R Under development (unstable) (2024-11-13 r87330 ucrt) -- "Unsuffered Consequences"
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> 
> library("tram")
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
> require("lme4")
Loading required package: lme4
Loading required package: Matrix
> options(digits = 2)
> 
> ## ----mtram-sleep_lmer, cache = FALSE------------------------------------------
> sleep_lmer <- lmer(Reaction ~ Days + (Days | Subject), 
+                    data = sleepstudy, REML = FALSE)
> 
> 
> ## ----mtram-sleep_mtram, cache = FALSE-----------------------------------------
> sleep_LM <- Lm(Reaction ~ Days, data = sleepstudy)
> sleep_LMmer <- mtram(sleep_LM, ~ (Days | Subject), data = sleepstudy)
> 
> 
> ## ----mtram-sleep_cmp----------------------------------------------------------
> logLik(sleep_lmer)
'log Lik.' -876 (df=6)
> logLik(sleep_LMmer)
'log Lik.' -876 (df=6)
> 
> 
> ## ----mtram-sleep_sd-----------------------------------------------------------
> (sdinv <- 1 / summary(sleep_lmer)$sigma)
[1] 0.039
> coef(sleep_LMmer)["Reaction"]
Reaction 
   0.039 
> 
> 
> ## ----mtram-sleep_beta---------------------------------------------------------
> fixef(sleep_lmer) * c(-1, 1) * sdinv
(Intercept)        Days 
      -9.82        0.41 
> coef(sleep_LMmer)[c("(Intercept)", "Days")]
(Intercept)        Days 
      -9.82        0.41 
> 
> 
> ## ----mtram-sleep_varparm------------------------------------------------------
> sleep_lmer@theta
[1] 0.929 0.018 0.223
> coef(sleep_LMmer)[-(1:3)]
gamma1 gamma2 gamma3 
 0.929  0.018  0.223 
> 
> 
> ## ----mtram-sleep_varcorr------------------------------------------------------
> sleep_LMmer$G * (1 / sdinv)^2
2 x 2 sparse Matrix of class "dsCMatrix"
           
[1,] 565 11
[2,]  11 33
> cov2cor(sleep_LMmer$G * (1 / sdinv)^2)
2 x 2 sparse Matrix of class "dsCMatrix"
                
[1,] 1.000 0.082
[2,] 0.082 1.000
> unclass(VarCorr(sleep_lmer))$Subject
            (Intercept) Days
(Intercept)         565   11
Days                 11   33
attr(,"stddev")
(Intercept)        Days 
       23.8         5.7 
attr(,"correlation")
            (Intercept)  Days
(Intercept)       1.000 0.081
Days              0.081 1.000
> 
> 
> ## ----mtram-sleep-Surv---------------------------------------------------------
> library("survival")
> sleepstudy$Reaction_I <- with(sleepstudy, Surv(Reaction - 20, Reaction + 20, 
+                                                type = "interval2"))
> sleepstudy$Reaction_I[1:5]
[1] [230, 270] [239, 279] [231, 271] [301, 341] [337, 377]
> 
> 
> ## ----mtram-sleep-interval, cache = FALSE--------------------------------------
> sleep_LM_I <- Lm(Reaction_I ~ Days, data = sleepstudy)
> sleep_LMmer_I <- mtram(sleep_LM_I, ~ (Days | Subject), data = sleepstudy)
> 
> 
> ## ----mtram-sleep-interval-results---------------------------------------------
> logLik(sleep_LMmer_I)
'log Lik.' -213 (df=6)
> 
> proc.time()
   user  system elapsed 
   13.2     1.4    14.6