Dear R-users
I am relatively new to R, i hope my many novice questions are welcome.
I have problems accessing some objects (specifically the random effects,
correlation structure and variance function) from an object of class gls and
lme.
I used the following models:
yah <- gls (outcome~ -1 + as.factor(Trial):as.factor(endpoint)+
as.factor(Trial):as.factor(endpoint):trt, data=datt[datt$Trial<4,],
correlation = corSymm(form=~1|as.factor(Trial)/as.factor(subject)),
weights=varIdent(form=~1|endpoint))
bm <- lme (outcome~ -1 + as.factor(endpoint)+ as.factor(endpoint):trt,
data=datt[datt$Trial<4,],
random=~-1 + as.factor(endpoint) + as.factor(endpoint):trt|as.factor(Trial),
correlation = corSymm(form=~1|as.factor(Trial)/as.factor(subject)),
weights=varIdent(form=~1|endpoint))
When i print the object "bm" i get the following output:
----------------------------------------------------------------------------------------------------------
> bm
Linear mixed-effects model fit by REML
Data: datt[datt$Trial < 4, ]
Log-restricted-likelihood: -52.23147
Fixed: outcome ~ -1 + as.factor(endpoint) + as.factor(endpoint):trt
as.factor(endpoint)-1 as.factor(endpoint)1 as.factor(endpoint)-1:trt
-3.663087 -1.772427 -3.661823
as.factor(endpoint)1:trt
-3.209671
Random effects:
Formula: ~-1 + as.factor(endpoint) + as.factor(endpoint):trt | as.factor(Trial)
Structure: General positive-definite, Log-Cholesky parametrization
StdDev Corr
as.factor(endpoint)-1 2.05744327 as.()-1 as.()1 a.()-1:
as.factor(endpoint)1 0.08400874 -0.976
as.factor(endpoint)-1:trt 1.90318009 0.975 -0.967
as.factor(endpoint)1:trt 3.25432832 -0.992 0.982 -0.972
Residual 6.48819860
Correlation Structure: General
Formula: ~1 | as.factor(Trial)/as.factor(subject)
Parameter estimate(s):
Correlation:
1
2 0.812
Variance function:
Structure: Different standard deviations per stratum
Formula: ~1 | endpoint
Parameter estimates:
1 -1
1.000000 1.764878
Number of Observations: 18
Number of Groups: 3
----------------------------------------------------------------------------------------------------
Can somebody tell me how to access the values in blue above?
Also, when i tried accessing these values i obtained the following
bm$modelStruct
corStruct parameters:
[1] -1.394879
varStruct parameters:
[1] 0.5680815
What do these values represent.
Thanks in advance..
Pryseley
sample data:
RowNames Trial subject VISUAL0 TRT VISUAL24 VISUAL52 TREAT outcome endpoint
trt
4 1 1003 65 4 65 55 2 0 1 1
8 1 1007 67 1 64 68 2 -3 1 -1
12 2 1110 59 4 53 42 2 -6 1 1
14 2 1111 64 1 72 65 2 8 1 -1
16 2 1112 39 1 37 37 2 -2 1 -1
18 2 1115 59 4 54 58 2 -5 1 1
24 3 1806 46 4 27 24 2 -19 1 1
26 3 1813 31 4 33 48 2 2 1 1
28 3 1815 64 1 67 64 2 3 1 -1
4 1 1003 65 4 65 55 2 -10 -1 1
8 1 1007 67 1 64 68 2 1 -1 -1
12 2 1110 59 4 53 42 2 -17 -1 1
14 2 1111 64 1 72 65 2 1 -1 -1
16 2 1112 39 1 37 37 2 -2 -1 -1
18 2 1115 59 4 54 58 2 -1 -1 1
24 3 1806 46 4 27 24 2 -22 -1 1
26 3 1813 31 4 33 48 2 17 -1 1
28 3 1815 64 1 67 64 2 0 -1 -1
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