Skip to content

Cross-over Data with Kenward-Roger correction

3 messages · knouri, Ben Bolker, Peter Dalgaard

Original
knouri
# 
Dear all:for the folowing data, a two-period, two treatment (A=1 vs. B=2) cross-over is fitted
using the folowing SAS code.? 
data one;
input? Sbj? Seq ?Per? Trt? PEF;
cards;
1???? ?1?? 1?? 1?? 310
1???? ?1?? 2?? 2?? 270
4???? ?1?? 1?? 1?? 310
4???? ?1?? 2?? 2?? 260
6???? ?1?? 1?? 1?? 370
6???? ?1?? 2?? 2?? 300
7????? 1?? 1?? 1?? 410
7????? 1?? 2?? 2?? 390
10??? 1?? 1?? 1?? 250
10??? 1?? 2?? 2?? 210
11??? 1?? 1?? 1?? 380
11??? 1?? 2?? 2?? 350
14??? 1?? 1?? 1?? 330
14??? 1?? 2?? 2?? 365
2????? 2?? 1?? 2?? 370
2????? 2?? 2?? 1?? 385
3????? 2?? 1?? 2?? 310
3???? ?2?? 2?? 1?? 400
5???? ?2?? 1?? 2?? 380
5????? 2?? 2?? 1?? 410
9????? 2?? 1?? 2?? 290
9????? 2?? 2?? 1?? 320
12??? 2?? 1?? 2?? 260
12??? 2?? 2?? 1?? 340
13??? 2?? 1?? 2??? 90
13??? 2?? 2?? 1?? 220
;
run;
proc mixed data=one method=reml;
class Sbj Per Trt;
?? model PEF = Per Trt /ddfm=kr;
?? repeated Trt / sub=Sbj type=un r;
?? lsmeans Trt / cl alpha=0.05;
?? estimate 'B vs. A' Trt -1? 1 / alpha=0.1 cl;
run;
(where kr option is for Kenward-Roger method).I need to use R to reproduce the results similar to what the above SAS code generates.
I have used several R functions including lme, lmer with no success so far.Any advice will be greatly appreciated,Sincerely,
Keramat
1 day later
Ben Bolker
# 
knouri <nouri4 <at> yahoo.com> writes:
[snip]
This is more appropriate for r-sig-mixed-models at r-project.org.
Please post followups there.

The lmerTest and lsmeans packages will probably be useful.

As a statistical point, I don't understand why you can't just
do a paired t-test on these data??

dat <- read.table(header=TRUE,text=
"Sbj Seq Per Trt PEF
1 1 1 1 310
1 1 2 2 270
4 1 1 1 310
4 1 2 2 260
6 1 1 1 370
6 1 2 2 300
7 1 1 1 410
7 1 2 2 390
10 1 1 1 250
10 1 2 2 210
11 1 1 1 380
11 1 2 2 350
14 1 1 1 330
14 1 2 2 365
2 2 1 2 370
2 2 2 1 385
3 2 1 2 310
3 2 2 1 400
5 2 1 2 380
5 2 2 1 410
9 2 1 2 290
9 2 2 1 320
12 2 1 2 260
12 2 2 1 340
13 2 1 2 90
13 2 2 1 220")

library(lmerTest)
library(ggplot2); theme_set(theme_bw())
ggplot(dat,aes(x=Per,y=PEF,colour=factor(Trt)))+geom_point()+
    geom_line(colour="gray",aes(group=Sbj))+
        scale_x_continuous(breaks=c(1,2))
        
m1 <- lmer(PEF~Per+Trt +(Trt|Sbj), data=dat)

## warning about unidentifiability
1 day later
Peter Dalgaard
#
On 08 Jun 2015, at 22:59 , Ben Bolker <bbolker at gmail.com> wrote:

            

      
      
      
    

        
It's a cross-over trial, so you need to account for the period effect. However, a standard way of treating it is by to calculate period differences within subjects and use a t-test (welch or classical) to see if the differ according to sequence (trt1-trt2 or v.v.).