Metric summary statistics of real, amount or compositional data
rplus

Amounts i.e. positive numbers analysed as objects of the real vector space
rDirichlet

Dirichlet distribution
NormalTests

Compositional Goodness of fit test
isoPortionLines

Isoportion- and Isoproportion-lines
rAitchison

Aitchison Distribution
gsipairs

Internal functions of the compositions package
rcompmargin

Marginal compositions in real geometry
aplusarithm

vectorial arithmetic for data sets with aplus class
rMahalanobis

Compute distributions of empirical Mahalanobis distances based on simulations
tryDebugger

Empirical variograms for compositions
acompscalarproduct

inner product for datasets with a vector space structure
parametricMat

Unique parametrisations for matrices.
summary.rcomp

Summary of compositions in real geometry
transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes
rmult

Simple treatment of real vectors
gsi.merge2signary

Auxiliary functions to compute user-defined ilr and ipt transforms.
names

The names of the parts
MahalanobisDist

Compute Mahalanobis distances based von robust Estimations
plot3Drmult

plot in 3D based on rgl
clr

Centered log ratio transform
outlierplot

Plot various graphics to analyse outliers.
totals

Total sum of amounts
summary.acomp

Summarizing a compositional dataset in terms of ratios
ult

Uncentered log transform
plotlogratioVariogram

Empirical variograms for compositions
simplemissingplot

Ternary diagrams
runif

The uniform distribution on the simplex
gsifiltercall

Calling from a function with the own parameters
ipt

Isometric planar transform
plot.aplus

Displaying amounts in scatterplots
zeroreplace

Zero-replacement routine
scalar

Parallel scalar products
rcomparithm

Arithmetic operations for compositions in a real geometry
print.acomp

Printing compositional data.
plot3Drplus

plot in 3D based on rgl
variograms

Variogram functions
straight

Draws straight lines.
simulatemissings

Artifical simulation of various kinds of missings
split

Splitting datasets in groups given by factors
mix.Read

Reads a data file in a mixR format
vgmFit

Compositional variogram model fitting
princomp.aplus

Principal component analysis for amounts in log geometry
rcomp

Compositions as elements of the simplex embedded in the D-dimensional real space
plot3D

plot in 3D based on rgl
varmlm

Residual variance of a model
sumprojector

Compute the global projector to the observed subspace.
variation

Variation matrices of amounts and compositions
rmultmatmult

inner product for datasets with vector scale
Activity10

Activity patterns of a statistician for 20 days
Metabolites

Steroid metabolite patterns in adults and children
R2

R square
dist

Distances in variouse approaches
cpt

Centered planar transform
gsi.csum

Internal function: row and column sums of matrices
gsi.svdsolve

Internal function: Solves singular and non square equation systems
rplusarithm

vectorial arithmetic for data sets with rplus class
summary.aplus

Summaries of amounts
ternaryAxis

Axis for ternary diagrams