robCompositions
Compositional Data Analysis
Methods for analysis of compositional data including robust
methods (
Robust Methods for Compositional Data
using robCompositions
data(expenditures)
p1 <- pcaCoDa(expenditures)
plot(p1)
What is it?
- Imputation of compositional data including robust methods, methods to impute rounded zeros
- Outlier detection for compositional data using robust methods
- Principal component analysis for compositional data using robust methods
- Factor analysis for compositional data using robust methods
- Discriminant analysis for compositional data (Fisher rule) using robust methods
- Robust regression with compositional predictors
- Anderson-Darling normality tests for compositional data
- log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations).
- In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.
Goals
- never use classical statistical methods on raw compositional data again.
Getting Started
The package has dependencies on
R (>= 2.10), utils, robustbase, rrcov, car (>= 2.0-0), MASS, pls
Installation
Installion of robCompositions is really easy for registered users (when the R-tools are installed). Just use
library(devtools)
install_github("robCompositions", "matthias-da")
Examples
k nearest neighbor imputation
data(expenditures)
expenditures[1,3]
expenditures[1,3] <- NA
impKNNa(expenditures)$xImp[1,3]
iterative model based imputation
data(expenditures)
x <- expenditures
x[1,3]
x[1,3] <- NA
xi <- impCoda(x)$xImp
xi[1,3]
s1 <- sum(x[1,-3])
impS <- sum(xi[1,-3])
xi[,3] * s1/impS
xi <- impKNNa(expenditures)
xi
summary(xi)
plot(xi, which=1)
plot(xi, which=2)
plot(xi, which=3)
pca
data(expenditures)
p1 <- pcaCoDa(expenditures)
p1
plot(p1)
outlier detection
data(expenditures)
oD <- outCoDa(expenditures)
oD
plot(oD)
transformations
data(arcticLake)
x <- arcticLake
x.alr <- addLR(x, 2)
y <- addLRinv(x.alr)
addLRinv(addLR(x, 3))
data(expenditures)
x <- expenditures
y <- addLRinv(addLR(x, 5))
head(x)
head(y)
addLRinv(x.alr, ivar=2, useClassInfo=FALSE)
data(expenditures)
eclr <- cenLR(expenditures)
inveclr <- cenLRinv(eclr)
head(expenditures)
head(inveclr)
head(cenLRinv(eclr$x.clr))
require(MASS)
Sigma <- matrix(c(5.05,4.95,4.95,5.05), ncol=2, byrow=TRUE)
z <- isomLRinv(mvrnorm(100, mu=c(0,2), Sigma=Sigma))
News
Changes in robCompositions version 2.1.0
- new functions cubeCoord, cubeCoordWrapper, tabCoord, tabCoordWrapper
- new data set employment2
- new data set manu_abs
Changes in robCompositions version 2.0.10
- updated documentation
- going back to old version of imputeBDLs
- mcd based robust variation (instead of mad) in function variation
Changes in robCompositions version 2.0.9
- new method in imputeBDLs
- minor change in imputeBDLs
- new function imputeUDLs
Changes in robCompositions version 2.0.8
- old Rd files management to meet new CRAN policy
Changes in robCompositions version 2.0.7
- bug in daFisher resolved
- additional argment in missPattern
- imputeBDLs now includes a new method
Changes in robCompositions version 2.0.6
- new method for imputation of rounded zeros in imputeBDLs
Changes in robCompositions version 2.0.5
- improved documentation
- version of robCompositions fits now to the Springer book
- orthbasis now times -1
- ilr.2x2 now fits to the formulas in the book, and not for the paper
- bug in daFisher resolved
- bug in external variables in pcaCoDa solved
- registering C-code
Changes in robCompositions version 2.0.4
- aDist now again works for vectors
- added following data sets:
socExp,
cancerMN,
educFM,
electionATbp,
employment,
employment_df,
GDPsatis,
govexp,
instw,
isic32,
mortality_tab,
precipitation,
rcodes, teachingStuff, unemployed - corrected documentation for ageCatWorld data
- new functions: coord, gmean, gmean_sum, ilr.2x2, ind2x2, indTab, int2x2, indTab, int2x2, intArray, intTab, pTab, rSDev, rSDev.test.R, SDev, stats
- bug in daFisher solved and new adapted predict function
Changes in robCompositions version 2.0.3
- new function perturbation() and powering()
- new function for inner product (iprod())
- new funciton balances()
- addLR, cenLR with optional different base in logrithm
- isomLR with more possibilites for a normalizing constant
- isomLR depricated, using now pivotCoord instead
- isomLRinv depricated, using pivotCoordInv instead
- orthbasis() now returns also the basis vectors
- bug in aDist solved
- aDist now much faster
- new function center()
- method symm (symmetric balances) in pivotCoord
Changes in robCompositions version 2.0.2
- new function balZav()
- new function daCoDa()
- new function clustCoDa()
- new function corCoDa()
- aDist for single matrix
- pcaCoDa() with external variables
- new data set alcoholreg
- new data set alcohol
- new data set econom
- new data set ageCatWorld
- new data set election
- new data set laborForce
- new data set payments
Changes in robCompositions version 2.0.1
- discriminant analysis (daFisher) for n-group case
- discriminant analysis (daFisher) including predict
- discriminant analysis (daFisher) including misclassification rates
Changes in robCompositions version 2.0.0
- combined help for some S3methods
- function robVariation is now called variation
- new data sets
Changes in robCompositions version 1.9.1
- now with roxygen2 documentation
- minor modifications in impRZilr
Changes in robCompositions version 1.9.0
- bug in robVariations solved
Changes in robCompositions version 1.8.0
- critical bug in function impRZilr solved (did worked only correct for constant sum data)
Changes in robCompositions version 1.7.0
- bug in function impRZilr solved
- new bootstrap procedure for estimating the number of components within impRZilr
- description in function impRZilr adapted
Changes in robCompositions version 1.6.4
- deprecated functions alr, ilr, clr, invalr, invilr, invclr deleted
- bugfix and enhancement of impRZilr.R
- improvement of isomLR for high-dimensional data
Changes in robCompositions version 1.6.3
+ function impAll included.
+ robGUI excluded (is now put in the compositionsGUI package)
Changes in robCompositions version 1.6.2
+ alr, clr, ilr, invalr, invclr, invilr are now deprecated. The new functions are called
addLR, cenLR, isomLR, addLRinv, cenLRinv, isomLRinv
+ new functions gm, orthbasis, missPatterns and zeroPatterns
+ return instead of invisible return for all log-ratio transformations
Changes in robCompositions version 1.5.0
+ variable names in expendiure data corrected
+ graphical user interface added
+ vignette about an overview of the package added
+ alrEM() function now renamed in impRZalr() to be consistent with notation
Changes in robCompositions version 1.4.6
+ correct transformation of the detection limit in impRZilr when having not constant sum 1.
Changes in robCompositions version 1.4.5
+ Bug in alrEM fixed.
+ impRZilr included, but without documentation.
Changes in robCompositions version 1.4.4
+ Description for the Expenditures data changed. Wrong variable description fixed.
+ Wrong formula in robVariation method robust=FALSE fixed after an comment
from from Mark Engle (thanks!).
+ Improved code in 'CITATION' file.