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compositions (version 1.40-1)

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

9,116

Version

1.40-1

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

June 7th, 2014

Functions in compositions (1.40-1)

getdetectionlimit

Gets the detection limit stored in the data set
cor.acomp

Correlations of amounts and compositions
gsiplotmargin

Internal functions of the compositions package
ilrBase

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

Proportions of sand, silt and clay in sediments specimens
gsi.margin

Internal function: Compute a desired compositional margin
missingsummary

Classify and summarize missing values in a dataset
ConfRadius

Helper to compute confidence ellipsoids
lines

Draws connected lines from point to point.
ClamWest

Color-size compositions of 20 clam colonies from West Bay
ClusterFinder1

Heuristics to find subpopulations of outliers
pwlrPlot

Plots of pairwise logratio against a covariable.
cpt

Centered planar transform
compOKriging

Compositional Ordinary Kriging
Boxite

Compositions and depth of 25 specimens of boxite
SerumProtein

Serum Protein compositions of blood samples
gsi.eq

Internal function: Checking equality of IEEE special numbers
CoDaDendrogram

Dendrogram representation of acomp or rcomp objects
DiagnosticProb

Diagnostic probabilities
ClamEast

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

An auxiliary functions to compute user-defined ilr and ipt transforms.
kingTetrahedron

Ploting composition into rotable tetrahedron
AnimalVegetation

Animal and vegetation measurement
gof

Compositional Goodness of fit test
as.data.frame

Convert "compositions" classes to data frames
lrvgram

vgram2lrvgram
boxplot

Displaying compositions and amounts with box-plots
outlierclassifier

Detect and classify compositional outliers.
variation

Variation matrices of amounts and compositions
Coxite

Compositions, depths and porosities of 25 specimens of coxite
iit

Isometric identity transform
Bayesite

Permeabilities of bayesite
PogoJump

Honk Kong Pogo-Jumps Championship
ult

Uncentered log transform
rMahalanobis

Compute distributions of empirical Mahalanobis distances based on simulations
SkyeAFM

AFM compositions of 23 aphyric Skye lavas
segments

Draws straight lines from point to point.
endmemberCoordinates

Recast amounts as mixtures of end-members
aplus

Amounts analysed in log-scale
ArcticLake

Artic lake sediment samples of different water depth
Firework

Firework mixtures
Supervisor

Proportions of supervisor's statements assigned to different categories
simplemissingplot

Ternary diagrams
barplot.acomp

Bar charts of amounts
CompLinModCoReg

Compositional Linear Model of Coregionalisation
balance

Compute balances for a compositional dataset.
biplot3D

Three-dimensional biplots, based on package rgl
fitdirichlet

Fitting a Dirichlet distribution
axis3D

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

Count compositions
parametricMat

Unique parametrisations for matrices.
ccompgof

Compositional Goodness of fit test
gsiCoorInfo

Internal functions of the compositions package
groupparts

Group amounts of parts
Hongite

Compositions of 25 specimens of hongite
ilt

Isometric log transform
HouseholdExp

Household Expenditures
summary.aplus

Summaries of amounts
isoPortionLines

Isoportion- and Isoproportion-lines
gsi.isSingleRow

Internal function: Can something be considered as a single multivariate data item?
Activity31

Activity patterns of a statistician for 20 days
clr2ilr

Convert between clr and ilr, and between cpt and ipt.
HotellingsTsq

Hotellings T square distribution
gsicall

Internal functions of the compositions package
outlierplot

Plot various graphics to analyse outliers.
acomp

Aitchison compositions
gsi.plain

Internal function: Convert to plain vector or matrix
ilr

Isometric log ratio transform
Kongite

Compositions of 25 specimens of kongite
Yatquat

Yatquat fruit evaluation
gsi.addclass

Internal function: give a derived subclass to an object
alr

Additive log ratio transform
compositions-package

library(compositions)
acomparith

Power transform in the simplex
dist

Distances in variouse approaches
ellipses

Draw ellipses
ShiftOperators

Shifts of machine operators
gsi.expandrcomp

Internal function: Scaling rcomp
gsi.mapin01

Internal functions: Storing integers as reals
WhiteCells

White-cell composition of 30 blood samples by two different methods
gsi.svdsolve

Internal function: Solves singular and non square equation systems
rpois

Simulate count compositions without overdispersion
ternaryAxis

Axis for ternary diagrams
fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model
gsiinternal3

Internal functions of the compositions package
oneOrDataset

Treating single compositions as one-row datasets
Glacial

Compositions and total pebble counts of 92 glacial tills
Metabolites

Steroid metabolite patterns in adults and children
SimulatedAmounts

Simulated amount datasets
R2

R square
meanrow

The arithmetic mean of rows or columns
aplusarithm

vectorial arithmetic for data sets with aplus class
Blood23

Blood samples
colorsForOutliers

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

The geometric mean
pairwiseplot

Creates a paneled plot like pairs for two different datasets.
gausstest

Classical Gauss Test
coloredBiplot

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

The policy of treatment of missing values in the "compositions" package
MahalanobisDist

