Bioequivalence and Bioavailability Forum • Potvin – all effects fixed (PHX/WNL vs. SAS, R)

Potvin – all effects fixed (PHX/WNL vs. SAS, R) [Two-Stage / GS Designs]

posted by ElMaestro – Denmark, 2012-10-27 00:05 (4622 d 16:25 ago) – Posting: # 9465
Views: 11,633

Hi Helmut,

check your coding, I thik there's an issue with seq.

I get:


Subj=as.factor(c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,

         11,11,12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19,20,20))

Seq=as.factor(c("TR","TR","TR","TR","TR","TR",   

                "TR","TR","TR","TR","TR","TR",  

                "RT","RT","RT","RT","RT","RT", 

                "RT","RT","RT","RT","RT","RT",

                "TR","TR","TR","TR",

                "TR","TR","TR","TR",

                "RT","RT","RT","RT",

                "RT","RT","RT","RT"))

Per=as.factor((rep(c(1,2), 20)))

Trt=as.factor(c(1,2,1,2,1,2,1,2,1,2,1,2, 

                2,1,2,1,2,1,2,1,2,1,2,1, 

                1,2,1,2,1,2,1,2,

                2,1,2,1,2,1,2,1))

Stg=as.factor(c(rep(1,24), rep(2,16)))



PK=c(4.8, 4.6, 1.4, 1.3, 3.9, 4.4, 1.5, 2.4, 3.8, 2.9, 3.3, 2.5, 1.7, 1.5, 1.3, 1.9, 2.1, 2.4, 11.4, 13.9, 1.5, 2.3, 2.6, 2.4,

4.0,4.2,0.7, 0.5, 10.3, 11.9,4.7, 4.8, 5.9,5.5, 3.8, 5.4, 4.3, 2.1, 3.6, 2.4)

options(digits=12)

M=lm(log(PK)~0+Trt+Seq+Subj%in%(Stg*Seq)+Per%in%Stg+Stg)

lnPE=coef(M)[1]-coef(M)[2]


df=anova(M)[6,1]


ct=qt(1-0.0294,df)

nps=length(Trt)/4

foo=sqrt(0.5*(anova(M)[6,3])* (1/nps+1/nps)   )  

U=lnPE+ct*foo

L=lnPE-ct*foo  

cat("Difference in treatment means is ", coef(M)[1]-coef(M)[2], "\n")

Difference in treatment means is  0.01443888498 

cat("PE: ", exp(lnPE), "\n")

PE:  1.01454362920 

> cat("The residual is ", anova(M)[6,3], "\n")

The residual is  0.0458955516532 

cat("Upper ", exp(U), "\n")

Upper  1.16377016091 

cat("Lower ", exp(L), "\n")

Lower  0.88445193916

We have a winner?

PS: With that coding for subject we will of course not talk about subject nested in sequence or stage :-D

. There is no subject 1 in sequence "RT" and no subject 1 in stage 2 and so forth. So we might just as well do:

M=lm(log(PK)~0+Trt+Stg+Seq+Subj+Per%in%Stg)

—
Pass or fail!
ElMaestro

Complete thread:

Potvin – all effects fixed (PHX/WNL vs. SAS, R) Helmut 2012-10-26 19:35 [Two-Stage / GS Designs]
- Potvin – all effects fixed (PHX/WNL vs. SAS, R) ElMaestro 2012-10-26 20:14
  - Potvin – all effects fixed (PHX/WNL vs. SAS, R) Helmut 2012-10-26 20:25
    - Potvin – all effects fixed (PHX/WNL vs. SAS, R)ElMaestro 2012-10-26 22:05
- Potvin – all effects fixed - SAS d_labes 2012-10-29 09:57
  - Potvin – all effects fixed (PHX/WNL resolved) Helmut 2012-11-06 01:43
    - Potvin – all effects fixed (PHX/WNL resolved) ElMaestro 2012-11-06 11:48
      - Potvin – all effects fixed (PHX/WNL resolved) Helmut 2012-11-06 13:48
        
        Mysterious ways ElMaestro 2012-11-06 15:27
        
        Mysterious ways Helmut 2012-11-06 17:06