| OHDSI Home | Forums | Wiki | Github |
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.
Thank you Dr.Schuemie!
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?
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()?
Thank you for your answer!
It seems I encounter the same package version problem when running another study. (My ATLAS webapi version is 2.7.7.)
Is there any method/documentation to check which version of the packages should I run for different studies?
Luckily that is one of the newer studies, where we’ve started using renv to manage the installation of the required package versions. I just can’t seem to find the instructions for running Charybdis with renv. @anthonysena: am I missing someting?
Hi Dr. Schuemie,
I’m trying to run Population-Level Estimation studies designed on our ATLAS WebAPI
I encountered errors when executing the study. The screenshots are from two packages I’ve run, there are some unexpected “n” in the code
code:
detailed error report: OHDSI_packages/Estimation_Study_error at main · ChenyuL/OHDSI_packages · GitHub
Is it something wrong with the study design? How can I troubles this problem?
Thank you!
The error you are seeing is unrelated to the ‘n’ characters you notice (those seem to be some weird artifact of printing the output).
I just posted information on this error and how to solve it.
Hi Dr. @schuemie, When I run an ATLAS generated PLE package, I got this error after updating some dependency packages. But not sure if it’s because of my study design or the dependencies.
Where could I find the dependencies version for study packages generated by ATLAS 2.7.7?
Thank you!
