Bioequivalence and Bioavailability Forum • lme() in bear

lme() in bear [🇷 for BE/BA]

posted by yjlee168 – Kaohsiung, Taiwan, 2015-04-18 13:12 (3716 d 06:17 ago) – Posting: # 14697
Views: 29,663

Dear Elmaestro,

❝ 1. Could you try and fit fixed effects as log(Cmax) ~ 0+ drug + seq + prd, and then extract your drug effects directly from that.

OK. add an intercept?

  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    0.149004554 drug1

drug2    0.122159679 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 + seq + prd + drug 

          Value  Std.Error DF   t-value p-value

seq1   7.356274 0.05636146 12 130.51957  0.0000

seq2   7.358938 0.05152645 12 142.81866  0.0000

prd2  -0.061700 0.04760132 39  -1.29618  0.2025

prd3  -0.059641 0.04760132 39  -1.25293  0.2177

prd4   0.003482 0.00164306 39   2.11917  0.0405

drug2  0.063740 0.04758714 39   1.33943  0.1882

Looks like the same.

❝ 2. Could you compare and check the presence and handling of na's in your comparisons?

in this demo dataset, there is no any NA involved.
any NA must be removed (as the entire period) first before doing lme(); otherwise, it will crash.

So there is no way to compare the difference.

—
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 bearyjlee168 2015-04-18 11:12
        
        lme() in bear ElMaestro 2015-04-18 11:28
        
        lme() in bear yjlee168 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