by Annette Gerritsen, Ph.D.
Cross-tabulation in cohort studies
Assume you have just done a cohort study. How do you actually do the cross-tabulation to calculate the cumulative incidence in both groups?
Best is to always put the outcome variable (disease yes/no) in the columns and the exposure variable in the rows. In other words, put the dependent variable–the one that describes the problem under study–in the columns. And put the independent variable–the factor assumed to cause the problem–in the rows.
Let’s take as example a cohort study used to see whether there is a causal relationship between the use of a certain water source and the incidence of diarrhea among children under five in a village with different water sources. In this case, the variable diarrhea (yes/no) should be in the columns. The variable water source (suspected/other) should be in the rows.
SPSS will put the lowest value of the variable in the first column or row. So in order to get those with diarrhea in the first column you should label ‘diarrhea’ as 1 and ‘no diarrhea’ as 2. The same is true for the exposure variable: label the ‘suspected water source’ as 1 and the ‘other water source’ as 2.
You will then be able to calculate the cumulative incidence (risk of developing the disease) among those with the exposure: a / (a + b) and among those without the exposure: c / (c + d).
In the case of the diarrhea study (Table 1), you could calculate the cumulative incidence of diarrhea among those exposed to the suspected water source, which would be (78 / 1,500 =) 5.2%.
You can also do this for those exposed to other water sources, which would be (50 / 1,000 =) 5.0%.
SPSS can give you these percentages immediately (in cell ‘a’ and ‘c’ respectively), when you ask to display row percentages in the Cells option (Table 2).
Cross-tabulation in Case-Control Studies
When you have used a case-control design for the diarrhea study, the actual cross-tabulation is quite similar, only “presence of diarrhea yes/no”, is now changed into “cases” and “controls.
Label the cases as 1, and the controls as 2. Be aware that row percentages have no meaning in terms of occurrence of disease in case-control studies. This is because in case-control studies the researcher determines how many patients and how many controls are included.
The ratio between the number of patients and controls (e.g. 2 : 1 or 4 : 1) influences the row percentages. So in a case-control study, the cumulative incidence cannot be calculated.
When having conducted a case-control study, you can ask to display column percentages. That gives you the proportion of those exposed to the suspected water source among the cases (in cell ‘a’) and among the controls (in cell ‘b’).
Table 3 gives the SPSS output for the same diarrhea study assuming that it had a case-control design. Using the data provided, (78 / 128 =) 60.9% of the cases were exposed to the suspected water source, while this was (1,422 / 2,372 =) 59.9% of the controls (asked for column percentages).
Another article will be devoted to measures of association: How do you actually compare cumulative incidence rates in cohort studies? And what measure of association can be used in case-control studies?
About the Author: With expertise in epidemiology, biostatistics and quantitative research projects, Annette Gerritsen, Ph.D. provides services to her clients focussing on the methodological soundness of each phase of an epidemiological study to ensure getting valid answers to the proposed research questions. She is the founder of Epi Result.
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.
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.
This year I hired a Quickbooks consultant to bring my bookkeeping up from the stone age. (I had been using Excel).
She had asked for some documents with detailed data, and I tried to send her something else as a shortcut. I thought it was detailed enough. It wasn’t, so she just fudged it. The bottom line was all correct, but the data that put it together was all wrong.
I hit the roof.Internally, only—I realized it was my own fault for not giving her the info she needed. She did a fabulous job.
But I could not leave the data fudged, even if it all added up to the right amount, and already reconciled. I had to go in and spend hours fixing it. Truthfully, I was a bit of a compulsive nut about it.
And then I had to ask myself why I was so uptight—if accountants think the details aren’t important, why do I? Statisticians are all about approximations and accountants are exact, right?
As it turns out, not so much.
But I realized I’ve had 20 years of training about the importance of data integrity. Sure, the results might be inexact, the analysis, the estimates, the conclusions. But not the data. The data must be clean.
Sparkling, if possible.
In research, it’s okay if the bottom line is an approximation. Because we’re never really measuring the whole population. And we can’t always measure precisely what we want to measure. But in the long run, it all averages out.
But only if the measurements we do have are as accurate as they possibly can be.
I recently received this question:
I have scale which I want to run Chronbach’s alpha on. One response category for all items is ‘not applicable’. I want to run Chronbach’s alpha requiring that at least 50% of the items must be answered for the scale to be defined. Where this is the case then I want all missing values on that scale replaced by the average of the non-missing items on that scale. Is this reasonable? How would I do this in SPSS?
My Answer:
In RELIABILITY, the SPSS command for running a Cronbach’s alpha, the only options for Missing Data (more…)
Two designs commonly used in epidemiology are the cohort and case-control studies. Both study causal relationships between a risk factor and a disease. What is the difference between these two designs? And when should you opt for the one or the other?
Cohort studies
Cohort studies begin with a group of people (a cohort) free of disease. The people in the cohort are grouped by whether or not they are exposed to a potential cause of disease. The whole cohort is followed over time to see if (more…)
In a previous post, Interpreting Interactions in Regression, I said the following:
In our example, once we add the interaction term, our model looks like:
Height = 35 + 4.2*Bacteria + 9*Sun + 3.2*Bacteria*Sun
Adding the interaction term changed the values of B1 and B2. The effect of Bacteria on Height is now 4.2 + 3.2*Sun. For plants in partial sun, Sun = 0, so the effect of Bacteria is 4.2 + 3.2*0 = 4.2. So for two plants in partial sun, a plant with 1000 more bacteria/ml in the soil would be expected to be 4.2 cm taller than a (more…)
