Bioequivalence and Bioavailability Forum • lme() in bear

lme() in bear [🇷 for BE/BA]

posted by yjlee168 – Kaohsiung, Taiwan, 2015-04-18 14:02 (3716 d 02:20 ago) – Posting: # 14699
Views: 29,698

Dear ElMaestro,

❝ No, take away an intercept.

I see.

❝ or equally good

❝ log(Cmax) ~ 0 + drug + seq + prd <-- I pick this one.

  Statistical analysis (lme) - replicate BE study               

-------------------------------------------------

  Dependent Variable: ln(Cmax)                                           

Linear mixed-effects model fit by REML

 Data: inputdata 

        AIC       BIC   logLik

  -174.2564 -153.2241 98.12818



Random effects:

 Formula: ~drug - 1 | subj

 Structure: General positive-definite, Log-Cholesky parametrization

         StdDev      Corr 

drug1    0.149004555 drug1

drug2    0.122159678 0.15 

Residual 0.007644172      



Variance function:

 Structure: Different standard deviations per stratum

 Formula: ~1 | drug 

 Parameter estimates:

        1         2 

1.0000000 0.4391939 

Fixed effects: log(Cmax) ~ 0 + drug + seq + prd 

          Value  Std.Error DF   t-value p-value

drug1  7.356274 0.05636146 38 130.51957  0.0000

drug2  7.420013 0.05152645 38 144.00398  0.0000

seq2   0.002664 0.05517303 13   0.04829  0.9622

prd2  -0.061700 0.04760132 38  -1.29618  0.2027

prd3  -0.059641 0.04760132 38  -1.25293  0.2179

prd4   0.003482 0.00164306 38   2.11917  0.0407

❝ order of effects has lexical importance and determines how many effect estimates you get per term. Accordingly, when you fit sequence as the first term you will not see one effect estimate for each drug.

Aha! Now I remember that. Thank you so much to refresh my memory. But now I don't know which one I should extract. :confused:

What do you think?

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

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Complete thread:

Reproducing Bear results in Phoenix mittyri 2015-04-14 08:35 [🇷 for BE/BA]
- Bug in bear? Helmut 2015-04-14 14:07
  - Bug in bear? mittyri 2015-04-14 20:43
    - Bug in bear? Helmut 2015-04-15 02:17
  - use the same dataset? yjlee168 2015-04-20 10:13
- Bugs in bear with replicated demo data set? yjlee168 2015-04-15 09:38
- Bugs fixed in bear? yjlee168 2015-04-17 01:21
  - Bugs fixed in bear? Helmut 2015-04-17 14:25
    - Bugs fixed in bear? yjlee168 2015-04-17 18:50
      - Bugs fixed in bear? ElMaestro 2015-04-17 23:14
        
        lme() in bear yjlee168 2015-04-18 11:12
        
        lme() in bear ElMaestro 2015-04-18 11:28
        
        lme() in bearyjlee168 2015-04-18 12:02
        
        lme() in bear ElMaestro 2015-04-18 13:42
        
        Mean means Helmut 2015-04-18 14:08
        
        Mean means ElMaestro 2015-04-18 16:01
        
        Mean means Helmut 2015-04-19 00:59
        
        Mean means ElMaestro 2015-04-19 09:14
        
        LL and AIC Helmut 2015-04-19 11:08
        
        Confused ElMaestro 2015-04-19 11:42
        
        lsmeans for mixed model in R yjlee168 2015-04-19 23:36
        
        lsmeans() & lme() Helmut 2015-04-20 01:28
        
        lsmeans() & lme() yjlee168 2015-04-20 10:23
        lsmeans() & lme() ElMaestro 2015-04-20 10:35
        
        keep it simple! Helmut 2015-04-20 14:34
        
        keep it simple! ElMaestro 2015-04-20 15:39
        
        ML vs. REML Helmut 2015-04-20 16:35
        
        lme() with NA in R yjlee168 2015-04-19 23:44
      - Dataset Helmut 2015-04-18 13:30
        
        Dataset and lme() in bear yjlee168 2015-04-18 23:14