1. Working with Data in Windows and Descriptive Statistics HRP223 – Topic 2 October 2 nd, 2013 Copyright © 1999-2013 Leland Stanford Junior University. All rights reserved. Warning: This presentation is protected by copyright law and international treaties. Unauthorized reproduction of this presentation, or any portion of it, may result in severe civil and criminal penalties and will be prosecuted to maximum extent possible under the law.

2. In this lecture… How SAS works in Windows – SAS vs EG files – Libraries vs. Folders Importing Data Subsets and creating new variables Describing Data Making better summary tables

3. Sources of Data Small data sets (aka Toy data) – You may be able to type in the data directly into a SAS code file with EG like in The Little SAS Book for EG. Excel – For small amounts of HIPAA safe data you can use Excel with validation. Text files with columns of numbers and text – Exports created by databases frequently provide a text file full of data and a program for loading it into SAS (like REDCap). – Data from the CDC Wonder database SAS – Native SAS datasets created by somebody else.

4. Types of Files SuffixFile Type.pdfAdobe portable document format.zipArchives full of compressed data.xlsExcel prior to 2007.xlsxExcel 2007 and later.csvComma separated values (text which Excel likes).txtText files (letters number and punctuation without formats.sasSAS code files.egpEnterprise Guide projects.sas7bdatSAS data files.htm or.htmlWeb pages.cssCascading style sheets for web pages

5. In this lecture… How SAS works in Windows – SAS vs EG files – Libraries vs. Folders Importing Data Subsets and creating new variables Describing Data Making better summary tables

6. SAS and EG files.sas files are text files full of instructions that a programmer can easily write and/or edit..egp files are not.

7. What is an EGP file? EGP files are actually zip archives (with a.egp suffix instead of.zip) which contain XML text and other text files.

8. Searching Because the contents of.egp files are compressed, the built in Windows file finder will not be able to find files by searching for keywords inside the projects. This affects me when I can’t remember the file name for a project and to find it I want to search for key words in the code (like the principal investigator’s name or the name of the source data file).

9. Searching Inside.egp files File Locator Pro can search inside the egp files: – Tools menu > Configuration … Add egp here. Without the. Click here

10. Files in Enterprise Guide Alternatively, you can save SAS code files outside of the EG project. Most people create EG projects that reference data files that live outside of EG. – SAS datasets – Excel files – Text files full of data Converted to SAS format Native Excel format

11. How SAS EG works SAS EG Saved output SAS Data (.xls,.sas7bdat, etc)

12. Shortcuts Windows indicates a “shortcut” to a file that lives elsewhere with an arrow in the bottom left corner of an icon. EG uses the same symbol to denote a shortcut to a file outside of the project.

13. What is in an EGP file? An EG project file ( a file with an.egp suffix) contains information and instructions but it will also have links to a lot of external files. Shortcut to a file NOT in the project. This is part of the project Shortcut to a file NOT in the project.

14. EG and Code Most of the time you will point and click to build an analysis but you can write and store your “code” instructions to SAS inside of the EG project or you can create a short cut to the code file which lives outside of EG. Right click and choose New > ProgramLook at the process flowNo shortcut icon

15. External SAS files You can easily save a code file outside of the project by choosing Save Program As… from the File menu or clicking the Save or Save As … from the program tab (when the code is open). Shortcut

16. In this lecture… How SAS works in Windows – SAS vs EG files – Libraries vs. Folders Importing Data Subsets and creating new variables Describing Data Making better summary tables

17. Where are SAS data sets Stored? While SAS can refer to files using their Windows path, it is easier to type a short name instead of a long path. SAS calls the short names “libraries”. EG automatically knows about a couple of places where data can be stored. – It creates a temporary work folder whenever EG starts. – It creates a permanent sasuser folder when EG is installed. The locations for data are called libraries.

