Dammit Jim! » tutorial http://scott.sherrillmix.com/blog I'm a biologist not a... Mon, 06 Feb 2012 05:19:08 +0000 en hourly 1 http://wordpress.org/?v=3.3 Getting Help with SAS http://scott.sherrillmix.com/blog/programmer/getting-help-with-sas/ http://scott.sherrillmix.com/blog/programmer/getting-help-with-sas/#comments Thu, 15 Nov 2007 06:01:35 +0000 ScottS-M http://scott.sherrillmix.com/blog/programmer/getting-help-with-sas/

There was some discussion in one of my SAS posts about where to find SAS help and communities. It seemed like a pretty useful topic so I thought I’d expand it a bit and make a post out of it. First, let me say I’m not the most knowledgeable since I’m more of a find-wall-bang-head type of programmer but I did my best to dig up some possible answers. If anyone has any other suggestions, feel free to leave them in the comments.

  • To start with, there’s always the official online documentation although this tends to be more for polishing something you already know how to do than starting cold.
  • Speaking of official, there’s also the official SAS forums. I didn’t know about these until I started looking around for this post so I can’t say much about them but the topics they have available seem rather specific and I can’t figure out where one would go to post a basic question.
  • Edit:There’s also the SAS Knowledge Base that has a lot of good papers and notes detailing SAS features complete with sample code and explanations. It’s really useful if you’re a learn by example type. (Thanks to Alison for pointing this one out).
  • Kelly Levoyer of SAS points out SAScommunity.org which seems like it is a little sparse but does have a surprisingly long list of SAS-related blogs.
  • The SAS company also appears to have jumped on the blogging band wagon although really only SAS Dummy looks helpful for learning SAS at the moment.
  • The only place that seem to be available for asking general question is the SAS-L email list (which I just found out is the same as the comp.soft-sys.sas Usenet group). There’s a nice paper on SAS-L etiquette (mostly do your homework first) (found via the sascommunity site).

Offline, there are also SAS user groups. I often get emails from our local one but I’ve never actually gone. The SAS company also has trainers that travel and teach quick classes. Our university stats department brought in one to teach a couple short two-day classes about statistical functions and macros. The classes were pretty good although I’m not sure how much it cost or how frequent they are. It might be worth checking on if you’re near a university.

Finally, you can also read my poor attempts at explaining SAS macro variables and SAS macros. Also, if you have any specific questions you can try asking in the comments here and if it’s not too time consuming I’ll try to lend a hand.

]]> http://scott.sherrillmix.com/blog/programmer/getting-help-with-sas/feed/ 2 SAS Macros: Letting SAS Do the Typing http://scott.sherrillmix.com/blog/programmer/sas-macros-letting-sas-do-the-typing/ http://scott.sherrillmix.com/blog/programmer/sas-macros-letting-sas-do-the-typing/#comments Sun, 04 Nov 2007 08:09:31 +0000 ScottS-M http://scott.sherrillmix.com/blog/programmer/sas-macros-letting-sas-do-the-typing/ I've been meaning to write up a bit on using macros in SAS to complement my previous post on macro variables for quite a while. Luckily Norwegian guy reminded me about the pain of starting programming in SAS and provided me some motivation. So here's my take on using macros in programming.

So what is a macro? Macros are a part of SAS that look through your code before the normal part of SAS sees it and writes out your code for you based on a special syntax. If you've ever found yourself copying and pasting code then you've probably been in a situation well suited for macros. They're also great if you need to perform different functions under different conditions. Once I learned macros, SAS seemed a lot more like a usable (although weird) programming language and tasks seemed to get a lot easier (except actually picking the statistical techniques to use).

Probably the easiest way to see what macros do is an example. So say we once again have a data set of tree heights

SAS:
  1. data trees;
  2. input name:$8. height;
  3. cards;
  4. Maple 123
  5. Maple 78
  6. Maple 90
  7. Elm 155
  8. Elm 65
  9. Elm 90
  10. Elm 120
  11. Birch 100
  12. Birch 30
  13. Maple 111
  14. run;

I already talked about how to find and use the mean and standard deviation for the whole data set. Now what if we wanted to standardize each species by its own seperate mean and deviation? We could cut and paste but once we get a few more species or want to change something later this really becomes a hassle. So this is where macros come in.

