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1. A lt matrix rnorm 100 nrow 10 diag A lt seq ncol A ncol A Make it diagonally dominant b lt rnorm ncol A sys time xl lt gaussSeidel A b function A b J Hard coded relative tolerance and max iterations tol lt 1 0e 4 maxItr lt 1le4 Validating A lt as matrix A b lt as numeric b if nrow A ncol A ncol A length b stop nrow A ncol A ncol A length b Begin Gauss Seidel step x lt b for k in 1 maxItr x01d lt x for i in 1 nrow A s lt ALi i1 xli for j in 1l ncol A s lt 6 Alis IJ IXL x i lt bLiT SJAL Check convergence continue if necessary if max abs x x01d x lt tol return x warning Solution does not converge n return x This code which involves a nested loop could be made more efficient but the intention is to illustrate the Gauss Seidel iteration in its most familiar form An example including the implementation of 24 Simple Examples An Application and a Called Routine CONNECT C is shown below and notice that by using the classes and methods of CONNECT C 4 this code closely resembles the equivalent computation in S PLUS The code begins by including the sconnect h header file to give us access to the CONNECT C library Next it includes the header file required for the Gauss Seidel code itself d include sconnect h d include gausssd1 h We then declare the gaussSeidel object as
2. O03a O04 005 ae 024 033 ae vA moot 210 moe 231 244 253 mee meri mga opg EE mpm Oe ar gie yol hozo R o25 026 027 030 034 035 036 4037 ee Es OO ES Pe T ee OE Te TP Oe Te pe S a a 202 203 204 205 maa ae PaE en o a a a eee mega 2a5 ano S Wagas 246 247 1250 254 255 256 257 aga gel ees AREE mere Mara a Me 367 O13 f wings R Dee A ORL 3 tai O14 i ea PES TE mpa mye E nae 200 206 wee 4 HET 4 242 YSI 260 YBF 27O a A207 Ee 5 TAZIO AZAS AZET 261 12707 LETT Note The set of characters allowed or disallowed in object names is not affected by the current locale The functions deparse parse dump dput source data dump and data restore are also unaffected by the choice of locale In PostScript Output The postscript function now uses the Latin1 encoding of its standard fonts by default This means you can more easily use non English Western European characters If you previously used octal escapes like 267 to get characters in the upper half of the standard PostScript encoding 267 was the bullet character you must either change such code 200 is now the bullet or use the arguments setfont ps setfont std and bullet ps bul
3. 50 e The decimal point argument controls the single character used to mark the decimal place in ASCII numbers The default is the period e The thousands separator argument controls the single character used as the digit grouping symbol in ASCII numbers The default is the comma You can also specify which locale to use within importData and exportData by setting the argument use locale to T the default is use 1ocale F Displaying Data Importing Exporting and Displaying Numeric Data The decimal marker used when displaying or reading numbers changes depending on LC_NUMERIC For example in many European locales the number pi is written 3 14159 approximately This affects how functions such as format print cat write table and html table display numeric data It also affects how as numeric and as character convert between strings and numbers Other functions like cut and factor in the labeling of levels are also affected 51 Chapter 3 Globalization 52 USER DEFINED HELP Introduction Creating Editing and Distributing a Help File Step 1 Creating the Help File Step 2 Copying the Help File to a Clean Directory Step 3 Running the CHAPTER Utility Step 4 Editing the Help File Step 5 Running Splus6 make install help Step 6 Viewing the Help File Step 7 Distributing the Help File Common Text Formats Contents of Help Files Descriptions of Fields Special Help File
4. CSPengineConnect CloseTopLevelEval and the Create method for the object type to be created CONNECT C 4 Architectural Features Table 2 1 CONNECT C classes and their S PLUS counterparts CONNECT C S PLus Class Class Example any CSPobject CSPobject x 2 numeric CSPnumeric CSPnumeric x 2 32 integer CSPinteger CSPinteger x 2 logical CSPlogical CSPlogical x c T F character CSPcharacter CSPcharacter abcd named CSPnamed CSPnamed c a 1 b 2 d 3 matrix CSPmatrix CSPmatrix A matrix 1 4 2 CSPnumericMatrix CSPnumericMatrix A matrix rnorm 12 6 CSPcharacterMatrix CSPcharacterMatrix A matrix letters 1 12 6 array CSParray CSParray B array 1 8 c 2 2 2 list CSPlist CSPlist list 1 2 6 700 function CSPfunction CSPfunction function x x 2 call CSPcall CSPcall Im 41 Chapter 2 CONNECT C 42 GLOBALIZATION Introduction Working With Locales Setting a Locale Changing a Locale Changing the Collation Sequence Using Extended Characters In Variable Names In PostScript Output Importing Exporting and Displaying Numeric Data Importing and Exporting Data Displaying Data 44 45 46 46 46 48 48 49 50 50 51 43 Chapter 3 Globalization INTRODUCTION 44 New in S PLUS 6 1 are a number of enhancements designed to improve global installation and use New functions have been added that allow you to sp
5. S PLUS on the Web Training Courses Technical Support Books Using S PLUS Typographic Conventions Oooo TNE wWH N e e ark eA A UOO o0 Chapter 1 Welcome WELCOME TO S Ptus 6 1 S PLUS 6 1 is a service upgrade for S PLUS 6 a significant new release of S PLUS based on the latest version of the powerful object oriented S language developed at Lucent Technologies S is a rich environment designed for interactive data discovery and is the only language created specifically for data visualization and exploration statistical modeling and programming with data S PLUS 6 continues to be the premier solution for your data analysis and technical graphing needs The Java graphical user interface gives you point and click access to graphing and statisticsWith S PLUS 6 you can also program interactively using the S PLUS programming language In a typical S PLUS session you can e Import data from virtually any source e View your data in a convenient Data window e Create plots with the click of a button e Control details of your graphics to produce stunning professional looking output for export to your report documents e Perform statistical analyses from convenient dialogs in the menu system e Create your own functions e Completely customize your user interface Installation INSTALLATION Supported Platforms and System Requirements S PLUS 6 1 for UNIX Linux is supported on the following e 32
6. SyncParseEval 22 try block 25 29 try catch block 25 connection classes 29 connectivity Oracle 82 See Oracle connectivity constructors 28 31 32 39 40 context sensitive help 10 conventions typographic 18 conversion operators 34 converting objects 34 Create 22 28 38 39 40 CSParray 35 CSPengineConnect 21 29 39 40 CSPevaluator 29 30 40 CSPnumeric 21 34 35 38 39 41 CSPobject 28 31 32 33 34 36 38 39 40 41 CSPproxy 36 CSPvector 35 D data object classes 28 decimal point argument 50 decimal markers 8 45 50 51 destructors 31 digit grouping symbols 50 displaying numerics 8 44 45 50 51 E evaluator classes 29 30 executeSQL function 82 91 92 93 exportData function 50 82 88 90 91 93 exporting numerics 8 44 50 F function evaluation classes 28 G Gauss Seidel method 23 24 25 generating functions 31 globalization 8 H help 10 54 function 13 at the command line 13 context sensitive 10 from the graphical user interface 10 help off function 10 help start function 10 help function 13 Help menu 10 help window navigation pane 10 12 Index page of 12 Search page of 12 Table of Contents page of 12 toolbar 10 11 buttons on 11 topic pane 10 12 keywords 12 Language Reference 74 help off function 10 help start function 10 help files user defined 9 54 57 BUILD_JHELP 58 HINSTALL 58 keywords 55 64 74 78 79 prompt function 55 56 57 58 77 Splus6 make
7. emp server ORACLEDB AUNE EMPNO 7369 7876 7900 7934 ENAME SMITH ADAMS JAMES MILLER Reading Data From an Oracle Database Using the sqlQuery argument gt importData type oracle user scott password tiger server 0RACLEDB sqlQuery SELECT FROM emp The next command returns the data from emp corresponding to employees who work as clerks gt importData type oracle user scott password tiger server ORACLEDB sqlQuery SELECT FROM emp WHERE job CLERK JOB CLERK CLERK CLERK CLERK MGR 7902 7788 7698 7782 HIREDATE 12 17 1980 00 00 00 000 05 23 1987 00 00 00 000 12 03 1981 00 00 00 000 01 23 1982 00 00 00 000 SAL 800 1100 950 1300 COMM NA NA NA NA DEPTNO 20 20 30 10 The next command selects only the EMPNO field from the table gt importData type oracle user scott password tiger server 0RACLEDB sqlQuery SELECT empno FROM emp EMPNO 1 7369 2 7499 3 252 4 7566 5 7654 6 7698 7 F782 8 7788 9 7839 10 7844 11 7876 12 7900 13 7902 14 7934 To select all data from emp and order the rows alphabetically according to employee name type the following gt importData type oracle user scott password tiger server ORACLEDB sqlQuery SELECT FROM emp ORDER BY ename 85 Chapter 5 Oracle Connectivity AN oa nO AUNG rPrPrPrPrF o FP wWhP FF OO 86 EMPNO 7876 7499 7698
8. lt p gt Wegman E J 1972 71 Chapter 4 User Defined Help BUGS SEE ALSO 72 Nonparametric probability density estimation lt it gt Technometrics lt it gt lt bf gt 14 lt bf gt 533 546 lt p gt Venables W N and Ripley B D 1997 lt it gt Modern Applied Statistics with S PLUS lt it gt 2nd ed New York Springer Verlag lt s section gt The tag for paragraph breaks lt p gt should be used to separate multiple references Please try to cite works that are widely available to users In this section you should document any known bugs a user might encounter while using the function The bugs section in S PLUS SGML files does not have a specific tag but uses lt s section name name gt and lt s section gt instead For example the following is a bug from the SGML help file for subplot lt s section name BUGS gt If you request it to draw outside the figure region lt s expression gt subplot lt s expression gt gets very confused and typically puts the subplot across the whole region lt s section gt This section provides links to related functions In general any function you reference in the text of a help file should be linked in this section The name of each function is wrapped in the tags lt s function name f77ename gt and lt s function gt this provides the hyperlinks in the formatted help file The f77ename is the name of the installed help file which is the linked functio
9. once for the text line and once for the blank line The lt br gt tag is not needed in preformatted sections Paragraph breaks lt p gt This is the recommended tag for including blank lines in a help file as it shows up in slynx as well as JavaHelp 62 CONTENTS OF HELP FILES Contents of Help Files Descriptions of Each S PLUS help file is composed of titled sections that appear in the Fields Table 4 3 Titled sections in S PLUS engine help files Titles in all capitals appear in a formatted help file order listed in Table 4 3 We discuss each of these sections below Titles in lowercase letters do not appear in a help file but the information in those sections do Section Title Quick Description SGML Tags Topic The name of the function lt s topics gt lt s topics gt Title The title that appears at the top of a lt s title gt formatted help file lt s title gt DESCRIPTION A short description of the function lt s description gt lt s description gt USAGE The function call with all of its arguments lt s usage gt lt s usage gt REQUIRED Descriptions of arguments that are lt s args required gt ARGUMENTS required by the function lt s args required gt OPTIONAL Descriptions of arguments that are lt s args optional gt ARGUMENTS optional lt s args optional gt VALUE The return value from the function lt s value gt lt s value gt SIDE E
10. 3 The S PLUS 6 1 release notes contain pointers to Web site where you can download these patches For complete installation instructions please see the plain text file INSTALL TXT located at the top level of your S PLUS 6 1 CD ROM or the manual PLUS 6 Installation and Maintenance Guide During installation you are prompted for your S PLUS serial number Note that the serial number format has changed dramatically in S PLUS 6 1 you can find your new serial number on the S PLUS 6 1 CD ROM jewel case The serial number you enter during installation is recorded and you can retrieve it later by typing Splus SERIAL at the UNIX prompt on your system Running S PLus Installation Do not install this release over any existing version of S PLUS Instead designate a clean installation directory for S PLUS 6 1 and proceed with the installation as described in either INSTALL TXT or the manual Before starting S PLUS you must do the following 1 Set your DISPLAY environment variable to your local machine 2 Create an S PLUS chapter to hold your work Setting your DISPLAY environment variable is necessary for the Java features in S PLUS To set your display from a C like shell csh tesh etc use the setenv command from the UNIX prompt setenv DISPLAY lt display_name gt where lt disp ay_name gt is the name of your local machine From the Bourne and Korn like shells including sh ksh bash etc use the following command
11. C Classes and methods discussed in this section are fully documented in the reference sections for the classes in the online help for CONNECT C CSPobject is the base class of most of the classes that represent S PLUS classes It provides common functionality to its derived classes and its most important data member is s_object CSPobject m_ps_object A class that represents an S PLUS class inherits m_ps_object because CSPobject is its base class As a smart pointer a derived class of CSPobject provides safer methods to manipulate the data pointed by m_ps_object as compared to using global C functions For example the constructor the destructor and the assignment operators automatically increment and decrement reference counts whenever appropriate to provide the same data sharing mechanism as that of the SV4 language All CSPobject derived classes have a method called IsValid which allows you to test whether the member m_ps_object is valid or not Often S generating functions are more convenient than the S method new Similarly constructors of CONNECT C classes can provide the same convenience They have the following form CSPclass CSPclass const char pszExpression pszExpression is a string representing valid S code where class is a CSPobject derived object This form of the object constructor parses and evaluates pszExpression and uses the resultant S PLUS object as its value Normally pszExpression shoul
12. Previously this feature was available only in S PLUS for Windows You can use CONNECT C to create C applications that access S PLUS functionality as well as C functions that are called from S PLUS via the Ca11 interface S PLUS 6 1 includes a C class library you can use to create and manipulate S PLUS functions parse and evaluate S PLUS expressions and return messages when objects have changed or databases have been attached or detached The CONNECT C 4 library is located in HOME newfun lib source code can be found in HOME sconnect and examples are in HOME sconnect samples Here SHOME is the home directory for your installation of S PLUS 6 1 You can see this directory path by typing either getenv SHOME at the command prompt in S PLUS or Splus SHOME from the UNIX prompt where Splus is the script you use to launch S PLUS 6 1 Aspects of S PLUS have been significantly enhanced to support globalization and locales The concept of a locale is akin to Regional Options or Regional Settings in Microsoft Windows setting a locale is a way of specifying which character sets number formats and collation sequences to use This allows S PLUS to support Western European character sets ISO 8859 1 as well as 8 bit ASCII characters ASCII codes 128 255 in character data and the names of objects Globalization also permits you to import export and display numbers written with decimal markers other than the period and thou
