122S:166Computing in StatisticsIntroductionLecture 1August 27, 2007Kate Cowles374 SH, [email protected] endeavors• applied statistics and data an a lysis• research in statistical theory and methods3Goals of this course are to develop:• intelligent use of appropriate compu ti ng toolsfor both statistical endeavors– R / Splus– S AS– WinBUGS– d atabase management software and con-cepts• understanding of important statistical com-puting algorithms– Newton’s method– EM algorithm– the bootstrap– M a rkov chain Monte Carlo• ability to de si g n a nd implement simulationstudies4• communication of statistical ideas in words,numbers, and graphics– LATEX– format of scientific reporting5Types of computer productsThis section and the next 2 borrow heavily from Chapter 1of the course notes for “Statistical Computing and Graph-ics” by Frank Harrellhesweb1.med.virginia.edu/biostat/teaching/statcomp• operating systems: make the computer itselfworke.g. Linux, Windows, Unix, MacOS• applications: perform specific taskse.g. Microsoft Word, Excel, S-Plu s, OpenOf-fice, R, SAS, . . .• commercial systems– code and lists of bugs are secret– expen si ve– require upgradin g and relicensin g– M icrosoft products, S-Plus, SAS, SPSS,Unix, etc.• free Open Source systems6– revolution in software availabi lity a nd func-tion from the open source movement– can see all code, change it, learn from it– qu a lity generally quite good∗ often better than that of commercially-developed software because Open Sourcesoftware has been tested by more p e o pleunder more different conditions– more rapid updates– most products have an active and helpfuluser n ew s group– generally lack some fancy features like ex-tensive GUI– Li nux, LATEX, OpenOffi ce, R7User interfaces: graphical vscommand line• graphical (GUI, mouse, menus)– easi e r to learn– l ess flexible– repetiti ve when the same tasks have to berepeated– h ard to document the exact steps taken– h ard to reproduce results• command line interfaces– h arder to learn– more flexible and powerful– can save commands in scripts to replaywhen the same tasks have to be performedrepeatedly– can write gen eri c commands to facilitaterunning different analyses with the samestructure8Types of user files• text• binary• graphics files9Linux historyThe material in this section borrows heavily from Section 1.1of Introduction to Linux: A Hands on Guide by MachteltGarrels.http://www.tldp.org/LDP/intro-linux/intro-linux.pdf• Unix– 1969: team of developers at Bell Lab o ra -tories began work on solution to problemof software incompatibility∗ at that time, every model of computerhad diff erent operating system∗ software was customized to specific pur-poses, and ran on only one type of com-puter system– UNIX operating system needed only smallpiece o f code specific to one type of com-puter: the kernel– opera ti ng system (and all other functions)built around kernel10– h igher-level programming language C spe-cially developed for creating UNIX– at first used only in very large comput-ing environments — universities, govern-ment, large corporation s with mainframesand min icomputers• developments in 1970’s and 1980 ’s– continued development of UNIX– support of UNIX in produc ts of increasingnumbers of hardware and software vendors– i nvention of personal computers– by end of 1980’s, several versions of UNIXavailable for PC architecture, but not free11• Linus Torvalds and Linux– computer science student at University ofHelsinki– goal: to create a freely-available op era ti ngsystem that was compliant with originalUNIX– began working on it in early 1990’s– other coders jumped aboard to developdrivers to make Linux usable with moreand more hardware– 12000 Linux users by 1993– all features of UNIX added over few moreyears12• Linux today– only operating system in the world thatruns on as wi de a range of hardware∗ desktop workstations∗ mid- and high-end servers∗ PDAs, mobiles, experimental wri stwatches,etc.– well known as a stable and reliable plat-form for servers– examples of users∗ Amazon (Internet book seller)∗ United States Post Office∗ German army∗ high-energy physics Grid13Logging in, activating the userinterface, and logging out• PC-based Linux systems have two basic modes:graphical and text• in graphical mode (usually the default)– l o gin requires inputting user name in onewindow and password in another– make sure mouse pointer is in the loginwindow; Click OK or else press Enter afterentering the userna me and after enteringthe password– open a terminal window by left cl ickingon icon of a computer screen at bottom ofscreen– l o g out by∗ closing a ll terminal windows and appli-cations∗ clicking RedHat icon at bottom of screenand selecting “Log Out”14– i n text mode∗ whole screen is black, with white char-acters∗ you are prompted for username and pass-word; press enter after typing in eachone∗ log out by entering logout commandand pressing enter15Linux student computer labs• UI Mathematica l Sciences educational com-puter labo rato ri e s:– 346 SH (primarily for statistics students)– B5 MLH and 301 MLH (primarily for mathand c. s. )• your username and password are a ssig ned byComputer Support Group– the first time you log in, you should i m-mediately change the password they giveyou– enter the passwd command in a terminalwindow and follow the instructions– requirements for passwords∗ from six to eight chara cters long∗ use both uppercase and lowercase let-ters and ei ther digits or non-alphabeticsymbols (or both)16∗ pick something you will remember with-out writin g it down∗ don’t use the same password on differentsystems• link to information from the Computer Sup-port Group (CSG) on student accounts onthe math/c.s./ stati sti cs networkwww.divms.uiowa.edu/help/orientation• must b ring your own printer paper if youwish to print• to access Internet, click icon of world wi th amouse around it at the bottom of the
View Full Document
Unlocking...