OHDSI Home | Forums | Wiki | Github

CohortMethod run outof time


#1


I run the CohortMethod package to create propensity score matching plots. The first time it was successful, but the second time I used the same code the createPs function never finishing running. If I interrupt the running, will get this error alert

  1. How could I troubleshoot this problem?
  2. Could we ATALS WebAPI to display the propensity score matching/Kaplan-Meier plot?

(Martijn Schuemie) #2

Depending on the size of the population, number of covariates, and especially the number of cores you assign, fitting a propensity can take a really long time (worst case: > 100,000 persons, > 100,000 covariates, 1 core will take weeks)

You can modify the behavior of Cyclops using the control argument of the createPs function. A first step would be to set the number of threads to however CPU cores you have available. I also recommend setting noiseLevel = "quiet" to get more information while it is running. See the Cyclops documentation for details.


#3

Thank you Dr.Schuemie!


#4

I successfully run the code and saw the result last week. It took me 48 minutes to run this single study.
Today I run the same code again and got this error.

Another problem I have is: I used ATLAS Estimation generated the package"Estimation1118", and tried to load it in R Studio to see the results in shiny app. I followed the readme.md steps. All the dependencies in readme.md in step 1 are attached but cannot run step 2. Are there any steps I missed?


(Martijn Schuemie) #5

The first error message suggests you’ve updated Cyclops to a newer version incompatible with the other packages. Note that ATLAS is behind the R packages, so you really must not update anything, to keep the code generated by ATLAS happy.

I’m not sure about the second error. R says it can’t find the manual pages and other documentation objects. Could you try clicking “Install and Restart” in R studio instead of calling install()?


t