13. Step 5 Running Splus6 make install help 58 lt s topic gt myfunc lt s topic gt lt s topics gt lt s title gt The first four lines of myfunc sgml are required in all SGML help files for S PLUS For this reason we recommend that you use prompt to create a template file rather than write SGML code from scratch The lt s function doc gt tag begins the contents of the help file you should see the end tag lt s function doc gt at the end of the file The start and end tags for most fields in an S PLUS help file are included in the skeleton files that prompt creates If your function does not require a certain field in its help file you can delete the corresponding tags If the text for a given section is particularly long be sure to start sentences or major phrases on new lines The SGML parser tends to break when a single line contains too much text When this occurs the help file is truncated at the point where the parser breaks and an error message is inserted Input string too long There is a great deal of information on the meaning and use of the SGML tags in S PLUS help files and this is described at length in the section Common Text Formats and the section Contents of Help Files that follow These sections have been omitted here for brevity Now that the SGML files have been edited view them in S PLUS to verify they have the proper content and formatting This requires another S PLUS utility to be run so at
14. above lt s section name gt categories lt s section gt SEE ALSO Links to related S PLUS functions and data sets lt s see gt lt s see gt EXAMPLES Coded S PLUS examples using the data lt s examp es gt lt s examples gt Keywords A list of keywords that place the help file in the lt s keywords gt Contents topics of the help system lt s keywords gt 79 Chapter 4 User Defined Help 80 ORACLE CONNECTIVITY Introduction Reading Data From an Oracle Database The importData Function The openData Function Writing Data to an Oracle Database Executing Arbitrary SQL Statements 82 83 84 87 90 92 81 Chapter 5 Oracle Connectivity INTRODUCTION S PLUS 6 1 for Solaris platforms extends connectivity with Oracle database clients This feature gives you more flexibility in reading data from an Oracle table inserting data into a table and running arbitrary SQL queries This enhanced Oracle connectivity is available from the S PLUS command line but not from the Import Data dialog in the S PLUS Java GUI In this chapter we briefly discuss the S PLUS functions involved in Oracle connectivity and provide examples illustrating this feature e The section Reading Data From an Oracle Database describes changes made to the importData and openData readNextDataRows closeData set of functions e The section Writing Data to an Oracle Database describes changes made to the exportData and openData w
15. an object of class s_object as required by the Ca11 interface s_object gaussSeidel s_object ps_A s_object ps_b As is typical for S PLUS code we declare the S_EVALUATOR and then embed the implementation in a try catch block Within the try block the tolerances are hard coded We then construct the C equivalents to the S PLUS objects A and b S_EVALUATOR try Hard coded relative tolerance and max iterations double tol le 4 long maxItr 1000 Constructing and validating C objects CSPnumericMatrix A ps_A CSPnumeric b ps_b if A nrow A ncol A ncol b length PROBLEM A nrow A ncol A ncol b length ERROR The actual Gauss Seidel step follows Begin Gauss Seidel step CSPnumeric x b for long k 1 k lt maxItr k i CSPnumeric xOld x for long i 1 i lt A nrow i 25 Chapter 2 CONNECT C 26 double ACT 7 Xi for long j 1 j lt A ncol j s Aij XC x i b ij s A i i Check convergence continue if necessary if Max abs x x01d x lt tol return x PROBLEM Solution does not converge WARN return x Cathl ass return blt_in_NULL return the built in NULL object The complete code for this example is in the directory SHOME sconnect samples gausssdl with the C code in the file gausssdl cxx To compile and execute the C code 1 Change the current directory to the directory cont
16. contains some useful overloading operators such as and These operators perform element by element operations in the same way as in the S language However for the matrix class the operator is different The operator for CSPmatrix is a real matrix multiplication operator equivalent to the S operator CSPclass amp CSPclass operator const CSPclass amp sObject CSPclass amp CSPclass operator const CSPclass amp sObject CSPclass amp CSPclass operator const CSPclass amp sObject CSPclass amp CSPclass operator const CSPclass amp sObject where class is a CSPobject derived object 33 Chapter 2 CONNECT C Converting C Objects to S PLUs Objects 34 An example using the CSPmatrix follows CSPevaluator s CSPaumeric x 1 4 s X lt 1 4 CSPnumeric y 4 1 yx 4 1 y FHM y lt yt x x CSPmatrix AC matrix 1 4 nrow 2 A lt matrix 1 4 nrow 2 CSPmatrix BC matrix 4 1 nrow 2 B lt matrix 4 1 nrow 2 CSPmatrix D A A BXB FID lt A 4 A B B Objects derived from class CSPobject are C representations of S PLUS objects within S PLUS S PLUS objects are represented as C objects of type s_object Sometimes an application needs to access the s_object directly For example the arguments and the return value of all Ca11 interfaces must be of type s_object The CSPobject class provides a convenient way to automatically convert to s_object Simply use a CSPobject
17. logical Q odbcConnection character 0 C module odbcSqlQuery character 0 readAsTa A sas contents 1 colNamesUpperCase F time in format decimal point Figure 4 1 JavaHelp is used to invoke the importData help file in S PLUS 6 1 Introduction The S PLUS function prompt generates a help file outline for any S PLUS function or data object you specify The outline includes the correct syntax for the function as well as the current definition of the function and headings under which you can supply the following information What the function does A brief description of the function A description of each argument with the option of specifying both required and optional arguments A description of the value returned by the function Side effects which are any effects of the function besides the return of a value The method behind the function that is how the function works Any references to the literature Cross references to other help files Keywords Keywords are used by the S PLUS help system in assembling its Category and Function menus The following sections describe the steps involved in creating editing viewing and distributing your customized help files 55 Chapter 4 User Defined Help CREATING EDITING AND DISTRIBUTING A HELP FILE Creating a help file for distribution in S PLUS 6 for UNIX involves the use of S PLUS commands and commands from a UNIX pro
18. lt s keyword gt models lt s keyword gt lt s keyword gt regression lt s keyword gt lt s keyword gt survival4 lt s keyword gt lt s keywords gt This places the coxph function in the following Contents topics Statistical Models Regression and Survival Analysis Table 4 4 lists the current keywords and the help topics they map to Table 4 4 Current keywords and the Contents topics they map to Keyword Topic Keyword Topic Keyword Topic aplot Add to design ANOVA bootstrap Bootstrap Existing Plot Models Methods category Categorical character Character Data cluster Clustering Data Operations complex Complex dplot Computations menudata Data Menu Numbers Related to Functions Plotting wdialogs Customizable wmenus Customizable attribute Data Attributes Dialogs pre Menus pre S PLUS 4 0 S PLUS 4 0 data Data manip Data sysdata Data Sets Directories Manipulation classes Data Types chron Dates Objects debugging Debugging Tools 74 Contents of Help Files Table 4 4 Current keywords and the Contents topics they map to Continued Keyword Topic Keyword Topic Keyword Topic defunct Defunct deprecated Deprecated documentation Documentation Functions Functions dynamic Dynamic error Error Handling device Graphical Graphics Devices hplot High Level file Input Output iplot Interacting Plots Files With Plots interface Interfaces to jackknife
19. s arg gt As in the section for required arguments the first word in each argument s description should not be capitalized and you should document whether exceptional values are accepted This section describes the return value of the function The first word in the description should not be capitalized Often the description of a function s return value begins with a phrase similar to a list containing the following components In this case you can use the tags lt s return component name name gt and lt s return component gt to format the individual components of the return list The first word in the description for each return component should not be capitalized As an illustration the value section of the density SGML file is provided below lt s value gt a list with two components lt s expression gt x lt s expression gt and lt s expression gt y lt s expression gt suitable for giving as an argument to one of the plotting functions lt s return component name x gt a vector of lt s expression gt n lt s expression gt points at which the density is estimated lt s return component gt 67 Chapter 4 User Defined Help SIDE EFFECTS GRAPHICAL INTERACTION 68 lt s return component name y gt the density estimate at each lt s expression gt x lt s expression gt point lt s return component gt lt s value gt You should include arcticles in the uncapitalized sentences of the valu
20. www seanet com pburns Spoetry Krause A and Olson M 2000 The Basics of S and S PLUS 2nd ed Springer Verlag New York Spector P 1994 An Introduction to S and S PLUS Duxbury Press Belmont CA Statistics and Data Analysis General Alzola C F and Harrell F E 2001 An Introduction to S PLUS and the Hmisc and Design Libraries Download for free from http hesweb1 med virginia edu biostat s doc splus pdf Atkinson A and Riani M 2000 Robust Diagnostic Regression Analysis Springer Verlag Bowman A and Azzalini A 1997 Applied Smoothing Techniques for Data Analysis The Kernel Approach with S PLUS Illustrations Clarendon Press Chambers J M and Hastie T J 1992 Statistical Models in S Chapman and Hall Crawley M 2002 Statistical Computing An Introduction to Data Analysis Using S PLUS Wiley Davison A C and Hinkley D V 1997 Bootstrap Methods and Their Applications Cambridge University Press 15 Chapter 1 Welcome 16 Efron B and Tibshirani R J 1994 An Introduction to the Bootstrap Chapman amp Hall Everitt B 1994 A Handbook of Statistical Analyses Using S PLUS Chapman amp Hall London Hardle W 1991 Smoothing Techniques with Implementation in S Springer Verlag New York Hastie T J and Tibshirani R J 1990 Generalized Additive Models Chapman amp Hall Hastie T J Tibshirani R J and Friedman J 2001 The Elements of Stati
21. 6 1 and tested supported on Red Hat 6 2 7 0 and 7 2 These releases contain the kernels and compilers listed in Table 1 2 Other Linux distributions such as SuSE are not officially supported or tested However if you want to use another Linux distribution you should use one that has similar Chapter 1 Welcome versions of the kernels and compilers for example SuSE 6 4 7 0 or 7 2 For more information on various Linux distributions see http www distrowatch com Table 1 2 Kernels and compilers for the supported versions of Red Hat Linux Java Runtime Red Hat OS Kernel GCC glibc 7 2 2 4 7 2 96 2 2 4 7 0 2 2 16 2 96 2 1 92 6 2 2 2 14 2 91 66 2 1 3 6 1 2 2 12 2 91 66 2 1 2 The Java runtime environment JRE version 1 3 is included in Environment JRE Installation Instructions S PLUS 6 1 Your operating system must support JRE 1 3 to run the Java enabled version of S PLUS The JRE provided by S PLUS is installed as part of the S PLUS distribution and under normal circumstances it is used only by S PLUS If you have a different version of the JRE on your system the JRE used by S PLUS should not interfere with your other JRE applications which will continue to use the version you ve previously installed See the S PLUS release notes for specific information regarding the JRE on your platform In particular Solaris operating environments require various patches from Sun to run Java 1
22. 7782 7902 7900 7566 7839 7654 7934 7788 7369 7844 7521 ENAME ADAMS ALLEN BLAKE CLARK FORD JAMES JONES KING MARTIN MILLER SCOTT SMITH TURNER WARD JOB MGR HIREDATE SAL COMM DEPTNO CLERK 7788 05 23 1987 00 00 00 000 1100 NA 20 SALESMAN 7698 02 20 1981 00 00 00 000 1600 300 30 MANAGER 7839 05 01 1981 00 00 00 000 2850 NA 30 MANAGER 7839 06 09 1981 00 00 00 000 2450 NA 10 ANALYST 7566 12 03 1981 00 00 00 000 3000 NA 20 CLERK 7698 12 03 1981 00 00 00 000 950 NA 30 MANAGER 7839 04 02 1981 00 00 00 000 2975 NA 20 PRESIDENT NA 11 17 1981 00 00 00 000 5000 NA 10 SALESMAN 7698 09 28 1981 00 00 00 000 1250 1400 30 CLERK 7782 01 23 1982 00 00 00 000 1300 NA 10 ANALYST 7566 04 19 1987 00 00 00 000 3000 NA 20 CLERK 7902 12 17 1980 00 00 00 000 800 NA 20 SALESMAN 7698 09 08 1981 00 00 00 000 1500 0 30 SALESMAN 7698 02 22 1981 00 00 00 000 1250 500 30 To select the subset of data corresponding to employees who make more than the average salary type the command below In this command only the fields DEPTNO ENAME and SAL are returned and the results are ordered by department number gt importData type oracle user scott password tiger server O0RACLEDB sqlQuery SELECT deptno ename sal FROM emp x WHERE sal gt SELECT AVG sal FROM emp WHERE x deptno deptno ORDER BY deptno DEPTNO ENAME SAL 10 KING 5000 20 JONES 2975 20 SCOTT 3000 20 FORD 3000 30 ALLEN 1600 30 BLAKE 2850 non AUNE The f
23. ELI is 10 and xi is 0 Some overloaded operators are available to support mixed mode arithmetic operations involving subscripting objects of classes derived from CSPobject These operators and perform mixed mode operations following the same rules as S PLUS long CSPproxy operator long double CSPproxy operator double An example using the arithmetic operators CSPevaluator s CSPnumeric x 1 4 X lt 1 4 CSPnumeric y x y lt x y shares data with x A lt matrix 1 4 nrow 2 CSPmatrix A matrix 1 4 nrow 2 CONNECT C 4 Architectural Features f e lt Afl 1 Afl 2 double e A 1 1 A 1 2 AL1 2 lt e A 1 1 A 2 1 A 1 2 e A 1 1 A 2 1 fi AC2 2 lt x L1J A 1 1 y 2 A2 1 A 2 2 x 1 A 1 1 y 2 A 2 1 ff X rray l 16 2 2 232 CSParray KC array 1s16 C222 ND ff X 1 1 1 1 lt gt X 2 1 1 1J e Xt1 1 1 1 4 2 1 1 1 e ff Rizal lt yl Xlll X2 dell yl 4t2 1 1 1 ff Bil ell All XLA L11 MCL fled ACL 211 1 Matrix Some overloaded functions are available for matrix computations double CSPmatrix ConditionNumber void CSPmatrix SPL_Multiply const CSPmatrix amp A const CSPmatrix amp B CSPnumeric SPL_Multiply const CSPmatrix amp A const CSPnumeric amp x For example CSPevaluator s CSPmatrix A matrix 5 8 nrow 2 A lt matrix 5 8 nrow 2 CSPmatrix B A B lt A CSPmatrix D SP
