Bioequivalence and Bioavailability Forum

Group effect: the endless river [General Statistics]

posted by Astea – Russia, 2019-12-22 22:23 (1730 d 18:59 ago) – Posting: # 21018
Views: 7,948

Dear Breathtakingly Smart People!

❝ I agree with PharmCat. Doable in R.

Please check my solution...
Below is my R-code:


library(readxl)

library(lmerTest)

options(contrasts=c("contr.treatment","contr.poly"))

Dataset<-read_excel("DS_01_group.xlsx", sheet = 1)

Model2 <- function(Dataset){

Dataset$Formulation<-factor(Dataset$Formulation, levels = c("R","T"))

Dataset$Sequence<-factor(Dataset$Sequence, levels = c("TRTR", "RTRT"))

Dataset$Period<-factor(Dataset$Period)

Dataset$Group<-factor(Dataset$Group)

mod.lmer <- (lmer(log(Data)~Sequence+Period/Group+Formulation+Group+Group*Sequence+(1|Subject/(Sequence)), data=Dataset))

FormulationEffect.lmer <- summary(mod.lmer)$coefficients["FormulationT","Estimate"]
cat("\n", "PE is", round(exp(as.numeric(FormulationEffect.lmer))*100, digits = 8), "\n")

FormulationT<-summary(mod.lmer)$coefficients["FormulationT",]  

CI_Lr<-round(exp(FormulationT[1]+FormulationT[2]*qt(0.05, FormulationT[3]))*100, 4)

CI_Ur<-round(exp(FormulationT[1]-FormulationT[2]*qt(0.05, FormulationT[3]))*100, 4)

cat("\n", "CI is", CI_Lr, "-", CI_Ur,"\n")}

Model2(Dataset)

In order to check whether it works properly I used Data set 1 from Q&A and added group-factor: first 30 subjects - group #1, and the last - group #2.

To compare the results I used the following SAS-code:


proc mixed data=SASuser.Dataset;

class Formulation Subject Period Sequence Group;

model PKlog= Sequence Formulation Period(Group) Group Sequence*Group;

random Subject(Sequence*Group);

estimate "test-ref" Formulation -1 1 / CL alpha=0.10;

run;

Cause I wasn't sure that my code works well I used the step-by-step approach and compared different models (they all may be meaningless by nature but whatever):
1). Sequence Formulation Period as Fixed, Subject(Sequence) as Random
2). Sequence Formulation Period Group as Fixed, Subject(Sequence) as Random
3). Sequence Formulation Period(Group) Group as Fixed, Subject(Sequence) as Random
4). Sequence Formulation Period(Group) Group Sequence*Group as Fixed, Subject(Sequence) as Random
5). Sequence Formulation Period(Group) Group Sequence*Group as Fixed, Subject(Sequence*Group) as Random

The results are as follows:

       SAS         SAS         SAS         R         R            R

#   PE         90%CI, L   90%CI, U   PE         90%CI, L   90%CI, U

1   115,7298   107,1707   124,9725   115,7298   107,1707   124,9725

2   115,7279   107,1680   124,9716   115,7279   107,1679   124,9716

3   115,7208   107,1080   125,0262   115,7208   107,1080   125,0262

4   115,7275   107,1136   125,0340   115,7275   107,1136   125,0340

5   115,7275   107,1136   125,0340   NA         NA         NA

And now, attention, the questions:
1). Looking the same is not proving to be the same, isn't it?
2). By the way, this is exactly an example where the design changes the decision of BE (of course if scaling was not stated in protocol). BE or not BE?
3). When I try to use Subject(Sequence*Group) as Random in R, it throws an error: "couldn't evaluate grouping factor (Sequence * Group):Subject within model frame: try adding grouping factor to data frame explicitly if possible". Is it right that we can simply neglect the structure of this term as we can do in standard models with Subject instead of Subject(Sequence)?

—
"Being in minority, even a minority of one, did not make you mad"

Complete thread:

Group by sequence interaction Mutasim 2019-08-07 13:16 [General Statistics]
- Group by sequence interaction, an urban myth? Helmut 2019-08-07 14:35
  - pristine, genuine, holy, magnificent, inexplicable beautiful variation ElMaestro 2019-08-08 10:06
    - I love your subject line! Helmut 2019-08-08 10:31
      - Group effect, did you miss it? Astea 2019-12-21 14:12
        
        Group effect, did you miss it? PharmCat 2019-12-22 01:37
        Group effect: the endless story Helmut 2019-12-22 10:30
        
        Group effect: the endless riverAstea 2019-12-22 21:23
        
        Group effect: the endless river PharmCat 2019-12-22 22:52
        replicateBE solution with interactions mittyri 2019-12-23 14:30
        
        replicateBE solution with interactions Astea 2019-12-23 17:26
        
        datasets issues mittyri 2019-12-24 10:53
        datasets Helmut 2019-12-24 11:03
        
        datasets Astea 2019-12-24 19:18
        
        lmer / lme Helmut 2019-12-25 19:12
        
        What do you mean exactly? Beholder 2019-12-27 13:44
        
        What do you mean exactly? Astea 2019-12-29 21:59
        
        ANOVA acc. to GL Helmut 2019-12-30 12:32

Group effect: the endless river [General Sta­tis­tics]

Complete thread:

Group effect: the endless river [General Statistics]