IASC-ERS Summer School CoDaCourse 2014

Transcription

1 IASC-ERS Summer School CoDaCourse Software Dept. Informàtica, Matemàtica Aplicada i Estadística Universitat de Girona Campus Montilivi, EPS-4 E Girona (Spain) [Coord: N E] webmaster@compositionaldata.com

2 Sotfware Organized by: Research Group on on Statistical MEthods in restricted spaces (METRICS) from the Computer Science, Applied Mathematics and Statistics Department of the University of Girona (UdG). The CoDaCourse is accredited by the International Association for Mathematical Geosciences ( and supported by the European Regional Section of the International Association for Statistical Computing ( Language: English Dates/Timetable: 2014 July 7-11; 5 days from 9:00-17:00, including coffeebreaks and lunches (i.e. 30 class room hrs). Language: English. Instructors from METRICS research group: J.J. Egozcue, V. Pawlowsky, C. Barceló, J. Daunis, J.A. Martín and G. Mateu. Support staff: M. Comas, I. Galván, and M. Vives. Material: PDF files, data files, and paper copy of slides and lab exercises will be provided. Certificate: Attendance certificate will be provided. Lab exercises are based on available software. Attendants are strongly encouraged to bring their own laptops for practicals with all the software previously installed. If some assistant is unable to bring any laptop or has troubles to install any software, please contact us at webmaster@compositionaldata.com. CoDaPack CoDaPack is an open source software, independent of any other software. The freeware package can be downloaded from the web site: The package comes with a setup file and requires having Java Virtual Machine (minimum version 1.5.0) installed. To get it working, it suffices to install and open the file CoDaPack.exe. CoDaPack is based on menus. Numerical results appear on the output part of the window, while graphs appear in new graphical windows. To use CoDaPack, one has to execute the le Codapack.exe. When a new version of CoDaPack is available, and Internet connection is working, the ~ 2 ~

3 package shows a message asking for the user to import the new version. In other words, CoDaPack updates itself. Data could be imported from Excel files or recovered from previous sessions. The observations are organized in rows and the variables in columns. The new CoDaPack has three different areas: the variables area; the data area; and the results area, which has a textual output window and independent graphical output. If you detect any bug or you have more ideas for coming versions, contact us via (mcomas@ima.udg.edu, thio@ima.udg.edu). R and its packages For more demanding statistical techniques, some packages [robcompositions, zcompositions, MASS or mvoultier] of the open source statistical environment R, are also used. See following sections for more detailed info about R. Websites: o Main website of R software: o Website to download the latest version: Comprehensive R Archive Network (CRAN) The latest release ( ) for windows is available in Download R for Windows INFOS from Youtube (examples!! look for other sources): Download and install R: Install and update packages in R: Step-by-step guideline to downloading and installing R 1. Select the mirror in click on CRAN mirror ~ 3 ~

4 2. Select the mirror from the list: e.g. Austria or Spain : 3. Select your system: e.g. click on Windows 4. Select the basic core of R: click on base 5. Download and save in your PC the latest release (47 megabytes approx.). ~ 4 ~

5 Once the Exe file is saved on your PC then double-click the Exe file and follow the instructions. 6. After the program R is installed, double-click the R icon on the desktop to start R program: A first simple example: mean of vector (3, 4.25, 5.75, 6). Write mean(c(3,4.25,5.75,6)) and press Enter 7. Demos: write demo(graphics) and press Enter 8. Help in R: for example, information about the mean function can be obtained writing help(mean) or?mean in the console window and press Enter. ~ 5 ~

6 Step-by-step guideline to installing and loading a R-package: The first time, any package needs to be installed. Once it is installed, one package must be previously loaded when one wants to use a function from the package. We are going to install and load the package MASS, the package from the book Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth edition. Springer. INSTALL a PACKAGE 1. In R, go to Packages menu. 2. Select Set CRAN mirror: 3. For example, select Spain and clic on OK 4. Install MASS package: If the list of packages is not automatically shown, then go again to Packages menu and select Install package ~ 6 ~

7 Select the package MASS and clic on OK LOAD a PACKAGE 5. Load the package MASS: Two possible options: One, on console, write library(mass) and press Enter Second, go to Packages menu and select Load package ~ 7 ~

8 Now we have available all the functions from the package MASS. On console, write help(package=mass) and press Enter to obtain a list of functions included in the package: 6. Help and data from a package: try to execute following instructions to obtain information of anorexia data set from package MASS. Function data load the data set and function head list it first rows. > help(anorexia) > data(anorexia) > head(anorexia) Treat Prewt Postwt 1 Cont Cont Cont Cont Cont Cont Please, install and load the packages: robcompositions, zcompositions, and mvoutlier. ~ 8 ~

9 Selected references : documentation (manuals, books, FAQ, Wiki, ) Quick-R : very useful page where you can easily find how to do plots or calculate statistics. Selected books: o Analyzing Compositional Data with R: van den Boogaart, K. Gerald, Tolosana-Delgado, Raimon New York: Springer, 2013, 258 p. o Applied econometrics with R: Kleiber, Christian, New York: Springer, o Applied spatial data analysis with R: Bivand, Roger, New York: Springer, o Biostatistics with R. An Introduction to Statistics Through Biological Data: Shahbaba, Babak. New York: Springer, 2012, 352p. o Bioinformatics and computational biology solutions using R and Bioconductor: Gentleman, R. (eds.), New York: Springer Science+Business Media, o A Handbook of statistical analyses using R: Everitt, B. Boca Raton: Chapman & Hall, o An R and S-PLUS companion to multivariate analysis: Everitt, Brian London: Springer, o The R book: Crawley, Michael J. New York: John Wiley & Sons, o R graphics: Murrell, Paul. Boca Raton: Chapman & Hall/CRC, o Statistical computing with R: Rizzo, M. L., Boca Raton: Chapman&Hall, o Using R for introductory statistics: Verzani, J., Boca Raton: Chapman&Hall, ~ 9 ~