Compositional Data Analysis

Aar | Composition of glaciar sediments from the Aar massif... |

acomp | Aitchison compositions |

acomparith | Power transform in the simplex |

acomp-class | Class '"acomp"' |

acompmargin | Marginal compositions in Aitchison Compositions |

Activity10 | Activity patterns of a statistician for 20 days |

Activity31 | Activity patterns of a statistician for 20 days |

alr | Additive log ratio transform |

amounts-class | Class '"amounts"' |

AnimalVegetation | Animal and vegetation measurement |

aplus | Amounts analysed in log-scale |

aplusarithm | vectorial arithmetic for data sets with aplus class |

aplus-class | Class '"aplus"' |

apt | Additive planar transform |

ArcticLake | Artic lake sediment samples of different water depth |

arrows3d | arrows in 3D, based on package rgl |

asdataframe | Convert "compositions" classes to data frames or matrices |

axis3d | Drawing a 3D coordiante system to a plot, based on package... |

backtransform | Automatic common backtransformation for compositions |

balancebase | Compute balances for a compositional dataset. |

barplot | Bar charts of amounts |

Bayesite | Permeabilities of bayesite |

binary | Treating binary and g-adic numbers |

biplot3d | Three-dimensional biplots, based on package rgl |

Blood23 | Blood samples |

Boxite | Compositions and depth of 25 specimens of boxite |

boxplot | Displaying compositions and amounts with box-plots |

ccomp | Count compositions |

ccomp-class | Class '"ccomp"' |

ccompgof | Compositional Goodness of fit test |

cdt | Centered default transform |

ClamEast | Color-size compositions of 20 clam colonies from East Bay |

ClamWest | Color-size compositions of 20 clam colonies from West Bay |

clo | Closure of a composition |

clr | Centered log ratio transform |

clr2ilr | Convert between clr and ilr, and between cpt and ipt. |

clusterfinder | Heuristics to find subpopulations of outliers |

codadendrogram | Dendrogram representation of acomp or rcomp objects |

coloredbiplot | A biplot providing somewhat easier access to details of the... |

colorsforoutliers | Create a color/char palette or for groups of outliers |

CompLinModCo | Compositional Linear Model of Coregionalisation |

compmiss | The policy of treatment of missing values in the... |

compOKriging | Compositional Ordinary Kriging |

compositional-class | Class '"compositional"' |

compositions | Compositional Data Analysis |

ConfRadius | Helper to compute confidence ellipsoids |

cor | Correlations of amounts and compositions |

Coxite | Compositions, depths and porosities of 25 specimens of coxite |

cpt | Centered planar transform |

DiagnosticProb | Diagnostic probabilities |

dist | Distances in variouse approaches |

ellipses | Draw ellipses |

endmemberCoordinates | Recast amounts as mixtures of end-members |

Firework | Firework mixtures |

fitdirichlet | Fitting a Dirichlet distribution |

fitsamemean | Fit Same Mean Different Variance Model |

gausstest | Classical Gauss Test |

geometricmean | The geometric mean |

getdetectionlimit | Gets the detection limit stored in the data set |

Glacial | Compositions and total pebble counts of 92 glacial tills |

goftests | Compositional Goodness of fit test |

groupparts | Group amounts of parts |

gsiadd | Internal functions: Parallel operations of single and... |

gsiaddclass | Internal function: give a derived subclass to an object |

gsicall | Internal functions of the compositions package |

gsiclosespread | Internal functions of the compositions package |

gsicoorinfo | Internal functions of the compositions package |

gsicsum | Internal function: row and column sums of matrices |

gsidiagExtract | Internal functions: Get the diagonal of a matrix |

gsidiagGenerate | Internal functions: Generate a diagonal matrix |

gsidrop | Internal functions: A conditional drop |

gsieq | Internal function: Checking equality of IEEE special numbers |

gsiexpandrcomp | Internal function: Scaling rcomp |

gsifiltercall | Calling from a function with the own parameters |

gsigetbalstruct | An auxiliary functions to compute user-defined ilr and ipt... |

gsigetD | Interal function: Get number of samples and number of parts... |

gsiinternal | Environment containing the old gsi functions |

gsiinvperm | Internal function: Invert a permutation |

gsiisSingleRow | Internal function: Can something be considered as a single... |

gsimap01 | Internal functions: Storing integers as reals |

gsimargin | Internal function: Compute a desired compositional margin |

gsimerge2signary | Auxiliary functions to compute user-defined ilr and ipt... |

gsipairrelativeMatrix | Internal functions of the compositions package |

gsipairs | Internal functions of the compositions package |

gsiplain | Internal function: Convert to plain vector or matrix |

gsiplotmargin | Internal functions of the compositions package |

gsiPrinBal | The canonical basis in the clr plane used for ilr and ipt... |

gsirecode | Internal function: Recode missings with IEEE number and vice... |

gsireset3d | Internal functions of the compositions package |

gsisimshape | Internal function: Reshape an object to the shape type of... |

gsispreadToIsoSpace | Internal functions of the compositions package |

gsisvdsolve | Internal function: Solves singular and non square equation... |

gsitextpanel | Internal function: A panel displaying a label only |

gsivarwithlosts | Internal function: computes variance of compositional data... |

