I’ve been working on the table 1 problem, and have the following solution (which will be wrong for everyone, I know, but at least it is something):
Using the upcoming version of the FeatureExtraction package one can generate cohort characteristics for a cohort of choice (the package allows many options, but that is another story). The resulting cohort characterization data object contains ‘covariates’ which have covariate IDs and analysis IDs. Given such a data object and a simple specification table like this one, a table 1 is generated as shown below. In this table I’ve used the concepts identified earlier by @Patrick_Ryan, for example looking them up in the analysis with ID 210 (occurrence in the condition_era table in the year prior to cohort_start_date). Note that race and ethnicity are not in the example, because these were not captured in the database.
For the average user, that means that with two R statements (one to generate the covariates, one to generate the table) you can have a table like below. For the power users they will have the flexibility to modify the variables that enter the table by modifying the specifications. But if people want more flexibility they’ll have to wrangle the data themselves.
Here’s the table (two parts), exported as PDF to preserve layout. Originally these are R data frames, so you can use them in many ways.
Part1.pdf (193.2 KB)
Part2.pdf (171.4 KB)
Still to add is the option to show two cohorts in one table, similar to this table 1 by Graham et al.
Still work in progress, but wanted to let everyone know what I’m working on.