Hi al,
I have a dataset (see attached), which basically involves 4 treatments for a
chemotherapy drug. Samples were taken from 2 biopsy locations, and biopsy were
taken at 2 time points. So each subject has 4 data points (from 2 biopsy
locations and 2 time points). The objective is to study treatment difference.
I used lme to fit a mixed model that uses "biopsy.site nested within pid" as a
random term, and used corAR1() as the correlation structure for between the 2
time points:
library(nlme)
test<-read.table("test.txt",sep='\t',header=T,row.names=1)
fit<-lme(y~age + time * trt, random=~1|pid/biopsy.site, data = test,
correlation=corAR1())
First, by above model specification, corAR1() is used for the correlation
between the 2 time points; what is the correlation structure implicitly used
for between biopsy locations? How do I specify a particular correlation
structure for between biopsy locations in this situation?
Second, does anyone know how to write the above mixed model in SAS? One of my
colleagues wrote the following, but it gave me different results:
proc mixed data=test;
class time trt pid biopsysite;
model y=age time trt time*trt;
random biopsysite
repeated pid / type=ar(1)
run;
Is there anyone familiar with SAS and know if the above SAS code does what the
R code does?
Many thanks
JohnX pid trt time biopsy.site y age
1 P8 B DAY 4 S2 0.748 62
2 P8 B DAY 4 S1 0.086 62
3 P8 B DAY 8 S2 0.09 62
4 P8 B DAY 8 S1 0.076 62
5 P13 B DAY 4 S1 -0.296 74
6 P13 B DAY 4 S2 -0.079 74
7 P13 B DAY 8 S1 -0.097 74
8 P13 B DAY 8 S2 0.135 74
9 P27 B DAY 4 S1 -0.128 82
10 P27 B DAY 4 S2 -0.401 82
11 P27 B DAY 8 S1 -0.01 82
12 P27 B DAY 8 S2 -0.249 82
13 P29 B DAY 4 S1 -0.45 51
14 P29 B DAY 4 S2 -0.086 51
15 P29 B DAY 8 S1 -0.407 51
16 P29 B DAY 8 S2 0.136 51
17 P9 C DAY 4 S2 0.789 53
18 P9 C DAY 4 S1 1.021 53
19 P9 C DAY 8 S2 0.29 53
20 P18 C DAY 4 S2 0.007 63
21 P18 C DAY 4 S1 0.053 63
22 P19 C DAY 4 S1 -0.048 63
23 P19 C DAY 4 S2 -0.121 63
24 P22 C DAY 4 S1 0.357 54
25 P22 C DAY 4 S2 0.407 54
26 P22 C DAY 8 S1 -0.171 54
27 P22 C DAY 8 S2 -0.038 54
28 P25 C DAY 4 S2 0.01 67
29 P25 C DAY 4 S1 0.102 67
30 P25 C DAY 8 S2 0.007 67
31 P25 C DAY 8 S1 0.09 67
32 P30 C DAY 4 S2 0.225 73
33 P30 C DAY 4 S1 0.018 73
34 P30 C DAY 8 S2 0.038 73
35 P30 C DAY 8 S1 -0.032 73
36 P33 C DAY 4 S2 -0.224 29
37 P33 C DAY 4 S1 0.122 29
38 P33 C DAY 8 S2 -0.346 29
39 P33 C DAY 8 S1 -0.161 29
40 P39 C DAY 4 S2 -0.005 70
41 P39 C DAY 4 S1 0.053 70
42 P39 C DAY 8 S2 -0.061 70
43 P39 C DAY 8 S1 0.016 70
44 P40 C DAY 4 S2 0.083 67
45 P40 C DAY 4 S1 0.13 67
46 P40 C DAY 8 S2 0.397 67
47 P40 C DAY 8 S1 0.388 67
48 P1 D DAY 4 S2 -0.195 57
49 P1 D DAY 4 S1 -0.267 57
50 P1 D DAY 8 S2 -0.042 57
51 P1 D DAY 8 S1 -0.255 57
52 P3 D DAY 4 S2 -0.312 39
53 P3 D DAY 4 S1 -0.338 39
54 P7 D DAY 4 S2 -0.216 61
55 P7 D DAY 4 S1 0.34 61
56 P7 D DAY 8 S2 -0.196 61
57 P7 D DAY 8 S1 -0.349 61
58 P10 D DAY 4 S2 0.108 57
59 P10 D DAY 4 S1 -0.073 57
60 P10 D DAY 8 S2 0.382 57
61 P10 D DAY 8 S1 0.461 57
62 P14 D DAY 4 S2 -0.003 71
63 P14 D DAY 4 S1 -0.156 71
64 P14 D DAY 8 S2 0.222 71
65 P14 D DAY 8 S1 0.016 71
66 P15 D DAY 4 S2 0.282 62
67 P15 D DAY 4 S1 0.463 62
68 P15 D DAY 8 S2 0.03 62
69 P15 D DAY 8 S1 0.42 62
70 P24 D DAY 4 S2 -0.345 72
71 P24 D DAY 4 S1 -0.2 72
72 P24 D DAY 8 S2 -0.285 72
73 P24 D DAY 8 S1 -0.059 72
74 P26 D DAY 4 S2 0.052 50
75 P26 D DAY 4 S1 0.256 50
76 P26 D DAY 8 S2 0.321 50
77 P26 D DAY 8 S1 0.197 50
78 P31 D DAY 4 S2 0.36 27
79 P31 D DAY 4 S1 0.108 27
80 P31 D DAY 8 S2 0.214 27
81 P31 D DAY 8 S1 0.012 27
82 P32 D DAY 4 S2 0.12 71
83 P32 D DAY 4 S1 0.033 71
84 P32 D DAY 8 S2 0.092 71
85 P32 D DAY 8 S1 -0.327 71
86 P36 D DAY 4 S1 0.059 40
87 P36 D DAY 4 S2 -0.046 40
88 P36 D DAY 8 S1 -0.22 40
89 P36 D DAY 8 S2 -0.175 40
90 P42 D DAY 4 S2 -0.116 67
91 P42 D DAY 4 S1 0.144 67
92 P42 D DAY 8 S2 -0.047 67
93 P42 D DAY 8 S1 0.342 67
130 P2 A DAY 4 S1 -0.122 49
131 P2 A DAY 4 S2 -0.442 49
132 P2 A DAY 8 S1 0.229 49
133 P2 A DAY 8 S2 -0.007 49
134 P4 A DAY 4 S2 -0.162 47
135 P4 A DAY 4 S1 -0.187 47
136 P4 A DAY 8 S2 -0.365 47
137 P4 A DAY 8 S1 -0.085 47
138 P5 A DAY 4 S2 0.004 70
139 P5 A DAY 4 S1 0.065 70
140 P5 A DAY 8 S2 -0.188 70
141 P5 A DAY 8 S1 -0.427 70
142 P6 A DAY 4 S1 0.14 38
143 P17 A DAY 4 S2 0.379 79
144 P17 A DAY 4 S1 0.117 79
145 P17 A DAY 8 S2 0.233 79
146 P17 A DAY 8 S1 0.13 79
147 P23 A DAY 4 S2 -0.266 45
148 P23 A DAY 4 S1 -0.286 45
149 P23 A DAY 8 S2 0.311 45
150 P23 A DAY 8 S1 0.283 45
151 P37 A DAY 4 S2 0.085 33
152 P37 A DAY 4 S1 -0.167 33
153 P37 A DAY 8 S2 0.361 33
154 P37 A DAY 8 S1 -0.096 33
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