Bioequivalence and Bioavailability Forum • Getting variance components from the lmer output

Getting variance components from the lmer output [🇷 for BE/BA]

posted by StatR – Turkey, 2017-02-03 14:53 (2632 d 19:57 ago) – Posting: # 17007
Views: 18,281

Hi dear all,

First of all, I am sorry if my question is too stupid.

I could not find the answer no matter how much I investigate. I am new in the area of bioequivalence, and recently I am interested in individual bioequivalence. Also, I am not so familiar with the lme4. I am trying to extract the variance components (sigmaBT^2, sigmaBR^2, sigmaWT^2, sigmaWR^2 and rho) of the model (Restricted Maximum Likelihood Estimation). My data is as follows:

head(mydata)

  Subject Formula Period Sequence      Yijk

1       1       1      1        1 100.11145

2       1       0      2        1 100.00666

3       1       1      3        1 100.06645

4       1       0      4        1  99.96603

5       2       1      1        1 100.04678

6       2       0      2        1 100.03281

I am trying to do it by lmer function as follows:

lmer(Yijk~Formula+Period+Sequence+(1|Sequence))

Linear mixed model fit by REML ['lmerMod']


Formula: Yijk ~ Formula + Period + Sequence + (1 | Sequence)

REML criterion at convergence: 60.4953

Random effects:

 Groups   Name        Std.Dev.

 Sequence (Intercept) 0.002309

 Residual             0.356224

Number of obs: 64, groups:  Sequence, 2

Fixed Effects:

(Intercept)      Formula       Period     Sequence  

  99.787798     0.178645     0.080047    -0.004724  

model <- lmer(Yijk~Formula+Period+Sequence+(1|Sequence))

summary(model)

Linear mixed model fit by REML ['lmerMod']


Formula: Yijk ~ Formula + Period + Sequence + (1 | Sequence)



REML criterion at convergence: 60.5



Scaled residuals: 

    Min      1Q  Median      3Q     Max 

-2.5750 -0.4585  0.1577  0.5746  2.2238 



Random effects:

 Groups   Name        Variance  Std.Dev.

 Sequence (Intercept) 5.331e-06 0.002309

 Residual             1.269e-01 0.356224

Number of obs: 64, groups:  Sequence, 2



Fixed effects:

             Estimate Std. Error t value

(Intercept) 99.787798   0.178187   560.0

Formula      0.178645   0.089056     2.0

Period       0.080047   0.039827     2.0

Sequence    -0.004724   0.089116    -0.1



Correlation of Fixed Effects:

         (Intr) Formul Period

Formula  -0.250              

Period   -0.559  0.000       

Sequence -0.750  0.000  0.000

I know, the estimated value of sigmaWR^2 = 1.269e-01 and the mean difference Ft-Fr = 0.178645.

But how can I get the estimated values of sigmaBT^2, sigmaBR^2, sigmaWT^2 and rho ? I appreciate any help.

Complete thread:

Bear vs. Phoenix & SAS Helmut 2015-04-20 17:34
- R vs. Phoenix & SAS? yjlee168 2015-04-20 19:36
  - R vs. Phoenix & SAS? Helmut 2015-04-21 01:02
    - lme() does not work with all fixed effects yjlee168 2015-04-21 23:41
      - lme() does not work with all fixed effects Astea 2016-11-04 00:13
        
        lmer: Method B (PE catched for imbalanced dataset!!!) and Method C mittyri 2016-11-05 17:38
        
        lmer: Method B (PE catched for imbalanced dataset!!!) and Method C Astea 2016-11-05 19:27
        
        lmer: Method B is ready for scaling mittyri 2016-11-05 20:01
        
        lmer: Method B is ready for scaling Astea 2016-11-06 11:50
        
        lmer: Method B is ready for scaling mittyri 2016-11-07 06:07
- info for lsmeans yjlee168 2015-04-20 21:34
  - info for lsmeans Helmut 2015-04-21 01:15
    - once more about R and replicate designes Astea 2016-11-02 23:43
      - once more about R and replicate designes VStus 2016-11-06 11:34
        
        Getting variance components from the lmer outputStatR 2017-02-03 13:53
        
        Getting variance components from the lmer output VStus 2017-02-03 15:47
        
        Getting variance components from the lmer output StatR 2017-02-03 17:12
        
        Getting variance components d_labes 2017-02-07 11:16
        
        Getting variance components StatR 2017-02-07 11:36
        Getting variance components StatR 2017-02-08 08:41
        
        Getting variance components d_labes 2017-02-08 10:13
        
        Getting variance components StatR 2017-02-08 10:19
        
        Data structure Helmut 2017-02-08 10:33
        
        Data structure StatR 2017-02-08 10:49