Data analysis work flow

Data Cleaning is a critically important part of any data analysis. Without properly prepared data, the analysis will yield inaccurate results. Correcting errors later in the analysis adds to the time, effort, and cost of the project.

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Knowing the right statistical analysis to use in any data situation, knowing how to run it, and being able to understand the output are all really important skills for statistical analysis.  Really important.

But they’re not the only ones.

Another is having a system in place to keep track of the analyses.  This is especially important if you have any collaborators (or a statistical consultant!) you’ll be sharing your results with.  You may already have an effective work flow, but if you don’t, here are some strategies I use.  I hope they’re helpful to you.

1. Always use Syntax Code

All the statistical software packages have come up with some sort of easy-to-use, menu-based approach.  And as long as you know what you’re doing, there is nothing wrong with using the menus.  While I’m familiar enough with SAS code to just write it, I use menus all the time in SPSS.

But even if you use the menus, paste the syntax for everything you do.  There are many reasons for using syntax, but the main one is documentation.  Whether you need to communicate to someone else or just remember what you did, syntax is the only way to keep track.  (And even though, in the midst of analyses, you believe you’ll remember how you did something, a week and 40 models later, I promise you won’t.  I’ve been there too many times.  And it really hurts when you can’t replicate something).

In SPSS, there are two things you can do to make this seamlessly easy.  First, instead of hitting OK, hit Paste.  Second, make sure syntax shows up on the output.  This is the default in later versions, but you can turn in on in Edit–>Options–>Viewer.  Make sure “Display Commands in Log” and “Log” are both checked.  (Note: the menus may differ slightly across versions).

2.  If your data set is large, create smaller data sets that are relevant to each set of analyses.

First, all statistical software needs to read the entire data set to do many analyses and data manipulation.  Since that same software is often a memory hog, running anything on a large data set will s-l-o-w down processing. A lot.

Second, it’s just clutter.  It’s harder to find the variables you need if you have an extra 400 variables in the data set.

3. Instead of just opening a data set manually, use commands in your syntax code to open data sets.

Why?  Unless you are committing the cardinal sin of overwriting your original data as you create new variables, you have multiple versions of your data set.  Having the data set listed right at the top of the analysis commands makes it crystal clear which version of the data you analyzed.

4. Use Variable and Value labels religiously

I know you remember today that your variable labeled Mar4cat means marital status in 4 categories and that 0 indicates ‘never married.’  It’s so logical, right?  Well, it’s not obvious to your collaborators and it won’t be obvious to you in two years, when you try to re-analyze the data after a reviewer doesn’t like your approach.

Even if you have a separate code book, why not put it right in the data?  It makes the output so much easier to read, and you don’t have to worry about losing the code book.  It may feel like more work upfront, but it will save time in the long run.

5. Put data manipulation, descriptive analyses, and models in separate syntax files

When I do data analysis, I follow my Steps approach, which means first I create all the relevant variables, then run univariate and bivariate statistics, then initial models, and finally hone the models.

And I’ve found that if I keep each of these steps in separate program files, it makes it much easier to keep track of everything.  If you’re creating new variables in the middle of analyses, it’s going to be harder to find the code so you can remember exactly how you created that variable.

6. As you run different versions of models, label them with model numbers

When you’re building models, you’ll often have a progression of different versions.  Especially when I have to communicate with a collaborator, I’ve found it invaluable to number these models in my code and print that model number on the output.  It makes a huge difference in keeping track of nine different models.

7. As you go along with different analyses, keep your syntax clean, even if the output is a mess.

Data analysis is a bit of an iterative process.  You try something, discover errors, realize that variable didn’t work, and try something else.  Yes, base it on theory and have a clear analysis plan, but even so, the first analyses you run won’t be your last.

Especially if you make mistakes as you go along (as I inevitably do), your output gets pretty littered with output you don’t want to keep.  You could clean it up as you go along, but I find that’s inefficient.  Instead, I try to keep my code clean, with only the error-free analyses that I ultimately want to use.  It lets me try whatever I need to without worry.  Then at the end, I delete the entire output and just rerun all code.

One caveat here:  You may not want to go this approach if you have VERY computing intensive analyses, like a generalized linear mixed model with crossed random effects on a large data set.  If your code takes more than 20 minutes to run, this won’t be more efficient.

8. Use titles and comments liberally

I’m sure you’ve heard before that you should use lots of comments in your syntax code.  But use titles too.  Both SAS and SPSS have title commands that allow titles to be printed right on the output.  This is especially helpful for naming and numbering all those models in #6.

9. Name output, log, and programs the same

Since you’ve split your programs into separate files for data manipulations, descriptives, initial models, etc. you’re going to end up with a lot of files.  What I do is name each output the same name as the program file.  (And if I’m in SAS, the log too-yes, save the log).

Yes, that means making sure you have a separate output for each section.  While it may seem like extra work, it can make looking at each output less overwhelming for anyone you’re sharing it with.

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