24. FFECTS Side effects from the function lt s side effects gt lt s side effects gt GRAPHICAL A description of graphical interactions See below INTERACTION expected of the user CLASSES A description of the classes the functionis See below applicable to if it is a default method 63 Chapter 4 User Defined Help Table 4 3 Titled sections in S PLUS engine help files Titles in all capitals appear in a formatted help file Titles in lowercase letters do not appear in a help file but the information in those sections do Continued Section Title Quick Description SGML Tags WARNING Anything the user should be warned about See below when using the function DETAILS Descriptions of algorithmic details and lt s details gt implementation issues lt s details gt BACKGROUND Background information on the function See below or method NOTE Any information that does not fit into the See below above categories REFERENCES Available texts and papers the user can See below refer to for additional information BUGS Descriptions of known bugs in the See below function SEE ALSO Links to related S PLUS functions lt s see gt lt s see gt EXAMPLES Coded S PLUS examples lt s examples gt lt s examples gt Keywords A list of keywords that place the help file lt s keywords gt in the Contents topics of the help system lt s keywords gt Topic The topic section c
25. ION Resources 20 CONNECT C is a tool used for interfacing C with the S language It is a convenient tool for integrating the S PLUS engine inside other programs written in C but it can also be used for integrating C code into the S PLUS environment To enable communication between the GUI Graphical User Interface and S PLUs CONNECT C was developed to provide a framework for the S language version 4 based engine used in S PLUS 6 0 for Windows In fact the S PLUS 6 GUI provides the most comprehensive example of using CONNECT C to integrate the S PLUS engine with C applications Similarly C developers could create their own GUI to interface with S PLUS using the same technique CONNECT C is a class library providing C classes with member functions that operate on S PLUS objects similar to S methods in the S language Users can use these classes and their member functions to create and manipulate persistent as well as local S objects CONNECT C provides various mechanisms for evaluating S expressions inside a C program and module S PLUS 6 x ships with several examples that illustrate how to use this library Some of these examples contain pairs of equivalent S and C functions that perform the same tasks The speed of the C functions can be many times faster than the S code depending on the code s complexity and the data sizes The examples are located in the SHOME sconnect directory where SHOME is your
26. Insightful gnt from data S PLus 6 1 for UNIX Linux Supplement May 2002 Insightful Corporation Seattle Washington Proprietary Notice Copyright Notice Insightful Corporation owns both this software program and its documentation Both the program and documentation are copyrighted with all rights reserved by Insightful Corporation The correct bibliographical reference for this document is as follows S PLUS 6 1 for UNIX Supplement Insightful Corporation Seattle WA Printed in the United States Copyright 1987 2002 Insightful Corporation All rights reserved Insightful Corporation 1700 Westlake Avenue N Suite 500 Seattle WA 98109 3044 USA ACKNOWLEDGMENTS S PLUS would not exist without the pioneering research of the Bell Labs S team at AT amp T now Lucent Technologies John Chambers Richard A Becker now at AT amp T Laboratories Allan R Wilks now at AT amp T Laboratories Duncan Temple Lang and their colleagues in the statistics research departments at Lucent William S Cleveland Trevor Hastie now at Stanford University Linda Clark Anne Freeny Eric Grosse David James Jos Pinheiro Daryl Pregibon and Ming Shyu Insightful Corporation thanks the following individuals for their contributions to this and earlier releases of S PLUS Douglas M Bates Leo Breiman Dan Carr Steve Dubnoff Don Edwards Jerome Friedman Kevin Goodman Perry Haaland David Hardesty Frank Harrell Richard Heiberg
27. Interface Experiments Programming Response Surfaces and Robust Design fracfac Fractional rsm Response taguchi Robust Factorial Surfaces Experimental Experiments Design modgarch GARCH geostat Geostatistical hexbin Hexagonal Module for Data Analysis Binning Modeling Time Series Volatility lattice Lattice Data pointpattern Point Pattern spatialreg Spatial Analysis Analysis Regression spatialstats Spatial WAVELETS Wavelet swt Discrete Statistics Analysis of Wavelet Module Data Signals Transform and Images Analysis Table 4 4 Current keywords and the Contents topics they map to Continued Contents of Help Files Keyword Topic Keyword Topic Keyword Topic transformld 1 D Wavelet transform2d 2 D Wavelet conv Wavelet and Cosine and Cosine Convolutions Transforms Transforms and Filters cpt Cosine wpt Wavelet Packet crystal Wavelet Packet Analysis Crystals Analysis molecule Wavelet wavemake Creating wavelets Wavelets Molecules Wavelets Module and Atoms Wavelet Functions Packets and Cosine Packets wavedata Wavelets Module Signals Images and Datasets Special Help Files Some S PLUS help files do not fit into the general format described above and instead require special fields The two most common types of special help files are those for class objects and data sets In this section we briefly list the fields in these types of help files We do not discuss each field in detail but refe
28. Jackknife libchron Library of Other Methods Chronological Languages Functions libcluster Library of libmaps Library of algebra Linear Algebra Clustering Maps Methods list Lists loess Loess Objects logic Logical Operators iteration Looping and math Mathematical array Matrices and Iteration Operations Arrays methods Methods and misc Miscellaneous missing Missing Values Generic Functions mixed Mixed nime3 Mixed Effects multivariate Multivariate Effects Models version Techniques Models 3 version 2 nonlinear Nonlinear nonparametric Nonparametric optimize Optimization Regression Statistics ode Ordinary print Printing distribution Probability Differential Distributions Equations and Random Numbers 75 Chapter 4 User Defined Help Table 4 4 Current keywords and the Contents topics they map to Continued 76 Keyword Topic Keyword Topic Keyword Topic programming Programming qc Quality Control regression Regression tree Classification release Release Notes resample Resampling and Bootstrap Regression Jackknife and Trees Permutations robust Robust environment S PLUS Session smooth Smoothing Resistant Environment Operations Techniques htest Statistical menustat Statistics Menu models Statistical Inference Functions Models survival4 Survival ts Time Series trellis Trellis Displays Analysis Library guifun User utilities Utilities DOX Design of
29. L files does not have a specific tag but uses lt s section name name gt and lt s section gt instead For example the background section in the hclust help file provides general information on clustering algorithms lt s section name BACKGROUND gt Cluster analysis divides datapoints into groups of points that are close to each other The lt s expression gt hclust lt s expression gt function continues to aggregate groups together until there is just one big group If it is necessary to choose the number of groups this can be decided subsequently Other methods see lt s expression gt kmeans lt s expression gt require that the number of groups be decided from the start lt p gt By changing the distance metric and the clustering method several different cluster trees can be created from a single dataset No one method seems to be useful in all situations Single linkage lt s expression gt connected lt s expression gt can work poorly if two distinct groups have a few stragglers between them lt s section gt NOTE REFERENCES Contents of Help Files Anything that does not fit into one of the above categories can be described in this section The note section in S PLUS SGML files does not have a specific tag but uses lt s section name name gt and lt s section gt instead The following is a note from the gamma help file lt s section name NOTE gt See lt s expression gt family lt s expres
30. L_Multiply A B D lt A B CSPnumeric x 1 2 ii x lt roormc2 CSPnumeric y SPL_Multiply A x y lt A x 37 Chapter 2 CONNECT C Printing to Standard Output Named Persistent Objects 38 You can use the following CONNECT C method to print to the S PLUS standard output stream void CSPobject Print void For example CSPevaluator s CSPcharacter message hello message lt hello message Print print message CSPmatrix M matrix 1 4 nrow 2 M lt matrix 1 4 nrow 2 M Print print M All CSPobject derived objects are placeholders for an s_object that exists in the engine So this C object can reference an s_object or none at all depending on whether the member s_object pointer points to a valid s_object All CSPobject derived classes have a method called IsValid which allows you to test whether it is pointing to a valid s_object or not All named objects are created in a permanent frame associated with an S PLUS database and are thus persistent between calls and between sessions in the S engine When you create a new CSPobject in your client program a new s_object is created in the S engine When you delete this CSPobject the s_object is also released in the engine However when you execute S PLUS expressions to remove the s_object that your CSPobject points to such as by using rm myObject or you call the Remove method on the object the CSPobject
31. S PLUs installation directory For more information on CONNECT C go to SHOME sconnect help ConnectC Class library htm This HTML file is a guide to the CONNECT C class library for C developers and it discusses how to connect to the S PLUS engine how to create data objects call S PLUS functions and evaluate S PLUS syntax Simple Examples An Application and a Called Routine SIMPLE EXAMPLES AN APPLICATION AND A CALLED ROUTINE Creating a Simple Application CONNECT C can be used for two distinct purposes to create C applications that can access S PLUS functionality and to create C functions that can be called via the S PLUS Ca11 interface We begin our investigation of CONNECT C with a simple example of each The CONNECT C 4 application used in this example is a console application that creates two S PLUS vectors It then uses S PLUS to compute a linear model relating the two vectors The code begins with the inclusion of sconnect h the CONNECT C library which all CONNECT C code must reference at the start It then declares a global S PLUS connection object with the CONNECT C 4 class CSPengineConnect before beginning the main application function The CSPengineConnect class generates a connection between the client application and S PLUS allowing you to create S PLUS objects in the permanent frame notifying you when the databases are attached or detached to the client and evaluating S language exp
32. S SGML files does not have a specific tag but uses lt s section name name gt and lt s section gt instead The following is the warning section from the gamma help file lt s section name WARNING gt lt s expression gt gamma x lt s expression gt increases very rapidly with lt s expression gt x lt s expression gt Use lt s expression gt lgamma lt s expression gt to avoid overflow lt s section gt Algorithmic details and implementation issues are described in this section For example the details section of the density help file explains the smoothing algorithm implemented in the function lt s details gt These are kernel estimates For each lt s expression gt x lt s expression gt value in the output the 69 Chapter 4 User Defined Help BACKGROUND 70 window is centered on that lt s expression gt x lt s expression gt and the heights of the window at each datapoint are summed This sum after a normalization is the corresponding lt s expression gt y lt s expression gt value in the output Results are currently computed to single precision accuracy only lt s details gt Details that apply to only one argument should be part of the affected argument s description and not part of the details section Background information on the function or method is described in this section The text here should be aimed at those with complete ignorance on the subject The background section in S PLUS SGM
33. Sys withlocale function 46 system requirements 3 T technical support 14 15 thousands separator argument 50 thousands separators 8 See digit grouping symbols toolbar help window 10 11 buttons on 11 topic pane help window 10 12 training courses S PLUS 14 try block 25 29 try catch block 25 Index typographic conventions 18 U unnamed objects 40 user defined help files See help files user defined V variable names characters allowed in 48 characters not allowed in 49 WwW Windows Regional Options 8 Windows Regional Settings 8 writeNextDataRows function 82 90 91 93 99 Index 100
34. UI in this release to the console of the machine on which S PLUS is installed that is treat this release of the Java based GUI as a workstation release rather than as a network client For specific details describing the limitations of Java GUI clients on remote displays see the S PLUS 6 includes two additional flags jit and helpoff The jit flag works with the g j and userapp flags and allows you to turn on the Java just in time compiler This makes the graphical user interface and help system run faster but introduces instabilities that often lead to crashes In particular the just in time compiler often crashes while repainting graphical user interface elements such as the JavaHelp window and the Data window The helpoff flag is useful only with the g flag It turns off the automatic invisible startup of the help system The invisible startup improves initial responsiveness of the help system but Installation adds a significant memory footprint to the current session If you want to optimize your available memory this flag may prove useful Chapter 1 Welcome WHAT S NEW IN S Ptus 6 1 CONNECT C Globalization In this section we briefly describe the new features in S PLUS 6 1 Detailed information can be found in the relevant chapters of this supplement For information on other enhancements and improvements in S PLUS 6 1 see the release notes CONNECT C 4 is now available with S PLUS for UNIX Linux
35. a UNIX prompt type Splus6 make install help Running the Splus6 make instal1 help utility invokes two other processes HINSTALL This copies myfunc sgml to Data __Shelp myfunc sgm and translates this sgm file to HTML and stores it as Data __Hhelp myfunc html Note the suffix is sgm and not sgml which preserves the original file BUILD_JHELP This creates the _ Jhelp directory and populates the directory with the XML files required to catalog and dispatch JavaHelp These XML files are described in Table 4 1 Step 6 Viewing the Help File Creating Editing and Distributing a Help File Table 4 1 Files within the _ Jhelp directory File Description hs The help set file which acts as an identifier to JavaHelp Index xml The index file which lists all the topics in the help set and is used as the text for the Index tab TOC xml The Table of Contents file which lists the topics in the help set by category and is used as the text for the Contents tab Map jhm The mapping file which maps topic names to specific URLs This is the most important file in the help set both the Index file and the TOC file rely on it mapsHelpSearch A directory containing the files used by JavaHelp s full text search facility on the Search tab This process also reveals any errors in SGML and warns you if there are any deficiencies If the Splus6 make install help should f