The first thing to do is to calculate the mean and standard deviations for each species. We can use proc means again to do this. Since we won't be using the output I'll add the noprint option and since we only want the means for the individual species and not the whole dataset I'll add the nway option. The class name; statement tells SAS to find the statistics seperately for each species and the output line tells SAS to save the mean and deviation in a dataset called meansd.

SAS:
  1. proc means data=trees nway noprint;
  2. class name;
  3. var height;
  4. output out=meansd mean=meanheight std=sdheight;
  5. run;

Now we just need to get the values from the meansd dataset into macro variables. We'll use the _NULL_ dataset and call symput again to create macro variables. This time we need to create seperate macro variables for each species. Luckily SAS automatically numbers each observation in a dataset in a column called _N_. Since each line of the dataset corresponds to a tree species, we can easily use this identifier to create the macro variables by using call symput('mean'||left(_N_), meanheight);. The left() and ()trim functions (numeric variables have extra spaces to the left and string variables have spaces to the right) removes any unnecessary spaces and the || concatenates (connects) the text "mean" with the line number to give give mean1, mean2, etc.. I'll do the same thing for standard deviation and tree name. Once the macro variables are created, there is still one problem remaining. We don't know how many species there were or how many macro variables were created. Luckily SAS will make another column that indicates the last line of the dataset when it sees end=newcolumnname following a set statement. Then we just need to check if SAS is on the last line and if so save the line number (_N_) to know the number of species of trees.

SAS:
  1. data _NULL_;
  2. set meansd end=last;
  3. call symput('mean'||left(_N_),meanheight);
  4. call symput('sd'||left(_N_),sdheight);
  5. call symput('name'||left(_N_),trim(name));
  6. if last then call symput('numspecies',_N_);
  7. run;

If you ever want to check what macro variables you have in your program, you can use %PUT _USER_; to print them all to the log file. Or if you want to see every macro variable available (SAS has quite a few automatic ones like operating system and date) use %PUT _ALL_;. Inserting %PUT _USER_; here produces:

SAS:
  1. GLOBAL NUMSPECIES            3
  2. GLOBAL NAME1 Birch
  3. GLOBAL NAME2 Elm
  4. GLOBAL NAME3 Maple
  5. GLOBAL MEAN1           65
  6. GLOBAL MEAN2        107.5
  7. GLOBAL MEAN3        100.5
  8. GLOBAL SD1 49.497474683
  9. GLOBAL SD2 38.837267326
  10. GLOBAL SD3 20.273134933

Now we've set a lot of macro variables but we still haven't created a real macro. In SAS, macros are started with %MACRO macroname; and finished with %MEND; (short for M[acro]END). %'s are used to indicate commands that the SAS macro facility will read and remove before normal SAS sees the code. Anything not with a % will be printed out by the macro facility. Macros don't spit out their code for SAS until they're are called using %macroname.

So I'll call my macro treestandardizer but you can call it whatever you want. I'm going to use a pretty simple and specific macro but if you were going to use this often and for different datasets you would want to program it better. The first thing to do is create the final dataset and set it to the trees dataset. Since we need to loop through each species of tree, we'll need a %DO loop. Everything between %DO and %END will be repeated while i increments from 1 to the number of tree species. If you want to combine text and a macro variable to reference another macro variable, you use the double ampersand && in SAS. For example, we want to get the mean for species 1 by looking in the macro variable &mean1 so we use &&mean&i. I think the macro processing part of SAS ends up running through the code twice, the first time finding the && and replacing it with & and the &i and replacing it with 1 to leave &mean1 and the second time finding &mean1 and pasting in the appropriate value (65). So we'll have the do loop write out a series of if statements to check what the name of the tree is and use the appropriate mean and deviation. Note that when using a string macro variable like &nameX, you need to surround it with double quotes (the macro processor doesn't look inside single quotes) so SAS doesn't think it is a variable name.

