I am running a linear mixed model on a longitudinal dataset.
How do I go about calculating a p-value for the interaction term 'trt*Category' at time = 2 (years)? In other words, I need the overall interaction p-value for 'trt * Category' when time = 2 years, irrespective of the values of trt and Category.
In the dataset df_new -
- base is a continuous variable, with longitudinal values at different time points
- base0 is a continuous variable at time=0 (baseline value)
- trt variable has 2 values: 0 and 1 with 0 as the reference level
- Category has 3 levels: A, B, C with A as the reference level
- time (in years) has 4 values: 0.1, 0.5, 1, 2
- time2 is just a quadratic term for time variable
- ID is the subject ID
Model has -
- 2-way interactions and one 3-way interaction
- intercept and time as random effects
Any help is appreciated.
> lmeFit.check <- lme(base ~ base0 + trt + Category + time + time2 + time:trt + time2:trt + time:Category + time2:Category + trt:Category+ time*trt*Category, data = df_new, random = ~ time| ID, na.action=na.exclude, method="ML")
> summary(lmeFit.check)
Linear mixed-effects model fit by maximum likelihood
Data: df_new
AIC BIC logLik
-1239.015 -1123.239 640.5077
Random effects:
Formula: ~time | ID
Structure: General positive-definite, Log-Cholesky parametrization
StdDev Corr
(Intercept) 0.1370508 (Intr)
Time 0.0861213 -0.021
Residual 0.1245289
Value Std.Error DF t-value p-value
(Intercept) 0.3342470 0.02907089 1228 11.497651 0.0000
base0 0.4862522 0.03065282 587 15.863210 0.0000
trt1 0.1581257 0.02858652 587 5.531477 0.0000
CategoryC -0.1561378 0.03683512 587 -4.238831 0.0000
CategoryB -0.0444300 0.02586699 587 -1.717634 0.0864
time 0.0048867 0.03813285 1228 0.128149 0.8981
time2 -0.0109739 0.01765595 1228 -0.621542 0.5344
trt1:time -0.0568882 0.03974451 1228 -1.431346 0.1526
trt1:time2 0.0205837 0.01633965 1228 1.259738 0.2080
CategoryC:time 0.1909650 0.06328872 1228 3.017362 0.0026
CategoryB:time 0.0648119 0.04091624 1228 1.584015 0.1134
CategoryC:time2 -0.0770699 0.02972717 1228 -2.592574 0.0096
CategoryB:time2 -0.0292700 0.01824750 1228 -1.604052 0.1090
trt1:CategoryC 0.1007911 0.05053169 587 1.994612 0.0465
trt1:CategoryB -0.0226765 0.03330770 587 -0.680819 0.4963
trt1:CategoryC:time -0.0526821 0.05042956 1228 -1.044668 0.2964
trt1:CategoryB:time 0.0196245 0.03078963 1228 0.637375 0.5240
I believe this can be accomplished using the contrast option? But, need some helpful pointers...