36. accented characters and uses a more natural sort order a then A then a 340 then A 300 In continental based locales the decimal marker is a comma In English based and French Canadian locales the decimal marker is a period Not every locale is supported on every computer To see which locales are supported on a computer running a version of UNIX run locale a Hint Choose a locale with 8859 1 in the name if there is a choice between this and Roman8 as S PLUS assumes you are using the ISO 8859 1 character set Your terminal emulator should be using an 8859 1 font This is an issue on HPUX where the default seems to be Roman8 45 Chapter 3 Globalization Setting a Locale Setting a locale gives you a way to tell S PLUS which character sets number formats and collation sequences to use The primary function for setting a locale is the Sys setlocale function This function allows you to set LC_ALL LC_COLLATE LC_CTYPE LC_MONETARY LC_NUMERIC or LC_TIME To use the default regional settings for locale type the following gt Sys setlocale locale This command tells S PLUS to follow the UNIX environment variables LANG LC_ CTYPE COLLATE NUMERIC Hint If you put the desired Sys set1ocale command into your S init file the command will be run automatically each time you launch S PLUS Changing a Locale Changing the Coll
37. ail in this event edit your SGML file before proceeding Now that the help files can be accessed by JavaHelp you can view your files in S PLUS and determine if any changes need to be made To view the edits in your help file first launch S PLUS Then attach the chapter and invoke your help file from the Commands window gt attach myfuncdir gt help myfunc 59 Chapter 4 User Defined Help Step 7 Distributing the Help File 60 You should see the help file for myfunc displayed in the help viewer and you can check for any formatting or content errors If you need to correct anything repeat steps 4 through 6 by editing the file running Splus6 make install help and viewing the file You can modify your S init file to attach the chapter where you created your help files each time you start S PLUS You can now distribute the files as necessary which you could package as a compressed archive or self extracting executable A utility such as compress or gzip could be used for this purpose The remaining sections in this chapter are devoted to the use and format of SGML tags in S PLUS help files which are necessary to understand the editing phase of step 4 COMMON TEXT FORMATS Common Text Formats Table 4 2 lists the most common text formats for S PLUS SGML files Note that this list is not exhaustive in general there might be many tags to format text in a particular way We suggest using tags with names that desc
38. aining the code cd SHOME sconnect samples gausssd 2 Build the share library Splus6 CHAPTER sconnectlib cxx Splus6 make 3 Run S PLUS Splus6 With the makefile created by CHAPTER compiling your code is simple just run the make command as an S PLUS utility as shown in step 2 The Splus6 in front of make allows S PLUS to set its environment variables appropriately before calling the standard make utility in particular it defines the SHOME environment variable used in the makefile Simple Examples An Application and a Called Routine The make utility executes the necessary commands to compile and link the C code into the shared object S so Note that sconnectlib is required to include the CONNECT C library The CONNECT C called via Ca11 implementation runs considerably faster than the S PLUS code Here is a comparison for a matrix A with 100 columns and 100 rows on a Solaris machine gt A lt matrix rnorm 10000 nrow 100 diag A lt seq ncol A ncol A Make it diagonally dominant gt b lt rnorm 100 gt sys time xl lt gaussSeidel A b 1 27 0 39 35 gt sys time x2 lt Call gaussSeidel A b 1 0 04 0 04 The CONNECT C 4 version ran about 1000 times faster than the pure S PLUS version 27 Chapter 2 CONNECT C CONNECT C CLASS OVERVIEW Data Object Classes Function Evaluation Classes 28 The class library provides a set of classes that can be used to create and m
39. anipulate persistent data objects run S PLUS functions parse and evaluate S PLUS expressions and receive output and notification when objects are changed or when databases are attached and detached The following sections provide an overview of specific categories of classes used to accomplish these operations Data object classes provide methods to create and operate on arrays matrices and vectors To use these classes to create a data object simply call the object constructor or call the Create method Fora persistent object specify the name of the object and an S language expression you want to parse evaluate and assign the result in order to initialize it with data Alternatively a data object can be constructed using a form of the constructor that takes an optional S language expression as an argument This is useful if named persistent objects are not required but intialization is required Once the object is created methods can be used to operate on the object To receive notification in a client application when a data object changes create a new class in the client application derived from the appropriate base class and override the virtual methods for handling object notification When a named object is modified or removed those virtual methods in the client are called The CSPcal1 class allows S PLUS functions to be evaluated with arguments passed to the function Arguments are any S_object as well as objects deriv
40. ation Sequence 46 Use the Sys setlocale and Sys getlocale functions to set and get locales respectively Use the Sys withlocale function if you want to evaluate an expression within a specified locale For example gt Sys getlocale Default 1 Es gt Sys setlocale locale en_US 1 en_US gt Sys getlocale 1 en_US Collation sequence refers to the ordering of characters by the sort and order functions For example in the C locale uppercase capital letters collate before lowercase letters In almost all other locales however collation sequence ignores case For example gt Sys setlocale locale C 1 ba ii gt Sortce as Axe rij Axe as Working With Locales gt Sys setlocale locale English United States 1 English_United States 1252 gt sorte as Axe i 1 as TAKE Changing LC_COLLATE affects the way S PLUS interprets the ordering of character data and thus can be used to change the behavior of functions like sort and order 47 Chapter 3 Globalization USING EXTENDED CHARACTERS In Variable Names 48 S PLUS 6 1 accepts more alphabetic characters than in earlier versions This set of alphabetic characters is fixed and is the set of characters considered alphabetic in ISO 8859 1 Latin1 Western European character set The set of characters that are displayed as octal codes changes depending on the cu
41. bit Solaris Solaris 2 6 7 or 8 e Red Hat Linux 6 1 6 2 7 0 7 2 Before installing S PLUS review the minimum system configuration information in Table 1 1 To determine the required RAM sum the base RAM and the per user RAM multiplied by the number of simultaneous users For example a single user Linux system should have at least 64 32 1 96MB of RAM Table 1 1 Minimum system configuration information for S PLUS 6 1 Linux Platforms Operating Platform System Disk Space Base RAM Per User RAM Sun SPARC Solaris 2 6 7 8 225MB 64MB 40MB Intel x86 Red Hat 6 1 6 2 7 0 7 2 225MB 64MB 32MB The base RAM and per user RAM listings can also be used to calculate minimum swap space requirements In general the minimum swap space required is twice the sum of the base RAM and the per user RAM multiplied by the number of simultaneous users For example on a Solaris system with three simultaneous S PLUS users the minimum swap space is 2 64 40 3 368MB These values are minima if you work with moderately sized data sets the numbers may be insufficient for your needs Note also that they are computed for simple command line S PLUS If you intend to run the Java GUI you should add approximately 100MB RAM per user to the numbers shown in Table 1 1 For example on Solaris Insightful Corporation recommends approximately 200 MB RAM for one user running the Java GUI S PLUS 6 1 was developed under Red Hat
42. connection Oracle connectivity is supported only in Solaris versions of S PLUS 6 1 and ODBC is supported only in Windows versions server A character string specifying the database server user A character string specifying the user name password A character string specifying the user s password for accessing the database database A character string specifying the database This must be the empty string when type oracle odbcConnection A character string containing an ODBC connection string when type odbc This argument is functional only in Windows versions of S PLUS 6 1 sqlQuery A character string specifying the SQL query to execute The return value from executeSQL is a character vector containing any messages from the database or NULL if no messages were generated Errors from the Oracle database do not cause errors in the S PLUS engine Executing Arbitrary SQL Statements The executeSQL function discards all data returned by the query You can use importData or openData to import data from an Oracle database see the section Reading Data From an Oracle Database on page 83 for details Whenever data is discarded executeSQL prints a warning message as notification Examples In the following sequence of commands we first create a table named test_2 in the Oracle database ORACLEDB and then write the first 20 rows of fuel frame to it To do this we use the openData function to open a conn
43. d contain an S PLUS expression that calls to an appropriate generating function However it works for any S PLUS expression that returns a valid S PLUS object and the 31 Chapter 2 CONNECT C Constructing From an Existing Object 32 constructor automatically coerces the returned object to the class that it represents It increments the reference count upon completion as well In case of errors the constructor throws an exception in the client application For example CSPevaluator s CSPinteger x 1 4 I x lt 1 4 CSPnumeric y fuel frame L 1 y lt as fuel frame 1 numeric CSPnumeric z new numeric z lt new numeric CSPmatrix A matrix 1 4 nrow 2 A lt matrix 1 4 nrow 2 CSPmatrix B 1 4 B lt as 1 4 matrix Do something with x y z A and B You can construct new objects from existing objects using one of the following forms CSPclass CSPclass const CSPclass amp sObject copy constructor CSPclass CSPclass s_object ps_object construct from s_object where class is a CSPobject derived object The copy constructor of a CONNECT C class behaves like an S PLUS assignment operator when the S PLUS object name is first used They both share the same data with the object names used to construct them However for the CONNECT C 4 classes sharing is not possible if the classes are incompatible It increments the reference count upon completion A
44. database named ORACLEDB This table describes employees at an imaginary company and includes fields for employee number name job manager number hire date salary commission and department number JOB MGR HIREDATE SAL COMM DEPTNO CLERK 7902 12 17 1980 00 00 00 000 800 NA 20 SALESMAN 7698 02 20 1981 00 00 00 000 1600 300 30 SALESMAN 7698 02 22 1981 00 00 00 000 1250 500 30 MANAGER 7839 04 02 1981 00 00 00 000 2975 NA 20 SALESMAN 7698 09 28 1981 00 00 00 000 1250 1400 30 MANAGER 7839 05 01 1981 00 00 00 000 2850 NA 30 MANAGER 7839 06 09 1981 00 00 00 000 2450 NA 10 ANALYST 7566 04 19 1987 00 00 00 000 3000 NA 20 PRESIDENT NA 11 17 1981 00 00 00 000 5000 NA 10 SALESMAN 7698 09 08 1981 00 00 00 000 1500 0 30 CLERK 7788 05 23 1987 00 00 00 000 1100 NA 20 CLERK 7698 12 03 1981 00 00 00 000 950 NA 30 ANALYST 7566 12 03 1981 00 00 00 000 3000 NA 20 CLERK 7782 01 23 1982 00 00 00 000 1300 NA 10 83 Chapter 5 Oracle Connectivity The importData Function 84 The principal tool for importing data from the S PLUS command line is importData This function accepts a type argument which is a character string specifying the file type of the data to be imported In older versions of S PLUS it is possible to specify type oracle to import data directly from an Oracle database When specifying type oracle you can define the appropriate Oracle server user name password and table with the server user password and table arguments respect
45. does not exist The writeNextDataRows appends rows of data to the table adding new fields as necessary You cannot use exportData or writeNextDataRows to overwrite an existing Oracle table See the examples in the section Executing Arbitrary SQL Statements on page 92 for examples using both exportData and writeNextDataRows Hints Another way of adding rows to an existing table is to write to a temporary table and then use an INSERT statement with executeSQL to merge the temporary table to an existing one This may reduce issues with a database being locked due to another process writing to it To overwrite an existing table in an Oracle database use the executeSQL function to drop the table first and then use exportData or openData with writeNextDataRows to create a new one See the section Executing Arbitrary SQL Statements below for information on executeSQL 91 Chapter 5 Oracle Connectivity EXECUTING ARBITRARY SQL STATEMENTS 92 S PLUS 6 1 includes a new function named executeSQL for executing arbitrary SQL statements This function has the arguments listed in Table 5 2 You can use executeSQL as an interface to your Oracle database for performing functions such as creating blank tables and inserting rows into an existing table Table 5 2 Arguments for the executeSQL function Argument Name Description type A character string either oracle or odbc specifying the type of database
46. e a mouse is required Clicking the selection button on a node results in the additional screens being filled with the information described above This process may be repeated any number of CLASSES WARNING DETAILS Contents of Help Files times Warnings result from selecting leaf nodes Clicking the exit button will stop the display process and return the list described above for the last node selected See lt s expression gt split screen lt s expression gt for specific details on graphic input and split screen mode lt s section gt This section lists the classes the function is applicable to if it is a default method Like the graphical interaction section the classes section in S PLUS SGML files does not have a specific tag Instead the tags lt s section name name gt and lt s section gt are used For example the classes section in the gamma help file is lt s section name CLASSES gt This function will be used as the default method for classes that do not inherit a specific method for the function or for the lt tt gt Math lt tt gt group of functions The result will retain the class and the attributes If this behavior is lt em gt not lt em gt appropriate the designer of the class should provide a method for the function or for the lt tt gt Math lt tt gt group lt s section gt Anything the user should be warned about when using the function should be described here The warning section in S PLU
47. e section That is you should write a list with two components instead of simply list with two components Side effects of the function plotting changing graphics devices changing session options etc are described in this section This is also the appropriate place to describe the lack of side effects if a user might expect one For instance the fact that many S PLUS editing functions do not actually change an object can be documented in the side effects sections of their SGML files Any function that updates the object Random seed must include the following message in its side effects section The function name causes the creation of the data set Random seed if it does not already exist Otherwise the value of Random seed is updated If the user is expected to interact with a graphical display the interaction is described in this section Help files that currently contain this section include burl tree hist tree and snip tree The graphical interaction section in S PLUS SGML files does not have a specific tag Instead the tags lt s section name name gt and lt s section gt are used For example the following excerpt is from the hist tree SGML file lt s section name GRAPHICAL INTERACTION gt This function checks that the user is in split screen mode A dendrogram of lt s expression gt tree lt s expression gt is expected to be visible on the current active screen and a graphics input device for exampl