Compute Mahalanobis distances based von robust Estimations
cdt

Centered default transform
rmultarithm

vectorial arithmetic for datasets in a classical vector scale
gsi.merge2signary

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

Interal function: Get number of samples and number of parts in a compositional object
gsi.add

Internal functions: Parallel operations of single and multiple datasets
gsi.diagExtract

Internal functions: Get the diagonal of a matrix
clo

Closure of a composition
gsi.recode

Internal function: Recode missings with IEEE number and vice versa
gsi.PrinBal

The canonical basis in the clr plane used for ilr and ipt transforms.
transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes
gsiinternal1

Internal functions of the compositions package
Hydrochem

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

Empirical variograms for compositions
gsi.simshape

Internal function: Reshape an object to the shape type of another
arrows3D

arrows in 3D, based on package rgl
idt

Isometric default transform
plot3Drmult

plot in 3D based on rgl
gsi.textpanel

Internal function: A panel displaying a label only
mix.Read

Reads a data file in a mixR format
ipt

Isometric planar transform
gsi2.invperm

Internal function: Invert a permutation
gsi.eps

Internal variable: Negligible differences
gsi.drop

Internal functions: A conditional drop
princomp.rplus

Principal component analysis for real amounts
plotmissingsummary

Plot a Missing Summary
jura

The jura dataset
print.acomp

Printing compositional data.
gsiinternal

Environment containing the old gsi functions
matmult

inner product for matrices and vectors
plot3Daplus

3D-plot of positive data
plot.aplus

Displaying amounts in scatterplots
powerofpsdmatrix

power transform of a matrix
princomp.acomp

Principal component analysis for Aitchison compositions
outliersInCompositions

Analysing outliers in compositions.
perturbe

Perturbation of compositions
princomp.rcomp

Principal component analysis for real compositions
princomp.rmult

Principal component analysis for real data
scale

Normalizing datasets by centering and scaling
scalar

Parallel scalar products
princomp.aplus

Principal component analysis for amounts in log geometry
ratioLoadings

Loadings of relations of two amounts
plot3D

plot in 3D based on rgl
runif

The uniform distribution on the simplex
clr

Centered log ratio transform
simulatemissings

Artifical simulation of various kinds of missings/polluted data
rcomp

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

Splitting datasets in groups given by factors
mean.acomp

Mean amounts and mean compositions
gsi.csum

Internal function: row and column sums of matrices
tryDebugger

Empirical variograms for compositions
varmlm

Residual variance of a model
Read standard data files

Reads a data file in a geoeas format
rmult

Simple treatment of real vectors
robustnessInCompositions

Handling robustness issues and outliers in compositions.
gsi.diagGenerate

Internal functions: Generate a diagonal matrix
acompmargin

Marginal compositions in Aitchison Compositions
plot.acomp

Ternary diagrams
rcompmargin

Marginal compositions in real geometry
acompscalarproduct

inner product for datasets with a vector space structure
rcomparithm

Arithmetic operations for compositions in a real geometry
NormalTests

Compositional Goodness of fit test
replot

Modify parameters of compositional plots.
rnorm

Normal distributions on special spaces
var.acomp

Variances and covariances of amounts and compositions
summary.acomp

Summarizing a compositional dataset in terms of ratios
variograms

Variogram functions
IsMahalanobisOutlier

Checking for outliers
plot3Drplus

plot in 3D based on rgl
rAitchison

Aitchison Distribution
names

The names of the parts
vcovAcomp

Variance covariance matrix of parameters in compositional regression
straight

Draws straight lines.
mvar

Metric summary statistics of real, amount or compositional data
rplusarithm

vectorial arithmetic for data sets with rplus class
norm

Vector space norm
normalize

Normalize vectors to norm 1
missingProjector

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

inner product for datasets with vector scale
totals

Total sum of amounts
rplus

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

Empirical variograms for compositions
vgmFit

Compositional variogram model fitting
summary.rcomp

Summary of compositions in real geometry
rlnorm

The multivariate lognormal distribution
zeroreplace

Zero-replacement routine
is.acomp

Check for compositional data type
Activity10

Activity patterns of a statistician for 20 days
Skulls

Measurement of skulls
gsipairs

Internal functions of the compositions package
gsi.varwithlosts

Internal function: computes variance of compositional data set with missing/zero values
plot3Dacomp

3D-plot of compositional data
rDirichlet

Dirichlet distribution
gsiinternal2

Internal functions of the compositions package
binary

Treating binary and g-adic numbers
qqnorm

Normal quantile plots for compositions and amounts
sumprojector

Compute the global projector to the observed subspace.
gsireset3D

Internal functions of the compositions package
apt

Additive planar transform
gsifiltercall

Calling from a function with the own parameters