18. Where are those folders? Look at the servers list and expand out the tree to show: Servers - Local - Libraries - WORK Right click on WORK and choose Properties. If the Server List display is not showing use view menu.

19. In this lecture… How SAS works in Windows – SAS vs EG files – Libraries vs. Folders Importing Data Subsets and creating new variables Describing Data Making better summary tables

20. Importing the Easy Way The most bulletproof way for importing with EG 5.1 is to use the import wizard and save into the Work library.

21. Always check this on.

22. Double check that it guesses the right Type, especially for dates.

23. Check this on By default you don’t see the library or path to the Excel file.

24. Libraries Prior to the version of EG that shipped with SAS 9.3, the default behavior was for EG to save all data into the same folder/library, sasuser. This is a very bad idea. – Naïve students would end up with every SAS data set in one folder. – Anybody using SAS can access that folder, so there are significant HIPAA issues. You can right click on a file and pick Properties to see where it is stored.

25. Change the Default File Location If you are working with an old SAS install, change the default file location to the work library. Do this once per machine.

26. Click 1st Click 2x

27. Permanent Store I suggest that you save your data into the temporary work library by default. If you have a huge file which you only want to import once, or if you want to keep a permanent copy of a SAS data file, you will want to set up a permanent library. – A library reference is just a fancy way of specifying what folder SAS should use to save the.sas7bdat data files.

28. Fix the Registry (Once) then Make a Library First fix the problematic registry entries that are described in my instructions on installing SAS. – If you do not do this, if you have mixtures of characters and number values in a column from Excel, programs reading the data (including SAS) can drop the cells that have character data without warning. Using Windows, make a folder c:\blah\libraryDemo to hold the data set. Using SAS, make a library to point to the folder where your data should be stored.

29. Tell SAS that there is a folder which can hold data by creating a library. This only makes SAS aware of the folder. It does not automatically put stuff into the folder.

30. It’s just a folder! When the library is created it is just a pointer to a preexisting folder. That folder can contain anything. When you want to use the folder you need to explicitly tell EG to store data in the folder. First rename your input the node and draw an arrow to indicate where the library is used. These changes are mostly just aesthetic.

31. Now it looks good but the import is still into work. 1 st rename the node to match the library name 2 nd add a line to the flowchart connecting the library to the import. It just looks good.

32. Find your library here.

33. Notice it is in the library. A “design feature” is that you have to Refresh the library to see the freshly added file. You can see it in Windows.

34. Working with Data in Windows and Descriptive Statistics HRP223 – Topic 2 October 7 th, 2013 Copyright © 1999-2013 Leland Stanford Junior University. All rights reserved. Warning: This presentation is protected by copyright law and international treaties. Unauthorized reproduction of this presentation, or any portion of it, may result in severe civil and criminal penalties and will be prosecuted to maximum extent possible under the law. New and improved... Now with more Windows advice!

35. Project Management in Windows Make a folder called projects. Make subfolders that contain each project/paper you are working on. The project subfolder will contain your – data or a subfolder with data – Enterprise guide and/or SAS files – A subfolder called Development to hold old versions of code Enterprise Guide projects. Your code will make subfolders to hold your results. – The results folders should be dates.

36. File names Name your files with a short label then the date written as: a four digit year then a two digit month and then a two digit day. This will make your files appear in chronological order. My folders are full of files named like this: carboAEs20110624.sas or LungImages2013-09-21.egp Dashes help readability. Just be consistent.

