Bioequivalence and Bioavailability Forum • "EMA crippled model"

"EMA crippled model" - CVwR estimation and ODA in R [🇷 for BE/BA]

posted by d_labes – Berlin, Germany, 2015-08-27 15:17 (3585 d 16:21 ago) – Posting: # 15358
Views: 12,755

Dear Mittyri,

❝ I mean the R code for CVwr estimation and outliers detection in Reference dataset according to ... EMA GL:

since I have to do my daily work with SAS I don't have an R solution for doing this out of the box.

But I think it should not that complicated to do the estimation of CVwR and this could be programmed even by a novice in R.
Part I: Estimation of CVwR

Make a subset of your data.frame containing only the PK metrics under R(eference)
dtaR <- subset(data, tmt=="R") dtaR$period <- as.factor(dtaR$period) dtaR$subject<- as.factor(dtaR$subject) dtaR$sequence<- as.factor(dtaR$sequence)
Fit an model containing period sequence and subject within sequence
muddleR <- lm(log(PKmetric) ~ period + sequence + subject%in%sequence, data=dtaR)
or according to our Captn's preferred implementation simply
muddleR <- lm(log(PKmetric) ~ period + sequence + subject, data=dtaR)
Extract the error mean square from that model and you calculate the CV from it
msewR <- sum(muddleR$residuals^2)/muddleR$df.residual CVwR <- sqrt(exp(msewR)-1)*100 # in %

Part II - ODA
It is another story and is a grey zone. An outlier test is not expected. So simply create a boxplot from the residuals, cross your fingers and hope that not suspected "outliers" are visible:

boxplot(muddleR$residuals)

This is of course only a rough description just in this moment came to my mind. Intended to give you a starting point. Needs to be tested and validated before going in production. Needs also to make a nice printout of the results. It's up to you.

—
Regards,

Detlew

Complete thread:

can't get information about outliers detection jerry 2015-08-26 08:37
- ODA in bear yjlee168 2015-08-26 08:53
  - ODA in bear jerry 2015-08-26 16:00
    - ODA in bear yjlee168 2015-08-26 17:40
      - ODA in bear jerry 2015-08-26 17:58
      - ODA for replicate designs d_labes 2015-08-27 08:12
        
        ODA for replicate designs yjlee168 2015-08-27 08:51
        
        ODA for replicate designs d_labes 2015-08-27 09:17
        
        ODA for replicate designs yjlee168 2015-08-27 09:30
        
        ODA for replicate designs - "EMA crippled model"? mittyri 2015-08-27 10:20
        
        ODA for replicate designs - "EMA crippled model"? d_labes 2015-08-27 10:53
        
        ODA for replicate designs - "EMA crippled model"? mittyri 2015-08-27 11:00
        
        "EMA crippled model" - CVwR estimation and ODA in Rd_labes 2015-08-27 13:17