48. e user can refer to for lt s section name gt additional information lt s section gt SEE ALSO Links to related S PLUS functions The function that lt s see gt creates the object should be included in the links lt s see gt Keywords A list of keywords that place the help file in the lt s keywords gt Contents topics of the help system lt s keywords gt 78 Data Sets Contents of Help Files The SGML sections in help files for data sets are listed in Table 4 6 For more details see the SGML files for solder and kyphosis Table 4 6 Titled sections in S PLUS help files for data sets Section Title Quick Description SGML Tags Topic The name of the data object lt s topics gt lt s topics gt Title The title that appears at the top of a formatted help lt s title gt file This should not be the name of the object lt s title gt itself SUMMARY A brief description of the experiment that lt s section name gt produced the data The name of the object should lt s section gt be included in this section DATA A short description of each of the variables in the lt s description gt DESCRIPTION object lt s description gt SOURCE The original references for the data lt s section name gt lt s section gt WARNING Anything the user should be warned about when lt s section name gt using the data lt s section gt NOTE Any information that does not fit into the
49. ecify a locale to be used by S PLUS Specifically S PLUS 6 1 now supports French and German locales Sorting and collating functions have been modified to support different locales The use of 8 bit characters Latinl1 Western European character set has been enabled The 8 bit characters can now be used in variable names and will properly display in data Functions that import export and display numeric data have been modified to support different locales S PLUS Setup has been improved to test for local settings and install localized DLLs as necessary In the sections that follow we describe these enhancements in greater detail Working With Locales WORKING WITH LOCALES A locale determines which characters are considered printable or alphabetic the format for numerals and the collating sequence of characters Note The implementation of locales in S PLUS does not cover date formats date formats are handled through a separate mechanism and messaging all messages in S PLUS are in the English language The default locale is C the locale used by the C language 7 bit ASCII characters and U S style numbers The C locale conforms to the behavior of earlier versions of S PLUS that is No accented characters are displayed backslash octal instead The decimal marker is a period e The sort order is all uppercase followed by all lowercase In European based locales however S PLUS prints
50. ection to the database writeNextDataRows to write the data to the table and closeData to close the connection gt executeSQL type oracle user scott password tiger server ORACLEDB sqlQuery create table test_2 x number gt dh lt openData type oracle openType write user scott password tiger table test_2 server ORACLEDB gt writeNextDataRows fuel frame 1 10 dh 10 gt writeNextDataRows fuel frame 11 20 dh 10 gt closeData dh ti T The next command uses exportData to write the next 30 rows of fuel frame to test_2 This command does not overwrite the table but instead appends the rows to it gt exportData fuel frame 21 50 type oracle user scott password tiger table test_2 server 0RACLEDB 1 40 93 Chapter 5 Oracle Connectivity 94 Finally we use an INSERT statement to append the 50 rows in test_2 to the test_1 table see the examples on page 88 for instructions on creating test_1 This illustrates a different way of adding rows to an existing table in an Oracle database which can reduce issues with the database being locked due to another process writing to it gt executeSQL type oracle user scott password tiger server ORACLEDB sqlQuery INSERT INTO test_1 SELECT FROM test_2 NULL INDEX Symbols Call interface 8 21 23 25 27 29 34 40 A arithmetic operators 36 Assign 22 assignment
51. ed from CSPobject which may include data objects and other S PLUS objects Results are returned as a CSPobject to the client To use this class simply call the object constructor with the name of the function to run and any arguments you wish to pass from the client to the function Client to Engine Connection Classes Evaluator Classes CONNECT C 4 Class Overview The CSPengineConnect class creates a connection between the client and the S PLUS engine This connection permits creation of objects in the permanent frame creation of persistent unnamed objects outside of Ca11 routines notification in the client when databases are attached or detached output routing to the client and evaluation of S language expressions To use CSPengineConnect create a new class derived from CSPengineConnect in the client override the virtual methods for receiving database attach detach notification and output notification and add a member variable to the client application class object to record a reference to a single instance of this derived class Use of the CSPengineConnect class is only necessary when one or more of the following features is desired in the client program e Integrate S engine shared library libSqpe so with another application client e Notification in the client when databases are attached or detached and when changes are made in persistent objects e Output redirected to the client For more information on usi
52. elp File By default this file is placed in your S PLUS working directory If you have a number of help files to create use prompt for each function The next step is to copy the SGML file s to a directory that will become an S PLUS chapter This chapter becomes the chapter you attach in your S PLUS session to access your user defined help files From a UNIX prompt create a new directory and copy the SGML files from the working directory mkdir myfuncdir cp myfunc sgml myfuncdir If you have a number of help files type cp sgml myfuncdir to copy all the SGML files to the directory Change directories to myfuncdir and proceed to the next step As mentioned in the previous step the CHAPTER utility must be run on the directory so myfuncdir can be recognized as an S PLUS chapter Splus6 CHAPTER This process creates the chapter s Data directory which includes the __Shelp and _ Hhelp directories that are required in step 5 to install the files so they can be accessed by JavaHelp You can view and edit the file in your text editor of choice such as emacs or vi For example if you want to invoke the vi editor to edit your file type the following command vi myfunc sgml Your skeleton help file should contain text similar to the following lt doctype s function doc system s function doc dtd lt lentity S OLD INCLUDE gt gt lt s function doc gt lt s topics gt 57 Chapter 4 User Defined Help
53. epts the new argument sq1Query which allows you to execute arbitrary SQL statements when importing Oracle data As with importData the sqlQuery argument to openData must be a single character vector and cannot be specified in conjunction with the table argument Note When openData is called with the table argument a new table is created if one by the specified name does not already exist 87 Chapter 5 Oracle Connectivity 88 Examples First we create a table named test_1 in the Oracle database ORACLEDB that is a copy of the built in data set fuel frame See the section Writing Data to an Oracle Database for information on the exportData function gt exportData fuel frame type oracle user scott password tiger table test_1 server ORACLEDB 1 60 Use openData to create a data handle that reads 10 rows at a time from the test_1 table gt dh lt openData type oracle rowsToRead 10 openType read user sScott password tiger table test_1 server ORACLEDB Read the first 10 rows from the table gt readNextDataRows dh WEIGHT DISP MILEAGE FUEL XTYPE 1 2560 97 33 3 030303 Smal 2 2345 114 33 3 030303 Small 3 1845 81 37 2 702703 Sia 4 2260 gi 32 3 125000 Small 5 2440 113 32 3 125000 Small 6 2285 97 26 3 846154 Small 7 2275 97 33 3 030303 Small 8 2350 98 28 3 571429 Small 9 2295 109 25 4 000000 Small 10 1900 is 34 2 941176 Small Read the second 10 rows fro
54. er Mia Hubert Richard Jones Jennifer Lasecki W Q Meeker Adrian Raftery Brian Ripley Peter Rousseeuw J D Spurrier Anja Struyf Terry Therneau Rob Tibshirani Katrien Van Driessen William Venables and Judy Zeh iii iv CONTENTS Acknowledgments Chapter 1 Welcome Welcome to S PLUS 6 1 Installation What s New in S PLUS 6 1 Help Support and Learning Resources Typographic Conventions Chapter 2 CONNECT C Introduction Simple Examples An Application and a Called Routine CONNECT C Class Overview CONNECT C Architectural Features Chapter 3 Globalization Introduction Working With Locales Using Extended Characters Importing Exporting and Displaying Numeric Data iii ow N 10 18 19 20 21 28 31 43 44 45 48 50 Contents Chapter 4 User Defined Help Introduction Creating Editing and Distributing a Help File Common Text Formats Contents of Help Files Chapter 5 Oracle Connectivity Introduction Reading Data From an Oracle Database Writing Data to an Oracle Database Executing Arbitrary SQL Statements Index vi 53 54 56 61 63 81 82 83 90 92 95 WELCOME Welcome to S PLUS 6 1 Installation Supported Platforms and System Requirements Installation Instructions Running S PLUS What s New in S PLUS 6 1 CONNECT C Globalization User Defined Help Oracle Connectivity Solaris Only Help Support and Learning Resources Online Help Online Manuals
55. er icons labeled with the name of the category To open a category double click the icon or label To select a topic within the category double click its page icon or the topic title The Index page lists available help topics by keyword Keywords are typically function names for S PLUS language functions Type a word in the text box and press ENTER to find the keywords that most closely match it e The Search tab provides a full text search for the entire help system Type the word or phrase you want to find in the text box and press ENTER JavaHelp displays in the list box all help files containing that keyword Double click a title to display the desired help topic Using the topic pane The topic pane appears on the right side of the help window and displays the help topics you choose It usually appears with both vertical and horizontal scroll bars but you can expand the JavaHelp window to increase the width of the right pane Many help files are too long to be fully displayed in a single screen so choose a convenient height for your JavaHelp window and then use the vertical scroll bars to scroll through the text Help at the Command Line Online Manuals Help Support and Learning Resources When working from the S PLUS command line you can obtain help for any S PLUS function using the he1p or functions For example to open the help file for anova simply type gt help anova or gt anova In addition to
56. ersen and Gill lt s description gt This section includes the function call with all of its arguments You should list optional arguments with the form name defau t Ifa default argument is complicated use the form name lt lt see below gt gt instead and describe the default in the argument s section of the SGML file Because the angle brackets lt and gt signify tags in SGML 65 Chapter 4 User Defined Help REQUIRED ARGUMENTS 66 however it is safest to type them as amp 1t and amp gt when tags are not intended Thus the form for a complicated default is name amp 1t amp lt see below amp gt amp gt If the help file describes more than one function the usage for each function should be listed on separate lines If the argument list for a function is more than one line long subsequent lines should be indented to one space past the opening parentheses Use spaces to indent each line instead of tabs For example the following is the usage section from the SGML file for 1m lt s usage gt lt s old style usage gt Im formula data amp lt amp lt see below amp gt amp gt weights amp 1t amp lt see below amp gt amp gt subset amp 1t amp lt see below amp gt amp gt na action na fail method qr model F x F y F contrasts NULL lt s old style usage gt lt s usage gt The tag lt s old style usage gt preformats the section so that it prints in a fixed width font This also causes newlin
57. es and blank lines to be recognized in the text Because of the preformatting no space is needed around the equals signs for each of the arguments In addition please ensure that the width of each line is no more than 60 characters so that the usage section displays nicely in conveniently sized help windows This section lists each required argument wrapped in the tags lt s arg name name gt and lt s arg gt The first word in the description of each argument should not be capitalized For example the following excerpt lists the three required arguments from the SGML file for ifelse lt s args required gt lt s arg name test gt logical object Missing values lt s object gt NA lt s object gt are allowed lt 7 s arg OPTIONAL ARGUMENTS VALUE Contents of Help Files lt s arg name yes gt vector containing values to be returned for elements with lt s expression gt test lt s expression gt equal to lt s expression gt TRUE lt s expression gt lt s arg gt lt s arg name no gt vector containing values to be returned for elements with lt s expression gt test lt s expression gt equal to lt s expression gt FALSE lt s expression gt lt s arg gt lt s args required gt In descriptions of arguments you should always state whether exceptional values NA NaN Inf etc are treated specially This section lists each optional argument wrapped in the tags lt s arg name name gt and lt
58. esources Kaluzny S P Vega S C Cardoso T P and Shelly A A 1997 SHSPATIALSTATS User s Manual Springer Verlag New York Meeker W and Escobar L 1998 Statistical Methods for Reliability Data John Wiley amp Sons Inc Millard S P and Krause A 2001 Applied Statistics in the Pharmaceutical Industry Springer Verlag New York Millard S P and Neerchal N K 2000 Environmental Statistics with S PLus CRC Press Selvin S 1998 Modern Applied Biostatistical Methods Using S PLUS Oxford University Press Therneau T M and Grambsch P M 2000 Modeling Survival Data Springer Verlag New York Graphical Techniques Chambers J M Cleveland W S Kleiner B and Tukey P A 1983 Graphical Methods for Data Analysis Duxbury Press Belmont CA Cleveland W S 1993 Visualizing Data Hobart Press Summit NJ Cleveland W S 1994 The Elements of Graphing Data Hobart Press Summit NJ S PLUS Programming Becker R A Chambers J M and Wilks A R 1988 The New S Language Wadsworth amp Brooks Cole Pacific Grove CA Chambers J M 1998 Programming with Data Springer Verlag New York Venables W N and Ripley B D 2000 S Programming Springer Verlag New York 17 Chapter 1 Welcome TYPOGRAPHIC CONVENTIONS Throughout this supplement the following typographic conventions are used e This font is used for S PLUS expressions and code samples This font i
