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Le livre de R - Apprentissage et Rˇfˇrence

(in french)


PACKAGES FOR R

This page provides various extensions for the statistical software R (see www.r-projects.org). Some of them are available on the CRAN (Comprehensive R Archive Network)) mirrors. The others are distributed only on this site and must be installed manually.

Here are instructions to install the packages, either from CRAN, or manually.

Note that some of the packages below have been written only for teaching purpose for my students at the Paris Ouest University and are not designed for production. You are free to modify or adapt them to suit your own needs. On the other hand, the packages which have been published on CRAN are intended for a much wider audience.

 clusterCrit

 Description

This package computes clusterization quality indices. It supports 42 internal indices (Calinski_Harabasz, Dunn, Ray_Turi, etc.) for cluster validation and 14 external indices (Phi, Jaccard, McNemar, etc.) to compare partitions.

A vignette is included and gives the exact definition of all the indices.

The package is written internally in Fortran and in C so you will need a Fortran and a C compiler if you want to compile it from sources. Alternatively, there are already compiled binary versions on the CRAN mirrors.

 Download

 

To install automatically from a CRAN mirror, execute the following command from R:

				> install.packages("clusterCrit")
				

Or go to the clusterCrit page.

 

 rcqp

 Description

This package is a front end in R for the CQP (Corpus Query Protocol) tool as defined by the CWB (Corpus Workbench) project (see CWB at SourceForge).

It lets you send queries to an indexed linguistic corpus and manipulate the results directly with R, in particular perform statistics, tests, etc.

A vignette is included and gives various examples.

 Download

 

To install automatically from a CRAN mirror, execute the following command from R:

				> install.packages("rcqp")
				

Or go to the rcqp page.

 

 conics

 Description

This package lets you plot 2D-conics (ellipses, hyperbolas, parabolas, etc.) that is to say curves defined by a quadratic polynomial in two variables.

Conics can be specified either by the polynomial or by the associated 3x3 symmetric matrix. There are functions to compute the various elements (center, axes, asymptotes, vertices) and options to include them in the graphic. Degenerate cases (pairs of lines) are also supported.

A vignette is included and gives various examples. For instance, the instructions:

					library(conics)
					v <- c(2,2,-2,-20,20,10)
					conicPlot(v, asp=1, sym.axes=TRUE, ax.col="red", ax.lty=2, 
					             col="blue", center=TRUE)
				
produce the following graphic:

 Download

 

To install automatically from a CRAN mirror, execute the following command from R:

				> install.packages("conics")
				

Or go to the conics page.

 

 diameter

 Description

This package calculates the euclidean diameter of a scatter plot (aka in french as "nuage de points"), that is to say the largest distance between pairs of points in the scatter plot. The diameter command works in any dimension.

The code is written internally in Fortran and makes use of the convex hull of the scatter plot. This makes the computations very efficient and very fast.

Here is an example where the diameter of 100000 points with two coordinates is computed in 12 milliseconds :

					> library(fraction)
					> set.seed(1)
					> m <- cbind(rnorm(100000),rnorm(100000))
					> diameter(m)
					[1] 9.084219
					> system.time(diameter(m))
					   user  system elapsed 
					  0.012   0.003   0.014 
				

 Download

 

Download the source code of the diameter package from this site. You will need a Fortran and a C compiler to compile it. If this is the case and if the archive is located in the current directory of R, you can compile and install the package with the following command:

				install.packages("diameter_0.4.tar.gz", repos=NULL, method="internal", type="source")
				
Here is an already compiled binary for Windows: diameter binary package for Windows. To install it, execute the following command from the R console:
				install.packages("diameter_0.4.zip", repos=NULL, type="win.binary")
				

 

 fraction

 Description

This package lets you perform symbolic calculations with rational numbers, that is to say manipulate a quotient like 1/3 as a fraction rather than as its numerical approximation 0.33333. It is used by the pivot package also available on this page.

Here is an example :

					> library(fraction)
					> a <- fract(5,6)
					> b <- fract(3,4)
					> a
					5/6
					> b
					3/4
					> a+b
					19/12
					> a-b
					1/12
					> a*b
					5/8
					> a/b
					10/9
					> a > b
					[1] TRUE
					> a <= b
					[1] FALSE
				

This package has been written for the Master1 course Mˇthodes Numˇriques at Paris-Ouest University.

 Download

 

Download the fraction package from this site.

 

 pivot

 Description

This package implements steps of the Gaussian elimination method (aka in french as "mˇthode du pivot de Gauss"). It can perform its calculations numerically or symbolically using fractions (it relies on the fraction package also available on this page). It is used by the simplex package and the dantzig package also available on this page.

This package has been written for the Master1 course Mˇthodes Numˇriques at Paris-Ouest University.

 Download

 

Download the pivot package from this site.

 

 simplex

 Description

This package implements the simplex algorithm for linear optimisation problems subject to linear inequalities constraints. It can perform its calculations numerically or symbolically using fractions (it relies on the fraction package and the pivot package also available on this page).

As a convenience, a function can produce the complete series of tables calculated at each step in LaTeX format.

This package has been written for the Master1 course Mˇthodes Numˇriques at Paris-Ouest University.

 Download

 

Download the simplex package from this site.

 

 dantzig

 Description

This package implements the Dantzig algorithm for quadratic optimisation problems subject to linear inequalities constraints. It can perform its calculations numerically or symbolically using fractions (it relies on the fraction package and the pivot package also available on this page).

As a convenience, a function can produce the complete series of tables calculated at each step in LaTeX format.

This package has been written for the Master1 course Mˇthodes Numˇriques at Paris-Ouest University.

 Download

 

Download the dantzig package from this site.

 

 dynprog

 Description

This package implements a simple discrete algorithm to solve optimisation problems by dynamic programming methods.

As a convenience, a function can produce the details of the calculations as a table in LaTeX format.

This package has been written for the Master1 course Mˇthodes Numˇriques at Paris-Ouest University.

 Download

 

Download the dynprog package from this site.

 

Date: 2013-11-16 15:57:28