SAS:
  1. %MACRO treestandardizer;
  2. data final;
  3. set trees;
  4. %DO i = 1 %TO &numspecies;
  5. if name="&&name&i" then stheight=(height-&&mean&i)/&&sd&i;
  6. %END;
  7. run;
  8. %MEND;

The previous code prepared the macro but nothing actually happens until we call it using %treestandardizer. Unlike almost everything else in SAS this line doesn't have to end in a semicolon (although it's pretty unlikely to hurt if you forget and add one). So to call the macro:

SAS:
  1. %treestandardizer

If you want to see what happens when you call a macro, you can have SAS print the code generated by the macro to the log file with the option option mprint; (make sure to set it before actually calling the macro). In this case, it gives:

SAS:
  1. MPRINT(TREESTANDARDIZER):   data final;
  2. MPRINT(TREESTANDARDIZER):   set trees;
  3. MPRINT(TREESTANDARDIZER):   if name="Birch" then stheight=(height- 65)/49.497474683;
  4. MPRINT(TREESTANDARDIZER):   if name="Elm" then stheight=(height- 107.5)/38.837267326;
  5. MPRINT(TREESTANDARDIZER):   if name="Maple" then stheight=(height- 100.5)/20.273134933;

So it worked and we now have the standardized heights in the stheight column of the final dataset. This particular example could be done a few different ways (the easiest and probably better way being to merge the meancv dataset with the trees) but I hope it gives a decent introduction to SAS macros. If you have any specific questions or something wasn't clear, feel free to ask in a comment.

Here is the SAS source code if you don't feel like copying and pasting.

]]> http://scott.sherrillmix.com/blog/programmer/sas-macros-letting-sas-do-the-typing/feed/ 13 Creating a (Better) Fake Post with a WordPress Plugin http://scott.sherrillmix.com/blog/blogger/creating-a-better-fake-post-with-a-wordpress-plugin/ http://scott.sherrillmix.com/blog/blogger/creating-a-better-fake-post-with-a-wordpress-plugin/#comments Sun, 20 May 2007 14:58:18 +0000 ScottS-M http://scott.sherrillmix.com/blog/blogger/creating-a-better-fake-post-with-a-wordpress-plugin/ I was looking to create a fake page in a WordPress plugin I'm working on in my (all too limited) spare time. It may seem a little silly to try to create a fake page with a plugin but this could be useful for any plugin that will display information to the readers of the blog (outside the admin panel), like statistics, contact pages or about pages. Luckily there is a handy tutorial for creating a fake posts. But although the plugin cleverly tricks WordPress into displaying a post created dynamically by the plugin itself, WordPress is clever enough to know something is wrong and sends a 404 error before sending the plugin-created content. Although many browsers will still display the page, this is a problem for any text-based browser or if you want the page to be indexed by search engines and (for me at least) just kind of grates to know my magnificent new plugin isn't actually performing correctly. Anyway, this happens because WP->handle_404() called by WP->main() in classes.php checks how many posts were found which, in this case, is 0 since there is no real post for the requested URL. To get around this problem, we need to make sure we trick WordPress before this function is called. Luckily we can catch WordPress immediately after it (unsuccessfully) looks for posts before any other function can figure out anything is wrong by using the the_posts filter.

So here is the new working code or just download it here. I'm not sure how many people will actually be interested in it but if you are feel free to leave a comment with any suggestions or questions.