59. hich should be called at the end of the overridden version in the client releases the member s_object from the CSPobject 39 Chapter 2 CONNECT C Storage Frames For Unnamed Objects 40 2 It can be removed by evaluating S PLUS expressions such as by calling CSPengineConnect SyncParseEval This also triggers a call to the OnRemove method of the CSPobject in the client program Normally when you create an unnamed CS Pobject in a client routine that you call via Ca11 the s_object corresponding to this CSPobject is alive or is valid until the routine ends and scope changes out of the routine If you create an unnamed CSPobject when the S PLUS evaluator is not open the s_object corresponding to this CSPobject may not be valid For most client applications this is usually inadequate Therefore you need to do the following to ensure that an unnamed CSPobject created in a client application does not get released until the end of the client routine e Create an instance of a CSPevaluator at the top of the scope a Pe e Create and use any unnamed CSPobject derived objects in the client For example CSPevaluator s CSPnumeric x 1 10 3 For named objects you do not have to use the above approach simply create named CSPobject derived objects using the constructor and a call to CSPobject Create For further information see the online help for the classes CSPengineConnect OpenTopLevelEval
60. inal command below returns the minimum and maximum salaries from each department as well as a count of the number of employees in each department gt importData type oracle user scott password tiger server O0RACLEDB sqlQuery SELECT deptno MIN sal MAX sal COUNT FROM emp GROUP BY deptno The openData Function Reading Data From an Oracle Database DEPTNO MIN SAL MAX SAL COUNT 1 10 1300 5000 3 2 20 800 3000 5 3 30 950 2850 6 To capture the results from any of these commands in S PLUS objects simply assign the output from the commands For example gt salary extremes lt importData type oracle user scott password tiger server 0RACLEDB sqlQuery SELECT deptno MIN sal MAX sal COUNT FROM emp GROUP BY deptno The openData function opens an external file so the data in the file may be read into S PLUS It returns a data handle which is an S PLUS object that can be passed to readNextDataRows to import sequential blocks of data from the file Together openData readNextDataRows and closeData the function for closing the external file when all data is imported provide the capability for reading arbitrarily large data sets into S PLUS The arguments to openData are structured similarly to those for importData In particular openData accepts a type argument you can set to oracle for importing data from an Oracle database In S PLUS 6 1 openData also acc
61. install help 56 58 59 60 text formats for 61 titled sections in 63 78 79 HINSTALL 58 I importData function 50 82 83 84 87 89 90 93 importing numerics 8 44 50 install help Splus6 make 56 58 59 60 installation 4 ISO 8859 1 character set 8 45 48 49 IsValid 31 38 J Java runtime environment 4 JavaHelp See help JRE 4 K keywords 12 55 64 74 78 79 L Language Reference 74 Index Latin1 44 48 49 locales 8 9 44 45 48 49 C 45 46 changing 46 setting 46 Sys getlocale function 46 Sys setlocale function 46 Sys withlocale function 46 M make 26 27 makefile 26 make install help Splus6 56 58 59 60 manuals online 13 viewing 13 markers decimal 8 45 50 51 methods CONNECT C 4 25 28 29 31 39 N named objects 38 39 40 names variables characters allowed in 48 characters not allowed in 49 navigation pane help window 10 12 Index page of 12 Search page of 12 Table of Contents page of 12 numerics displaying 8 44 45 50 51 exporting 8 44 50 importing 8 44 50 O objects named 38 39 40 unnamed 40 OnModify 38 39 OnRemove 38 39 40 97 Index 98 openData function 82 83 87 88 90 91 93 operators arithmetic 36 assignment 31 32 33 conversion 34 overloading 33 35 36 subscripting 35 36 Oracle 9 Oracle connectivity 82 83 90 92 closeData function 82 83 87 90 93 executeSQL function 82 91 92 93 exportData funct
62. ion 82 88 90 91 93 importData function 82 83 84 87 89 90 93 openData function 82 83 87 88 90 91 93 reading data 83 readNextDataRows function 82 83 87 90 SQL queries 82 84 87 92 writeNextDataRows function 82 90 91 93 writing data 90 order sort 45 order function 46 47 overloading operators 33 35 36 P platforms supported 3 postscript function 49 prompt function 55 56 57 58 77 Q queries SQL 9 R readNextDataRows function 82 83 87 90 reference counts 31 32 33 34 Regional Options Windows 8 regional settings 46 Regional Settings Windows 8 Remove 38 39 resources 10 runtime environment Java 4 S S init file 46 60 S so 27 S_EVALUATOR 25 s_object 25 28 34 38 39 40 sconnect h 21 25 sequences collation 8 45 46 settings regional 46 Setup S PLUS 44 sort function 46 47 sorting 44 sort order 45 S PLUS books using graphical techniques 17 introductory 15 S PLUS programming 17 statistics and data analysis general 15 specialized 16 installing 4 running 5 Setup 44 starting 5 with command line supporting Java 6 with command line without Java 5 with graphical user interface 6 training courses in 14 Web site 14 SQL queries 9 82 84 87 92 Standard Generalized Markup Language SGML 54 subscripting operators 35 36 support technical 14 15 swap space 3 symbols digit grouping 50 SyncParseEval 22 Sys getlocale function 46 Sys setlocale function 46
63. is 0 n n x 2 n lt ntas integer x 2 f n is still 0 The following is another example using the subscripting operator for a matrix CSPevaluator s CSPmatrix AC matrix c 1 6 2 0 8 0 9 ZY if ASe wWatrix eto 1 he 0 8 09 23 double d A 1 1 I7 d lt AC1 1 d is 0 1 d d A 2 1 ff d lt d A 2 1 d is 0 3 long e long A 2 1 e lt as integer A 2 1 e is 0 long n A 1 1 n lt as integer A 1 1 n is 0 n n A 2 1 n lt ntas integer A 2 1 n is still 0 35 Chapter 2 CONNECT C Subscript and Replacement Operations Subscript and Arithmetic Operations 36 If a subscript operator of a CSPobject derived class returns an 1value object of CSPproxy the operation involves replacing an element of the S PLUS object Since writing data is not possible for a shared S PLUS object CSPproxy must determine whether to copy data before replacing its elements This action occurs in one of its overloaded assignment operations CSPproxy amp CSPproxy operator long CSPproxy amp CSPproxy operator double CSPproxy amp CSPproxy operator const CSPproxy amp For example CSPevaluator s CSPnumeric x 1 4 7 X 154 xC1L 0 0 x 1 lt 0 x is not share simply set x 1 to 0 0 x2 x1 x 2 lt x 1 x is not share simply set x 2 to 0 0 CSPnumeric y x y lt x y shares data with x y 1 10 0 y 1 lt 10 copy and replace ff Y
64. is not deleted in your client The OnRemove method of the CSPobject in your client is called and the base class version of this method disconnects your CSPobject from the now released s_object by setting the member s_object pointer to NULL After this event calling IsValid on the CSPobject returns FALSE Deleting the CSPobject in your client program does not automatically remove the permanent frame s_object in the S PLUS engine that this CSPobject refers to You must call the method Remove to remove the s_object from the engine You can create named objects using the Create method of the various object classes derived from CSPobject such as CSPnumeric Whenever these objects are modified the OnModify method is CONNECT C Architectural Features called in your client program Whenever these objects are removed the OnRemove method is called in your client program Only named objects support this kind of client program notification To create a named object in your client first derive a new class from the appropriate CSPobject derived class such as CSPnumeric Then construct an instance of this derived class using the constructor then call the Create method to specify the name you wish to give the object It is important to derive a new class from the CSPobject derived class instead of just using the base class directly in your client because the OnModify and OnRemove methods are virtual and must be overridden in
65. ively The contents of the designated table are imported into S PLUS and returned as a data frame In S PLUS 6 1 you can also specify the new sq1Query argument when type oracle which allows you to execute arbitrary SQL queries with importData This allows more flexibility in the structure of data you can read from Oracle databases The sq1Query argument must be a single character vector for example select from mytable where Type Van S PLUS pastes multi element character vectors together using newlines as separators The return value from a call to importData that includes sq Query is the result from the query as an S PLUS data frame If the query produces no output the return value is NULL Any errors or warnings from the database that the query causes are stored as a message attribute to the return object messages from the database do not cause errors in the S PLUS engine The server user and password arguments to importData remain identical in function in S PLUS 6 1 You can still provide the table argument if you do not specify sqlQuery providing both arguments causes S PLUS to return an error To illustrate the following two argument settings are equivalent e table mytable e sqlQuery select from mytable Examples The following two commands are equivalent and return all data from the emp table Using the syntax table emp gt importData type oracle user sScott password tiger table
66. let std in calls to postscript The Symbol and Zapf family of fonts are not changed The Latin1 encoding is not quite the ISO 8859 1 standard in that the bullet character was added at position 200 49 Chapter 3 Globalization IMPORTING EXPORTING AND DISPLAYING NUMERIC DATA S PLUS 6 1 supports importing exporting and displaying numeric data written in regional notation This means you can import export and display numbers written using decimal markers and thousands separators other than the period and comma respectively For example you can specify a comma as your decimal marker and a period as your digit grouping symbol or you can use a period as the decimal marker and an apostrophe as your digit grouping symbol This feature is supported for the functions scan print read table and write table It is also supported for tick labels in graphics Note however that it is not supported for use within S PLUS expressions within x1ab and ylab in graphics or by default within the importData and exportData functions Hint The default values for x1ab and ylab do not use the numeric locale information because the default values are made with deparse However if you make up your labels with as character or paste the locale information is used Importing and The functions importData and exportData now have two Exporting Data additional arguments for use in reading and writing ASCII numbers
67. m the table gt readNextDataRows dh WEIGHT DISP MILEAGE FUEL TYPE 1 2390 97 29 3 448276 Small 2 2079 B9 35 2 857143 Small 3 2330 109 26 3 846154 Small 4 3320 305 20 5 000000 Sporty 5 2885 153 27 3703704 Sporty 6 3310 302 lf 5 263158 Sporty 7 2695 8 2170 2710 i 2775 133 97 125 146 30 33 27 24 Reading Data From an Oracle Database Sa 333333 3 030303 3 703704 4 166667 Sporty Sporty Sporty Sporty As with importData assign the output from the commands to capture the results in S PLUS objects For example gt rows 21 thru 30 lt readNextDataRows dh When all data has been read into S PLUS close the connection to the Oracle database gt closeData dh 1 T 89 Chapter 5 Oracle Connectivity WRITING DATA TO AN ORACLE DATABASE 90 The primary functions for writing data to an Oracle database are e exportData to export data directly or e writeNextDataRows in conjunction with openData and closeData to write sequential blocks of data to a table in the database As its name suggests the exportData function is the counterpart to importData In S PLUS 6 1 the arguments in Table 5 1 have been added to exportData to enhance Oracle connectivity on Solaris installations of S PLUS These new arguments are analogs to the corresponding importData arguments and function in generally the same way to write data to an Oracle database Likewise the writeNextDataRows function is the counter
68. mpt In general the steps are as follows 1 Use the prompt function to generate a SGML file in your working directory 2 Copy the SGML file to a new directory 3 Run Splus6 CHAPTER on this directory to create an S PLUS chapter 4 Edit the SGML file with your editor of choice Run Splus6 make install help to install the file so it can be accessed by JavaHelp 6 Launch S PLUS attach the S PLUS chapter and test the help file by typing gt help myfunc Repeat steps 4 6 until you are satisfied with the results If you have a number of files you want to add to your distribution you can also run this process on a number of help files at once Your working directory may change but as long as you attach the chapter that contains your help files you can always access them To illustrate this process we create a sample help file and detail each of the steps involved in distributing it in the following sections Step I Let s suppose you create a new S PLUS function named myfunc Creating the er Help File function x r eturntx 2 Use the prompt function to create a template help file named myfunc sgml gt prompt my func created file named myfunc sgml in the current directory edit the file according to the directions in the file 56 Step 2 Copying the Help File to a Clean Directory Step 3 Running the CHAPTER Utility Step 4 Editing the Help File Creating Editing and Distributing a H
69. n example of creating new objects from existing objects follows CSPevaluator s CSPnumeric x 1 4 x lt 1 4 CSPnumeric u x u lt x u shares data with x CSPmatrix A x A lt as x matrix A shares data with x Assignment Operators Overloading Operators CONNECT C Architectural Features CSPcharacter v x v lt as x character no sharing s_object ps_object x GetPtr Get pointer to s_object CSPnumeric U ps_object U shares data with x CSPmatrix a ps_object a shares data with x The assignment operator of an CONNECT C class behaves like an S PLUS assignment operator when the S PLUS object name is already used However the left hand side object of the operator is an existing and valid object The assignment operator decrements the reference count on the old object and increments the reference count on the new object before swapping the two object pointers CSPclass amp CSPclass operator const CSPclass amp sObject where class is a CSPobject derived object An example of the assignment operator follows CSPevaluator s CSPnumeric x 1 4 x lt 1 4 CSPnumeric u x u lt new numeric u lt x u shares data with x CSPmatrix A x A lt new matrix A lt as x matrix no sharing CSPnumeric y y lt new numeric u y u lt y u switches to share data with y A y A lt as y matrix A switches to share data with y CONNECT C 4
70. n followed by sgm For example the links in the SGML file for subplot are lt s see gt lt s function name symbols sgm gt symbols lt s function gt lt s function name locator sgm gt locator lt s function gt lt s function name par sgm gt par lt s function gt lt s see gt Functions that rely on the self doc mechanism for their help files cannot be linked in this section EXAMPLES Contents of Help Files Although newlines are not recognized in the see also section of S PLUS SGML files spaces are Thus be sure to include spaces between each link even if you type them on separate lines In the SGML file for subplot two spaces are included at the end of each line immediately after the lt s function gt tags The examples in this section should help the user understand the function better The goal is to provide the user with clear examples that are easily copied and run either from the commands window or from a script window Therefore do not include the S PLUS prompt character gt in your examples and comment any output you include So that the examples are self contained use built in data sets or create simple data sets in the code For clarity do not abbreviate argument names in your code and be sure to test your examples before including them in a help file The following is an excerpt from the examples section of the coxph help file lt s examples gt lt s example type text gt Create the sim
