search

OHDSI / PheValuator

An R package for evaluating phenotype algorithms.
https://ohdsi.github.io/PheValuator/
17 stars 6 forks source link

randomSplitter error #27

Closed SSMK-wq closed 4 years ago

SSMK-wq commented 4 years ago

Hello,

I encountered the below error while I was trying to execute the createevaluationcohort function under PheValuator

Warning: This function is deprecated. Use 'randomSplitter' instead.
Error in randomSplitter(population = population, test = test, train = train,  : 
  Outcome only occurs in fewer than 10 people or only one class

Though this error didn't occur when I ran the same code couple of days back with same cohort definitions, am just trying to understand why this happens now? Because my outcome (XSpec) cohort has 2324 patients. So basically the outcome is occurring in more than 2000 cases. Why does the error message say that it's only for 10 people. Moreover, why doesn't it pull the negative cases from the population. Earlier, during model creation we saw that the code would pull the corresponding negative cases to match the prevalence. May I know why doesn't it happen now?

I see that the population size is set to cases count. Can I kindly check with you on this please? I might be wrong here but whoever runs the code, won't they encounter the same issue? Because if our population size is going to be cases count (which is only one class) and doesn't consider the negative cases at all. Your inputs to help me understand this would be very much appreciated

SSMK-wq commented 4 years ago

I found out that this error message is coming from the PLP package repository but in my case, the positive case count is more than 2000 and test fraction is set to 0.25. I didn't encounter this error earlier for the same cohort definition and positive cases count. But not sure why is this issue showing up when nothing hasn't changed at my end. was there any update to this part of PheVal/PLP? But, when I went through the code, I couldn't find any.

Update

This issue can be closed. I updated PLP package, this issue seems to have gone now and this issue can be closed