37. Dated results Data exported from ONCORE database Programs with: label yyyy-mm-dd in the file name Development holds earlier versions of my code and projects

38. Dated Analysis Folders index.html file will display the results/graphics if I move this folder to WWW PDF to share with UCSF

39. In this lecture… How SAS works in Windows – SAS vs EG files – Libraries vs. Folders Importing Data Subsets and creating new variables Describing Data Making better summary tables

40. SAS and Windows In *modern* SAS you can give it paths.

41. Library for less typing You can specify the path once and then use the shortcut name:

42. Playing with Data Once the data is imported you can add code “nodes” to the flowchart or use the graphical user interface to tweak the data and do analyses. Complex changes Quick and easy subset and sorting Select all variables for the new dataset

45. Push Validate to see the SQL code. Notice the tabs in the output.

46. Notice Analysis.css hidden in the voodoo. It has the appearance scheme (color, bold, etc.)

47. Convert From a Character to a Number Remember that page that I mentioned that has functions? /lefunctionsref.hlp/p0w6napahk6x0an0z2dzozh2ouzm.htm Hold the control key and type f to bring up the find box.

49. 2 nd 3 rd Click New 4 th Click Advanced expression 5 th Click Next

50. Convert to a 4 digit number with the input function: input( t1.score, 4. )

51. Before After Context sensitive menus help you describe the data you are browsing.

52. In this lecture… How SAS works in Windows – SAS vs EG files – Libraries vs. Folders Importing Data Subsets and creating new variables Describing Data Making better summary tables

53. Descriptive Statistics drag

55. Turn on Higher Quality Graphics Tools > Options > Tasks > Custom Code

58. This is SAS code that can be cut and pasted into a.SAS file and run outside of EG.

61. I like this color scheme.

62. Fixing the title is too advanced for now but it is trivial to cut it in Illustrator or to mask it in PowerPoint.

63. Clean the Project 2 nd Right click and rename. 3 rd Right click and link it to the code 1 st Right click and rename it.

64. In this lecture… How SAS works in Windows – SAS vs EG files – Libraries vs. Folders Importing Data Subsets and creating new variables Describing Data Making better summary tables

65. Table 1 Table 1 in a manuscript describes data grouped by something, typically a treatment. – Frequency count by gender – Means for age

66. Drowning…. is bad SCUBA divers practically never drown. Can I find any patterns in who dies? Load the fakeDrowningData Excel file. It is real data based on the CDC’s mortality data from 1999-2007: wonder.cdc.gov/controller/datarequest/D53 The actual ages are sampled from the age bins the CDC gives and the SCUBA rate is simulated. wonder.cdc.gov/controller/datarequest/D53

67. For each treatment table 1 always has… For continuous data, a measure of central tendency and variability. Number of people Mean and standard deviation Median, min, max, 25 th and 75 th percentiles For categorical data – Frequency counts, percentages

68. Too Many Nodes Continuous You can request lots of tables. Typically people do one node per variable.

74. .M (dot M)

75. Add ageFixed

76. Now there is a useful dataset Now the analysis is running on the wrong data. Select the new input data and modify the node to run on the new variable.

77. The new variable N is not the number of observations. The minimum is not -1.

78. Notice the bug… it lost the 5 year bins. Right click the node and reset it.

80. Categorical: several variables cross tabulated

82. Exposure Outcome Notice the table request

83. Typically I want row not column percentages. Watch the code change as you click.

84. Women don’t drown while diving and there is no evidence of a SCUBA effect You can rinse and repeat building this table but then you need to copy and paste a LOT for your paper.

85. Bug with Reports If your table has missing data you may get an Unable to read SAS Report file error. Use the Tools > Options menu to turn on the procedure titles in the output.

86. Categorical and continuous… pretty tables. I am going to want to count people. The easiest way to do this is to add a new column. Every person should have the value 1 then I can count or sum that variable. I am going to write a program to do this… Add a programming node to the project by right clicking on the process flow and choosing new program.

88. Make a new dataset called analysisFinal Base the new dataset on everything in the analysis dataset. Make a new variable call it one and have it contain the number one. What library will the new dataset live in? Is the variable one character or numeric? Rename and link the program… Describe> Summary Tables…

92. Add Race then State.

94. This is too confusing with row and column percentages.

99. It is too advanced for now but you can do fancy formatting like using colors for big or impossible values/patterns. You can save this as HTML and open it in Excel to do final touches.