71. ng CSPengineConnect please see the section on this class in SHOME sconnect help ConnectC Class library htm The CSPevaluator class manages memory resources errors the top evaluation frame and a set of local evaluation frames Although it is optional instantiating an object of CSPevaluator class at the top of a try block can speed up the code and the corresponding catch block receives an exception error when an unexpected error occurs in the S PLUS engine To use CSPevaluator create an instance of this class at the top of a try block as shown below double minValue 0 try Open top level evalutor frame 1 if it is closed CSPevaluator sEvaluator CSPnumeric myNumeric sEvaluator eval 1 10 minValue myNumeric Min minValue 1 29 Chapter 2 CONNECT C 30 Close top level evaluator when sEvaluator is out of scope catcht Unexpected error occurred in the engine l For more information on using CSPevaluator please see the section on this class in SHOME sconnect help ConnectC Class library htm CONNECT C 4 Architectural Features CONNECT C ARCHITECTURAL FEATURES CSPobject Constructors and Generating Functions The following sections describe the basic architectural featues in the class library and some of the specific programming features available in the library that make it possible to perform S PLUS operations efficiently in client programs and modules written in
72. ontains the function name wrapped in the tags lt s topic gt and lt s topic gt In the myfunc sgml example the topic looks like lt s topi s gt lt s topic gt myfunc lt s topic gt lt s topics gt 64 Title DESCRIPTION USAGE Contents of Help Files In help files containing multiple functions each function name should be wrapped in the lt s topic gt tags For example the following is an excerpt from the common SGML file for cor and var lt s topics gt lt s topic gt cor lt s topic gt lt s topicrvar lt s topic gt lt s topics gt The topic section is not visible in a formatted help file but is used to index the file in the help system The title section contains the title that appears at the top of a formatted help file For example the title from the coxph SGML file is lt s title gt Fit Proportional Hazards Regression Model lt s Title gt All words in a title should begin in uppercase letters For clarity avoid S PLUS jargon such as function names and class names in the title section A title should be short enough to fit on one line in the help file This section contains a short description of the function The description in the coxph SGML file is lt s description gt Fits a Cox proportional hazards regression model Time dependent variables time dependent strata multiple events per subject and other extensions are incorporated using the counting process formulation of And
73. operators 31 32 33 B BUILD_JHELP 58 C C See CONNECT C catch block 29 characters allowed in variable names 48 not allowed in variable names 49 character sets 8 44 46 48 ISO 8859 1 8 45 48 49 classes CONNECT C 20 21 25 28 31 32 35 36 38 40 41 connection 29 data object 28 evaluator 29 30 function evaluation 28 class library 20 28 31 C locale 45 46 closeData function 82 83 87 90 93 collating 44 collation sequences 8 45 46 Commit 39 CONNECT C 20 Call interface 21 23 25 27 29 34 40 Assign 22 catch block 29 classes 20 21 25 28 31 32 35 36 38 40 41 connection 29 data object 28 evaluator 29 30 function evaluation 28 class library 20 28 31 Commit 39 constructors 28 31 32 39 40 converting objects 34 Create 22 28 38 39 40 CSParray 35 CSPengineConnect 21 29 39 40 CSPevaluator 29 30 40 CSPnumeric 21 34 35 38 39 41 CSPobject 28 31 32 33 34 36 38 39 40 41 CSPproxy 36 CSPvector 35 destructors 31 generating functions 31 95 Index 96 IsValid 31 38 make utility 26 27 methods 25 28 29 31 39 objects named 38 39 40 unnamed 40 OnModify 38 39 OnRemove 38 39 40 operators arithmetic 36 assignment 31 32 33 conversion 34 overloading 33 35 36 subscripting 35 36 printing 38 reference counts 31 32 33 34 Remove 38 39 S so 27 S_EVALUATOR 25 s_object 25 28 34 38 39 40 sconnect h 21 25 sconnectlib 27 See C
74. part to readNextDataRows You can use writeNextDataRows to insert data into a table in an Oracle database Before calling writeNextDataRows to do this however you must open a connection to the table using openData with the table argument not the sqlQuery argument see page 87 for details Table 5 1 New arguments to exportData that support Oracle connectivity Argument Name Description server A character string specifying the database server user A character string specifying the user name password A character string specifying the user s password for accessing the database database A character string specifying the database This must be the empty string when type oracle table A character string specifying the name of the table to write to when type oracle If a table by the specified name already exists exportData appends data to it If the table does not exist exportData creates it Writing Data to an Oracle Database When writing to a table exportData creates a new table if one by the specified name does not exist otherwise it appends rows of data to the existing table If some or all of the column names in the exported S PLUS data frame do not correspond to fields in the table exportData adds additional fields as necessary The same is true for openData and writeNextDataRows when openData is called with the table argument it creates a new table if one by the specified name
75. plest test data set testi amp lt list time c 4 3 1 1 2 2 3 status c 1 1 1 0 1 1 0 Rec 21 11 OO sex c 0 0 0 0 1 1 1 Fit a stratified model coxph Survitime status x strata sex testl lt s example gt lt s examples gt The tag lt s example type text gt preformats the examples section so that it prints in a fixed width font This also causes newlines and blank lines to be recognized in the text Thus you can include spaces between different examples to enhance readability So that the examples display nicely in conveniently sized help windows please ensure that the width of each line is no more than 60 characters In your examples always use the left assignment operator lt instead of the underscore _ for assignments Because the angle bracket lt signifies a tag in SGML it is safest to type the left assignment operator using amp 1t instead Thus the operator is amp 1t in SGML 73 Chapter 4 User Defined Help Keywords All help files should have keywords listed at the bottom immediately before the closing tag lt s function doc gt The help system uses keywords to organize the engine functions in the Contents tab of the help window open the Language Reference from the S PLUS menu and click on the Contents tab to see this Each keyword should be wrapped in the tags lt s keyword gt and lt s keyword gt For example the keywords section in the SGML file for coxph is lt s keywords gt
76. r you to specific help files for more information and example SGML code As with help files for functions you can use prompt to create template SGML files and delete the tags that are not applicable to your objects 77 Chapter 4 User Defined Help SV4 Class Objects The SGML sections in an SV4 class type help file are listed in Table 4 5 For more details see the SGML files for class timeSeries class vector and class matrix Table 4 5 Titled sections in S PLUS help files for SV4 class objects Section Title Quick Description SGML Tags Topic The name of the object lt s topics gt lt s topics gt Title The title that appears at the top of a formatted help lt s title gt file lt s title gt DESCRIPTION A short description of the object lt s description gt lt s description gt CLASS SLOTS A list of descriptions for the slots in the object Each lt s slots gt slot can be formatted with the list tags lt s class lt s slots gt slot name gt and lt s class slot gt EXTENDS A list of classes the object extends Each class is lt s contains gt formatted with lt s contains class name gt and lt s contains gt lt s contains class gt DETAILS Descriptions of implementation issues lt s details gt lt s details gt NOTE Any information that does not fit into the above lt s section name gt categories lt s section gt REFERENCES Available texts and papers th
77. ressions Here s what the code looks like so far include sconnect h A global connection object CSPengineConnect g_engineConnect int main int argc char argv The first step in the main function is to create the actual connection object which opens a connection to S PLUS Create the connection to S PLUS g_engineConnect Create argc argv We then create the variables x and y to use in the regression The CONNECT C 4 class CSPnumeric is used to store S PLUS numeric vectors The CSPnumeric class is one of many in CONNECT C that are used to represent S PLUS objects within C Similar classes 21 Chapter 2 CONNECT C exist for most of the standard atomic objects in S PLUS see Table 2 1 The Create method creates instances of the class the Assign method assigns the class to an S PLUS database Create S object with name x in the current database Same as x lt 1 10 at the command line CSPnumeric sx Sx Creavet l 10 2 Squaring sx which is the same as S expression sy lt x x in a local frame but here we set it to local C variable sy CSPnumeric sy sx Sx Assign the result as S object with name y in the current database sy Assign y Finally we fit the linear model passing the appropriate call to S PLUS via the CONNECT C 4 method SyncParseEval Evaluate z lt 1Im y x g_engineConnect SyncParseEval z lt 1m y x return 1 The comple
78. ribe the formats themselves Thus instead of using lt tt gt and lt tt gt for code we encourage you to use lt s expression gt and lt s expression gt or lt code gt and lt code gt to save typing Table 4 2 Common text formats in S PLUS SGML files Format SGML Tags Notes Fixed width code font lt s expression gt lt s expression gt lt code gt lt code gt lt tt gt lt tt gt Although lt tt gt and lt tt gt still exist in some older help files please use the other tags instead Preformatted text lt pre gt lt pre gt This is usually for code samples that extend over multiple lines With lt pre gt you are responsible for line breaks and blank space as SGML does no formatting for you Enumerated lists lt enum gt lt enum gt lt item lt item gt lt tag gt lt tag gt Italics lt it gt lt it gt Emphasis lt em gt lt em gt Bold lt bf gt lt bf gt Lists lt descrip gt lt descrip gt The lt descrip gt and lt enum gt tags create the lists Use lt item gt and lt item gt or lt tag gt and lt tag gt to format the individual list elements See the nlminb help file for an example 61 Chapter 4 User Defined Help Table 4 2 Common text formats in S PLUS SGML files Continued Format SGML Tags Notes Line breaks lt br gt To include a blank line in a help file lt br gt must be used twice
79. riteNextDataRows closeData set of functions e The section Executing Arbitrary SQL Statements describes executeSQL a new function for executing arbitrary SQL commands S PLUS 6 1 was fully supported and tested with the Oracle 8 1 7 and 9i clients These clients may be used to communicate with Oracle 8 1 6 and Oracle 9i servers Note The extended Oracle connectivity discussed in this chapter is available on Solaris installations of S PLUS 6 1 only Linux installations do not support this feature 82 Reading Data From an Oracle Database READING DATA FROM AN ORACLE DATABASE AN oO oO AUNGA EMPNO 7369 7499 7521 7566 7654 7698 7782 7788 7839 7844 7876 7900 7902 7934 ENAME SMITH ALLEN WARD JONES MARTIN BLAKE CLARK SCOTT KING TURNER ADAMS JAMES FORD MILLER The primary functions for reading data from an Oracle database are e importData to import data directly or e readNextDataRows in conjunction with openData and closeData to read sequential blocks of data from a table in the database The importData and openData functions have been modified in S PLUS 6 1 to enhance Oracle connectivity on Solaris installations of S PLUS In particular a new sq Query argument has been added to both functions In this section we describe the changes to importData and openData and provide examples illustrating them In many of the examples we use the following hypothetical table emp from an Oracle
80. rrent locale specifically LC_CTYPE For example in all locales that use Latin characters 341 is displayed as This affects how functions such as format print and cat display character data Because S PLUS now supports Western European character sets ISO 8859 1 you can include 8 bit ASCII characters ASCII codes 128 255 within character data and within the names of S PLUS objects For example you can include names such as Furtw ngler and Garcia Iniguez in your character data and they will properly display S PLUS uses your locale settings to determine the appropriate character set to use in printing output The characters allowed in S PLUS object names are sIphantmer ies f BE eT TI T TA TE A gg Per TET Pe A E TT Te TTE TE TE MA ES Ana R E MWe N O P Wa E G EPA a E a PS M E T a T a MI Te W TEM SE ee S To A ES Te W Tma T mPa S CPT CPS TT TW Ty W TR e Eg 212 TZI RAIG Ae TAZA RESO A237 LIO FRSO MRIUZ MAJIT AIO 305 300r PUSET EST TFS A I Ay hole RILES ORT PRO gs MAGLI An ABER T324 LAZO AEG TASO MV SSIs T AZT ASSO SIE SSO gy ARGS ABST MASI ASAI PV SEZ RAT aa BAS PASAO ASAT Te ASSO ASSL VSL MISST oe TRIOS ys TIISE MEIT Vee YSGl ABOL A263 MSGI TAIG T360 A370 VSrl ANATS EES g TASTAT MaS Te ISTO a TIS Using Extended Characters The characters not allowed in names are non alphanumerics lt O01 x002
81. s DISPLAY lt display_name gt export DISPLAY Creating an S PLUS chapter is necessary for storing the data objects and external files you create in S PLUS The following commands create an S PLUS chapter named mysplus for you to work in be sure you don t have a mysplus directory in your home directory before typing these commands cd mkdir mysplus cd mysplus Splus CHAPTER You are now ready to start S PLUS S PLUS may be launched in a variety of modes The following lists each mode and the corresponding UNIX command line expression for launching it In all of the commands below Splus refers to the script you use to launch S PLUS 6 1 on your system e PLUS command line without Java Splus Chapter 1 Welcome S PLUS command line supporting Java calls Java graphics and the Java help interface Splus j S PLUS graphical user interface Splus g or Splus g amp The second command using the ampersand amp puts the GUI process into the background freeing your xterm for other uses The e flag may be added to either of the first two modes to enable command line editing The Commands window in the graphical user interface always allows basic editing Note server release S PLUS 6 1 release notes Java has a number of known problems displaying on a remote display using the X Window System For this reason Insightful Corporation suggests if possible that you limit your use of the Java based G
