Bioequivalence and Bioavailability Forum • Bugs fixed in bear?

Bugs fixed in bear? [🇷 for BE/BA]

posted by yjlee168 – Kaohsiung, Taiwan, 2015-04-17 20:50 (3661 d 13:09 ago) – Posting: # 14695
Views: 29,363
(edited on 2015-04-17 21:48)

Dear Helmut,

Estimate(test-ref) here is obtained from lme() (red color number),

  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) ~ seq + prd + drug 

                Value  Std.Error DF   t-value p-value

(Intercept)  7.356274 0.05636146 38 130.51957  0.0000

seq2         0.002664 0.05517303 12   0.04829  0.9623

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

drug2        0.063740 0.04758714 38   1.33943  0.1884

 Correlation: 

      (Intr) seq2   prd2   prd3   prd4  

seq2  -0.573                            

prd2  -0.520  0.199                     

prd3  -0.520  0.199  0.999              

prd4  -0.015  0.000  0.017  0.017       

drug2 -0.519  0.000  0.000  0.000  0.000

...

Point estimate is calculated from 100*e^{Estimate(test-ref)}.
The means are calculated directly from dataset.

Fdata<-split(TotalData, list(TotalData$drug))

RefData<-Fdata[[1]]

TestData<-Fdata[[2]]

ref_lnCmax<-mean(RefData$lnCmax)   ### MEAN-ref

test_lnCmax<-mean(TestData$lnCmax) ### MEAN-test

[edited] do we use the same dataset?: confused:

—
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

Thread locked

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 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