PHP:
  1. /**
  2. * Plugin Name: Fake Page Plugin 2
  3. * Plugin URI: http://scott.sherrillmix.com/blog/blogger/creating-a-better-fake-post-with-a-wordpress-plugin/
  4. * Description: Creates a fake page without a 404 error (based on <a href="http://headzoo.com/tutorials/wordpress-creating-a-fake-post-with-a-plugin">Sean Hickey's Fake Plugin Page</a>)
  5. * Author: Scott Sherrill-Mix
  6. * Author URI: http://scott.sherrillmix.com/blog/
  7. * Version: 1.1
  8. */
  9.  
  10. class FakePage
  11. {
  12.     /**
  13.      * The slug for the fake post.  This is the URL for your plugin, like:
  14.      * http://site.com/about-me or http://site.com/?page_id=about-me
  15.      * @var string
  16.      */
  17.     var $page_slug = 'about-me';
  18.    
  19.     /**
  20.      * The title for your fake post.
  21.      * @var string
  22.      */
  23.     var $page_title = 'About Me';
  24.    
  25.     /**
  26.      * Allow pings?
  27.      * @var string
  28.      */
  29.     var $ping_status = 'open';
  30.        
  31.     /**
  32.      * Class constructor
  33.      */
  34.     function FakePage()
  35.     {
  36.         /**
  37.          * We'll wait til WordPress has looked for posts, and then
  38.          * check to see if the requested url matches our target.
  39.          */
  40.         add_filter('the_posts',array(&$this,'detectPost'));
  41.     }
  42.  
  43.    
  44.     /**
  45.      * Called by the 'detectPost' action
  46.      */
  47.     function createPost()
  48.     {
  49.    
  50.         /**
  51.          * What we are going to do here, is create a fake post.  A post
  52.          * that doesn't actually exist. We're gonna fill it up with
  53.          * whatever values you want.  The content of the post will be
  54.          * the output from your plugin.
  55.          */  
  56.        
  57.         /**
  58.          * Create a fake post.
  59.          */
  60.         $post = new stdClass;
  61.        
  62.         /**
  63.          * The author ID for the post.  Usually 1 is the sys admin.  Your
  64.          * plugin can find out the real author ID without any trouble.
  65.          */
  66.         $post->post_author = 1;
  67.        
  68.         /**
  69.          * The safe name for the post.  This is the post slug.
  70.          */
  71.         $post->post_name = $this->page_slug;
  72.        
  73.         /**
  74.          * Not sure if this is even important.  But gonna fill it up anyway.
  75.          */
  76.         $post->guid = get_bloginfo('wpurl') . '/' . $this->page_slug;
  77.        
  78.        
  79.         /**
  80.          * The title of the page.
  81.          */
  82.         $post->post_title = $this->page_title;
  83.        
  84.         /**
  85.          * This is the content of the post.  This is where the output of
  86.          * your plugin should go.  Just store the output from all your
  87.          * plugin function calls, and put the output into this var.
  88.          */
  89.         $post->post_content = $this->getContent();
  90.        
  91.         /**
  92.          * Fake post ID to prevent WP from trying to show comments for
  93.          * a post that doesn't really exist.
  94.          */
  95.         $post->ID = -1;
  96.        
  97.         /**
  98.          * Static means a page, not a post.
  99.          */
  100.         $post->post_status = 'static';
  101.        
  102.         /**
  103.          * Turning off comments for the post.
  104.          */
  105.         $post->comment_status = 'closed';
  106.        
  107.         /**
  108.          * Let people ping the post?  Probably doesn't matter since
  109.          * comments are turned off, so not sure if WP would even
  110.          * show the pings.
  111.          */
  112.         $post->ping_status = $this->ping_status;
  113.        
  114.         $post->comment_count = 0;
  115.        
  116.         /**
  117.          * You can pretty much fill these up with anything you want.  The
  118.          * current date is fine.  It's a fake post right?  Maybe the date
  119.          * the plugin was activated?
  120.          */
  121.         $post->post_date = current_time('mysql');
  122.         $post->post_date_gmt = current_time('mysql', 1);
  123.  
  124.         return($post);   
  125.     }
  126.    
  127.     function getContent()
  128.     {
  129.         return '<p>Hi there!  You are viewing my fake post!</p>';
  130.     }
  131.  
  132.     function detectPost($posts){
  133.         global $wp;
  134.         global $wp_query;
  135.         /**
  136.          * Check if the requested page matches our target
  137.          */
  138.         if (strtolower($wp->request) == strtolower($this->page_slug) || $wp->query_vars['page_id'] == $this->page_slug){
  139.             //Add the fake post
  140.             $posts=NULL;
  141.             $posts[]=$this->createPost();
  142.        
  143.             /**
  144.              * Trick wp_query into thinking this is a page (necessary for wp_title() at least)
  145.              * Not sure if it's cheating or not to modify global variables in a filter
  146.              * but it appears to work and the codex doesn't directly say not to.
  147.              */
  148.             $wp_query->is_page = true;
  149.             //Not sure if this one is necessary but might as well set it like a true page
  150.             $wp_query->is_singular = true;
  151.             $wp_query->is_home = false;
  152.             $wp_query->is_archive = false;
  153.             $wp_query->is_category = false;
  154.             //Longer permalink structures may not match the fake post slug and cause a 404 error so we catch the error here
  155.             unset($wp_query->query["error"]);
  156.             $wp_query->query_vars["error"]="";
  157.             $wp_query->is_404=false;
  158.            
  159.         }
  160.         return $posts;
  161.     }
  162. }
  163.  
  164. /**
  165. * Create an instance of our class.
  166. */
  167. new FakePage;

