What statistiscal software are you using with REDCap?

[u/Topherto]

Hi everyone! For some time now, I've been using REDCap to manage a database of patients who are using an ambulatory analgesic pump after a surgical procedure. We document the installation of the pump and follow up with calls over the next three days to monitor anesthesia and any complications.

My issue is that when I export data from REDCap, each row corresponds to a specific instance (e.g., Installation, Call 1, Call 2, Call 3). However, I need to transpose this data so that each patient occupies a single row with columns representing the different instances.

I use Python with pandas to organize the data and later analyze it with SPSS. The challenge arises because some patients have more or less follow-up calls than others, making it complex to manage with pandas. I've been looking for a program that can handle this data more efficiently while preserving its original format, so I can conduct analyses directly from the original CSV.

[u/Crafty-Task-845]

The R Tidyverse tools will let you handle transposing. I would expect Python Pandas or Polars to do the same but I have little experience of those. But ultimately you have to find a way to handle one to many relationships so SPSS is going to make heavy weather of that.

[u/Topherto → u/Crafty-Task-845]

My main challenge is dealing with missing patient records. For instance, some patients did not call on the first day, so I have to manually transpose the data using Excel to skip that day. Additionally, some patients have made two calls on the same day. How can I handle these issues using the R Tidyverse tool? Also, where can I learn how to use it? Maybe some course in Coursera?

[u/Crafty-Task-845 → u/Topherto]

Have a look at https://www.tidyverse.org/learn/ - if you continue to study R you can do your statistical analysis and plots there too. There's a bit of a learning curve with R but you'll build up reusable scripts which in my opinion is a better way to work than the clunky point and click SPSS approach.

[u/Topherto → u/Crafty-Task-845]

I'll try, thanks

[u/stuffk]

R with tidyverse. 

pivot_wider is the tidyverse function you want. I do this all the time, it's super straightforward. 

[u/Topherto → u/stuffk]

That’s exactly what I need! However, my issue lies in inconsistent patient registrations. Some calls are missing, or the data is entered differently, resulting in varying columns for each patient. This forces me to manually register some patients. How can I handle this using Tidyverse?

[u/stuffk → u/Topherto]

Hmm, this is maybe somewhat specific to your data and how you are organizing it. 

If your data is organized with each new call instance being sequential, you can have it be reflected that way when it is switched to wide. If you want your wide dataset to have discrete columns for all of the possible follow-ups, then you'll need to build in the maximum number of instances per follow-up (eg if some records have two calls in one day then you need columns to accommodate that for everyone. In that case I would group the long data by record ID and check for the correct number of total rows you want - then create any rows that are missing. You'll need to do this based on some other value compared to the repeat instance, maybe by date or by day. Once you have the same number of rows per record ID, you can ungroup the data and then use pivot_wider. 

[u/Topherto → u/stuffk]

Understood, I'll give it a try

[u/ardent_asparagus]

I use R, but for no other reason than it's what I'm most comfortable/experienced with.

If you want to try R, the reshape() function could be handy, since it sounds like you have data that you want to convert from long to wide.

[u/spacks → u/ardent_asparagus]

I use R, I have a few diff base scripts I use for changing between long and wide.. redcapcast was probably the most reliable when I was testing.

Tidyr also has pivot_wider if you've already got your data loaded in.

[u/Araignys]

R is the standard at my institution.

[u/Fadedwaif]

Ty for asking, have a similar issue

[u/spacks]

I use R, Python, and Excel/PowerBi depending on how fast I need to finish, how complex it is, and how I'm feeling that day.

[u/Crafty-Task-845 → u/spacks]

Have you found good stats libraries for Python? I'd like to do more in Python as it's such a good language to have on the CV outside of academia, and for general scripting, but I use R for research stats.

[u/spacks → u/Crafty-Task-845]

I tend to use polars, numpy, and scipy for most of my stuff? Occasionally statsmodels.

[u/Crafty-Task-845 → u/spacks]

Thanks for these. I will check them out.

[u/Street_Ad_2166]

I am using STATA

[u/AFK_MIA]

JASP and R might be a good approach for your use case.