Hongite | Compositions of 25 specimens of hongite |

HotellingsTsq | Hotellings T square distribution |

HouseholdExp | Household Expenditures |

Hydrochem | Hydrochemical composition data set of Llobregat river basin... |

idt | Isometric default transform |

iit | Isometric identity transform |

ilr | Isometric log ratio transform |

ilrBase | The canonical basis in the clr plane used for ilr and ipt... |

ilt | Isometric log transform |

ipt | Isometric planar transform |

isAcomp | Check for compositional data type |

ismahalanobisoutlier | Checking for outliers |

isoportion | Isoportion- and Isoproportion-lines |

jura | The jura dataset |

kdeDirichlet | Density estimation on the simplex with Dirichlet kernel |

kingtetrahedron | Ploting composition into rotable tetrahedron |

Kongite | Compositions of 25 specimens of kongite |

lines | Draws connected lines from point to point. |

logratioVariogram | Empirical variograms for compositions |

lrvgram | vgram2lrvgram |

mahalanobisdist | Compute Mahalanobis distances based von robust Estimations |

matmult | inner product for matrices and vectors |

matmultacomp | inner product for datasets with a vector space structure |

meanAcomp | Mean amounts and mean compositions |

meanrow | The arithmetic mean of rows or columns |

Metabolites | Steroid metabolite patterns in adults and children |

missingProjector | Returns a projector the the observed space in case of... |

missingsummary | Classify and summarize missing values in a dataset |

mix2compositions | Transformations from 'mixtures' to 'compositions' classes |

mixRead | Reads a data file in a mixR format |

mvar | Metric summary statistics of real, amount or compositional... |

names | The names of the parts |

norm | Vector space norm |

normalize | Normalize vectors to norm 1 |

oneOrDataset | Treating single compositions as one-row datasets |

outlierclassifier | Detect and classify compositional outliers. |

outlierplot | Plot various graphics to analyse outliers. |

outliers | Analysing outliers in compositions. |

pairwisePlot | Creates a paneled plot like pairs for two different datasets. |

panelAcomp | Pairs plot method for compositions |

parametricMat | Unique parametrisations for matrices. |

perturbe | Perturbation of compositions |

plot | Ternary diagrams |

plot3d | plot in 3D based on rgl |

plot3dacomp | 3D-plot of compositional data |

plot3daplus | 3D-plot of positive data |

plot3drmult | plot in 3D based on rgl |

plot3drplus | plot in 3D based on rgl |

plotlogratioVariogram | Empirical variograms for compositions |

plotmissingsummary | Plot a Missing Summary |

plotpos | Displaying amounts in scatterplots |

PogoJump | Honk Kong Pogo-Jumps Championship |

powerofmatrix | power transform of a matrix |

princompacomp | Principal component analysis for Aitchison compositions |

princompaplus | Principal component analysis for amounts in log geometry |

princomprcomp | Principal component analysis for real compositions |

princomprmult | Principal component analysis for real data |

princomprplus | Principal component analysis for real amounts |

Printing compositional data. | |

pwlr | Pairwise log ratio transform |

pwlrPlot | Plots of pairwise logratio against a covariable. |

qqnorm | Normal quantile plots for compositions and amounts |

R2 | R square |

raitchison | Aitchison Distribution |

ratioLoadings | Loadings of relations of two amounts |

rcomp | Compositions as elements of the simplex embedded in the... |

rcomparithm | Arithmetic operations for compositions in a real geometry |

rcomp-class | Class '"rcomp"' |

rcompmargin | Marginal compositions in real geometry |

rDirichlet | Dirichlet distribution |

readgeoeas | Reads a data file in a geoeas format |

replot | Modify parameters of compositional plots. |

rlnorm | The multivariate lognormal distribution |

rmahalanobis | Compute distributions of empirical Mahalanobis distances... |

rmult | Simple treatment of real vectors |

rmultarithm | vectorial arithmetic for datasets in a classical vector scale |

rmult-class | Class '"rmult"' |

rmultmatmult | inner product for datasets with vector scale |

rnorm | Normal distributions on special spaces |

robustness | Handling robustness issues and outliers in compositions. |

rplus | Amounts i.e. positive numbers analysed as objects of the real... |

rplusarithm | vectorial arithmetic for data sets with rplus class |

rplus-class | Class '"rplus"' |

rpois | Simulate count compositions without overdispersion |

runif | The uniform distribution on the simplex |

scalar | Parallel scalar products |

scale | Normalizing datasets by centering and scaling |

Sediments | Proportions of sand, silt and clay in sediments specimens |

segments | Draws straight lines from point to point. |

SerumProtein | Serum Protein compositions of blood samples |

ShiftOperators | Shifts of machine operators |

simplemissingplot | Ternary diagrams |

SimulatedAmounts | Simulated amount datasets |

simulatemissing | Artifical simulation of various kinds of missings/polluted... |

Skulls | Measurement of skulls |

SkyeAFM | AFM compositions of 23 aphyric Skye lavas |

split | Splitting datasets in groups given by factors |

straight | Draws straight lines. |

subsetting | Subsetting of compositions |

summaryAcomp | Summarizing a compositional dataset in terms of ratios |

summaryAplus | Summaries of amounts |

summaryRcomp | Summary of compositions in real geometry |

sumprojector | Compute the global projector to the observed subspace. |

Supervisor | Proportions of supervisor's statements assigned to different... |

ternaryAxis | Axis for ternary diagrams |

tests | Compositional Goodness of fit test |

totals | Total sum of amounts |

tryDebugger | Empirical variograms for compositions |

ult | Uncentered log transform |

varAcomp | Variances and covariances of amounts and compositions |

variation | Variation matrices of amounts and compositions |

variograms | Variogram functions |

varmlm | Residual variance of a model |

vcovAcomp | Variance covariance matrix of parameters in compositional... |

vgmFit | Compositional variogram model fitting |

WhiteCells | White-cell composition of 30 blood samples by two different... |

wrapped_functions | Standard R functions wrapped for compatibility |

Yatquat | Yatquat fruit evaluation |

zeroreplace | Zero-replacement routine |

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