This is just an example to get you started creating a fake page with a plugin. After loading this plugin, you will be able to visit your fake page at http://site.com/about-me/ or for the non-pretty link people http://site.com/?page_id=about-me. Hope it helps someone out and good luck with your plugin.

Change Log:

  • v1.1 6-5-2007
    • Fixed 404 error on more complicated permalink structures
  • v1.0 5-20-2007
]]> http://scott.sherrillmix.com/blog/blogger/creating-a-better-fake-post-with-a-wordpress-plugin/feed/ 30 SAS Macro Variables: How to Take a Mean in SAS http://scott.sherrillmix.com/blog/programmer/sas-macros/ http://scott.sherrillmix.com/blog/programmer/sas-macros/#comments Sat, 16 Sep 2006 02:03:52 +0000 ScottS-M http://scott.sherrillmix.com/blog/programmer/sas-macros/ I just thought I'd do a quick post about SAS macro variables. They're a pretty important part of SAS but when I had just started people told me not to worry about them and to just enter values by hand. After I finally got tired of constantly looking up results and entering them into programs over and over again, I decided I had better figure out how real programmers did it. As a side note, I've had a couple people tell me SAS was dying out but I see it appears to be in the top 20 of programming languages so I guess it's going strong.

So SAS is very good at working on rows of data but not quite so good at working with columns. For example if you have a column of tree heights and want to standardize by the mean and standard deviation, there is no easy way to do this without using macros or manually getting the mean and entering it into your program (this works the first couple times but it gets old quickly trust me).

Macros seem to me to be sort of a patch that sits on top of the main SAS program to allow this sort of thing. Macros work by scanning through your program for special commands and replacing things before sending it onto the real SAS program. In effect, the macro processor writes your program for you.

So back to our example of trees. Here is some data:

SAS:
  1. data trees;
  2. input name $1-8 height 9-11;
  3. cards;
  4. Maple   123
  5. Oak     78
  6. Birch   90
  7. Elm     155
  8. Poplar  65
  9. run;

I never actually use the cards statements in real code but it's handy for portable examples. Also the spaces between the two columns are significant since we told SAS to look the 1st through 8th column ($1-8) for tree name

So we now need to find the mean and s.d. of the heights:

SAS:
  1. proc means data=trees mean std;
  2. var height;
  3. output out=meansd mean=meanheight std=sdheight;
  4. run;

Now our mean is stored in the meanheight and sdheight columns of the meantrees dataset. So to get it into the macro part of SAS we need to use call symput(anyname,column). You can only use call symput in data statements. This is a little silly since we don't actually want to do anything with the data but I don't make the rules. Luckily, SAS does provide the _NULL_ dataset which just dumps whatever you put in it after you finish the data step. SAS variables often have extra spaces attached so it's probably smart to stick a trim(left(column)) in the call symput.

SAS:
  1. data _null_;
  2. set meansd;
  3. call symput('treemean',trim(left(meanheight)));
  4. call symput('treesd',trim(left(sdheight)));
  5. run;

So after call symput we can access the stored values with &treemean and &treesd. They're called macro variables by the way. If you ever need to check the contents of your macro variables you can use %PUT _users_; to put them all into the log file. So now we can make a column of our standardized tree heights:

SAS:
  1. data trees;
  2. set trees;
  3. standardized=(height-&treemean)/&treesd;
  4. run;

Now the trees dataset contains the standardized tree heights. This is a lot easier than looking in the results and entering it manually every time something changes.

]]> http://scott.sherrillmix.com/blog/programmer/sas-macros/feed/ 4