82. s 54 56 56 57 57 57 58 59 60 61 63 63 77 53 Chapter 4 User Defined Help INTRODUCTION 54 When an S PLUS function is made available system wide a help file should always accompany it Without a help file use of the function is likely to be limited to those in close contact with the person who wrote it Starting with S PLUS 5 1 the S Language version 4 provides the flexibility of creating and editing your own SGML Standard Generalized Markup Language help files to document your user defined functions in S PLUS Using the built in functions distributed in your S PLUS installation you can use and distribute help via JavaHelp the help system from Sun Microsystems included with S PLUS 6 x JavaHelp is used to display the importData help file as shown in Figure 4 1 lt gt S S oc ace Ty xerrwv Import Data ga DESCRIPTION D can s Import data from a file or database into a data frame double USAGE Q executeSq exportData importDataCfile type keep character 0 d z colNames character 0 rowNamesCol C importData filter character 0 format charact C is double delimiter lt lt see below gt gt startCol 1 is loaded startRow 1 endRow 1 pageNumber se tes server user password da D is single table stringsAsFactors lt lt see be java xml string valueLabelAsNumber F centuryCutoff Dy library separateDelimiters
83. s used for elements of the S PLUS user interface for operating system files and commands and for user input in dialog fields This font is used for emphasis and book titles e CAP SMALLCApP letters are used for key names For example the Shift key appears as SHIFT When more than one key must be pressed simultaneously the two key names appear with a hyphen between them For example the key combination of SHIFT and F1 appears as SHIFT F1 e Menu selections are shown in an abbreviated form using the arrow symbol to indicate a selection within a menu as in File gt New 18 CONNECT C Introduction Resources Simple Examples An Application and a Called Routine Creating a Simple Application Example of Calling a C Function Via Ca11 CONNECT C Class Overview Data Object Classes Function Evaluation Classes Client to Engine Connection Classes Evaluator Classes CONNECT C Architectural Features CSPobject Constructors and Generating Functions Constructing From an Existing Object Assignment Operators Overloading Operators Converting C Objects to S PLUS Objects Subscripting Operators Subscript and Replacement Operations Subscript and Arithmetic Operations Matrix Computations Printing to Standard Output Named Persistent Objects Storage Frames For Unnamed Objects 20 20 21 21 23 28 28 28 29 29 31 31 31 32 33 33 34 35 36 36 37 38 38 40 19 Chapter 2 CONNECT C INTRODUCT
84. sands separators other than the comma S PLUS 6 1 fully supports French and German locales What s New in S PLUS 6 1 Note The implementation of locales within S PLUS does not apply to date formats because they are handled through a separate mechanism in the timeDate set of functions Also it does not apply to messaging all messages in S PLUS are in the English language User Defined In S PLUs 6 1 the process for creating and distributing custom S PLUS Help help files has been greatly streamlined and better documented Oracle S PLUS 6 1 expands connectivity with Oracle database clients This Connectivity allows you to read data from an Oracle table insert data into a table Solaris Only and run arbitrary SQL queries all from the S PLUS command line This feature is available on Solaris installations of S PLUS 6 1 only Linux installations do not support this feature Chapter 1 Welcome HELP SUPPORT AND LEARNING RESOURCES There are a variety of ways to accelerate your progress with S PLUS This section describes the learning and support resources available to S PLUS users Online Help S PLUS offers an online JavaHelp system to make learning and using S PLUS easier Under the Help menu in the S PLUS GUI you will find detailed help on each function in the S PLUS language You can access the help system from the S PLUS prompt or the Commands window in the GUI by typing help start Context sensitive help is a
85. sion gt for the family generating function lt s expression gt Gamma lt s expression gt used with the lt s expression gt glm lt s expression gt and lt s expression gt gam lt s expression gt functions See lt s expression gt GAMMA lt s expression gt for the functions related to the gamma distribution lt s expression gt dgamma lt s expression gt density lt s expression gt pgamma lt s expression gt probability lt s expression gt qgamma lt s expression gt quantile lt s expression gt rgamma lt s expression gt sample lt s section gt References for functions are listed alphabetically and should follow The Chicago Manual of Style The format for a book reference is similar to Venables W N and Ripley B D 1999 Modern Applied Statistics with S PLUS 3rd ed New York Springer Verlag Inc The format for a journal article is similar to Andersen P and Gill R 1982 Cox s regression model for counting processes a large sample study Annals of Statistics 10 1100 1120 The references section in S PLUS SGML files does not have a specific tag but uses lt s section name name gt and lt s section gt instead The following is an excerpt from the references in the SGML help file for density which cites a number of different works lt s section name REFERENCES gt Silverman B W 1986 lt it gt Density Estimation for Statistics and Data Analysis lt it gt London Chapman and Hall
86. stical Learning Data Mining Inference and Prediction Springer Verlag New York Huet S et al 1996 Statistical Tools for Nonlinear Regression A Practical Guide with S PLUS Examples Springer Verlag New York Marazzi A 1992 Algorithms Routines and S Functions for Robust Statistics Wadsworth amp Brooks Cole Pacific Grove CA Newton H J and Harvill J L 1997 StatConcepts A Visual Tour of Statistical Ideas Duxbury Press Nolan D and Speed T P 2000 Stat Labs Mathematical Statistics Through Applications Springer Verlag Pinheiro J C and Bates D M 2000 Mixed Effects Models in S and S PLUS Springer Verlag New York Schumaker R E and Akers A 2001 Understanding Statistical Concepts Using S PLUS Lawrence Erlbaum Associates Mahwah NJ Venables W N and Ripley B D 1999 Modern Applied Statistics with S PLUS 3rd ed Springer Verlag New York Wilcox R 1997 Introduction to Robust Estimation and Hypothesis Testing Academic Press Statistics and Data Analysis Specialized Bruce A and Gao H Y 1996 Applied Wavelet Analysis with S PLUS Springer Verlag New York Everitt B and Rabe Hesketh S 2001 Analyzing Medical Data Using S PLUS Statistics for Biology and Health Springer Verlag Harrell F E 2001 Regression Modeling Strategies with Applications to Linear Models Logistic Regression and Survival Analysis Springer Verlag Help Support and Learning R
87. t will be remove OPTIONAL ARGUMENTS n classes the number of cells into which the observations are to be all cut points is supplied then n classes is set to length c is recommended by Moore 1986 cut points vector of cutpoints that define the cells x i is allocated to cut points j 1 If x i is less than or equal to the firs last cutpoint then x i is treated as missing If the hypothe cut points must be supplied EZ ZEEE gt Figure 1 1 The S PLUS JavaHelp window Using the toolbar Table 1 3 lists the four buttons on the help window toolbar Table 1 3 Toolbar buttons in the JavaHelp window Button Description Returns to previously viewed help topic Previous Ki Moves to next help topic in a previously Next displayed sequence of topics Prints the current help topic amp Print a 11 Chapter 1 Welcome 12 Table 1 3 Zoolbar buttons in the JavaHelp window Continued Button Description Ey Determines the orientation of the page for Page Setup printing purposes Using the navigation pane The navigation pane appears on the left side of the JavaHelp window Like the help window itself the left pane is divided into three parts the Table of Contents a Index a and Search pages The Table of Contents page organizes help topics by category so related help files can be found easily These categories appear as small fold
88. te code for this example is in the directory SHOME sconnect samples splm and the C code is in the file spllm cxx Run the application as follows 1 Change the current directory to the directory containing the code cd SHOME sconnect samples splm where SHOME is your S PLUS installation directory 2 Build the program Splus6 CHAPTER sconnectapp cxx Splus6 make 22 Example of Calling a C Function Via Call Simple Examples An Application and a Called Routine 3 Run the program Splus6 EXEC S app To verify the results start S PLUS Splus6 S PLUS Copyright c 1988 2002 Insightful Corp S Copyright Lucent Technologies Inc Version 6 1 2 Release 1 for Sun SPARC SunOS 5 6 2002 Working data will be in Data and look at the objects x y and z gt X fil 2 22 4 6 6 7 g o 10 gt y 1 1 4 9 16 25 36 49 G4 8 amp 1 100 2 2 Caris Im formula y x Coefficients Intercept 22 11 Degrees of freedom 10 total 8 residual Residual standard error 8 124038 The Gauss Seidel method is a familiar technique for solving systems of linear equations The algorithm is straightforward and easy to implement in S PLUS gaussSeidel lt d gaussSeidel solves a linear system using Gauss Seidel d iterative method REQUIRED ARGUMENTS df A and b are numeric matrix and vector respectively df VALUE i a vector x solution of Ax b 23 Chapter 2 CONNECT C tf tf Usage
89. this supplement the booklet Getting Started with S PLUS 6 for UNIX Linux the User s Guide the Programmer s Guide and both volumes of the Guide to Statistics are available online Getting Started with S PLUS 6 provides a tutorial introduction to the product and so is particularly useful for those new to S PLUS To view a manual online navigate to S HOME doc and open the desired PDF file See Table 1 4 for the names of the PDF files Table 1 4 Online documentation available in SHOME doc Manual PDF File S PLUS 6 1 for UNIX Linux Supplement unixsupp61 pdf S PLUS 6 Installation and Maintenance Guide instman pdf Getting Started with S PLUS 6 for UNIX Linux getstart pdf S PLUS 6 User s Guide unixug pdf S PLUS 6 Guide to Statistics Volume 1 statman L pdf S PLUS 6 Guide to Statistics Volume 2 statman2 pdf S PLUS 6 Programmer s Guide pguide pdf 13 Chapter 1 Welcome Note The online manuals are viewed using Adobe Acrobat Reader It is generally useful to turn on bookmarks under the View entry of the menu bar while using Acrobat Reader rather than rely on the contents at the start of the manuals Bookmarks are always visible and can be expanded and collapsed to show just chapter titles or to include section headings S PLUS on the Web Training Courses Technical Support 14 You can find S PLUS on the World Wide Web at http www insightful com support In these pages
90. vailable by clicking the Help buttons in dialogs JavaHelp JavaHelp in S PLUS uses Java to display the help files To access JavaHelp do one of the following From the main menu in the S PLUS GUI choose Help gt Contents Help gt Index or Help gt Search to view the help system s table of contents index and search pages respectively e From the S PLUS prompt or the Commands window in the GUI type help start To turn the help system off type help off at the S PLUS prompt As shown in Figure 1 1 the JavaHelp window has three main areas the toolbar the navigation pane and the topic pane 10 S PLUS Help lt gt SiS Help Support and Learning Resources Gs Resampling Bootstrap Cf Robust Resistant Tech Cf 5 PLUS Session Enviro C Smoothing Operations Cf Statistical Inference GB binom test j binomial sample si Q cdf compare C chisq gof GB chisq Rest Ly cor test QA fisher test QA htest object QA ks gof GB mantelhaen test C mcnemar test b normal sample size Bi prop test Bi shapiro test G ssType3 bi ssType3 aovlist G ssType3 default x EEE gt Chi square Goodness of Fit Test DESCRIPTION Performs a chi square goodness of fit test USAGE chisq gofCx n classes ceiling 2 ClengthCx AC2 5 A cut points NULL distribution normal n pa REQUIRED ARGUMENTS numeric vector NAs and Infs are allowed bu
91. wherever a s_object is required It automatically invokes a conversion operator that returns the s_object as appropriate s_object CSPobject operator s_object CSPobject operator amp For example s_object myCal1 CSPnumeric x 1 10 return x s_object pReturn myCall1 The return statement return x first typecasts x to type s_object This invokes the conversion operator s_object of the CSPnumeric class derived from CSPobject which ensures that the destructor of x does not delete the object even if the reference count drops to zero Subscripting Operators CONNECT C 4 Architectural Features CONNECT C contains some useful overloading subscripting operators for the derived classes of CSPvector and CSParray such as CSPnumeric and CSPmatrix The proxy class of the returned object provides supports for read write and mixed mode operations const double CSPnumeric operator long 1Index const Fortran style indexing starting from index 1 rvalue only CSPproxy CSPnumeric operator long 1Index Fortran style indexing and ordering value and rvalue An example using the subscripting operators CSPevaluator s CSPnumeric x e 0 1 0 2 0 8 0 97 A7 X lt cfO 1 0 2 0 9 fi 0 8 double d x 1 d lt x 1 dis 0 1 d d x 2 d lt d x 1 d is 0 3 double e long x 1 e lt as integer x 2 e is 0 long n x 1 n lt as integer x 1 n
92. you will find a variety of information including Product information e FAQ pages The most recent service packs e Training course information Information on classroom use and related educational materials Insightful Corporation s Educational Services offers a number of courses designed to quickly make you efficient and effective at analyzing data with S PLUS The courses are taught by professional statisticians and leaders in statistical fields Courses feature a hands on approach to learning dividing class time between lecture and online exercises All participants receive the educational materials used in the course including lecture notes supplementary materials and exercise data For further information see http www insightful com services training asp North Central and South America Contact Technical Support at Insightful Corporation Telephone 206 283 8802 or 1 800 569 0123 ext 235 Monday Friday 6 00 a m PST 9 00 a m EST to 5 00 p m PST 8 00 p m EST Fax 206 283 8691 Books Using S PLUS Help Support and Learning Resources E mail support insightful com Web http www insightful com support All Other Locations Contact the European Headquarters of Insightful Corporation Christoph Merian Ring 11 4153 Reinach Switzerland Telephone 41 61 717 9340 Fax 41 61 717 9341 E mail info ch insightful com Introductory Burns P 1998 S Poetry Download for free from http
93. your derived class in the client in order to be notified when these events occur A CSPobject can be modified in one of two ways It can be modified in the client program by using the operators available for the object to assign and operate on the elements of the object When this kind of modification is done it is necessary to call the Commit method on the object to commit it to the S PLUS engine before any changes to the object are reflected in the persistent s_object that is referenced by the object in the client Another way it can be modified is by evaluating S PLUS expressions such as by using CSPengineConnect SyncParseEval When this kind of modification is done it is not necessary to call Commit on the object as the s_object is automatically updated by the S PLUS engine For both kinds of modification the OnModify method of the CSPobject is called in the client program It is important to call the base class OnModi fy in your override of OnModify This allows the base class to update the member s_object pointer to point to the newly modified s_object in the engine The s_object member of a CSPobject can be removed invalidated in one of two ways 1 It can be removed in the client program by calling the Remove method on the CSPobject This method removes the s_object from the permanent frame and triggers a call to the OnRemove method of the CSPobject in the client program The base class version of OnRemove w

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