bear v1.0.0 - a data analytical tool for ABE in R [🇷 for BE/BA]
❝ From this I get the impression that the ANOVA in fact is based on lm, not GLM; for example "lm(LnAUC0INF ~ seq + subj + prd + drug, data = TotalData)"?! Is this intended - shouldn't it be glm?
❝
❝ 2. The intrinsic R glm function does afair not allow for random effects (in contrast to glm in SAS); analysing datasets with a syntax like "glm(LnAUC0INF ~ seq + subj + prd + drug)" might treat subj as fixed.
Exactly. You're right. We use "lm" function to run anova, not "glm" from R. However, the outputs we have tested with one BE dataset are exactly the same with those generated by SAS with
proc glm;
statement. Yes, we tried "glm" at the beginning, and got some different results from it. Then we changed to "lm". Bingo! Your comments exactly help to solve something that we don't know before.
❝ 3. As far as I remember, both lm and glm are unsafe in cases with imbalance for crossover studies (can't find a ref right now, though, sorry about it). I am under the impression that this type of analysis should be done explicitly with a mixed model (LME, using the REML approach) to ascertain you get the correct sigma.
Our package is built currently only for the 2-trt x 2-per x 2-seq, balanced, non-replicated, cross-over designed BE study. The mixed model (such as
proc mixed;
in SAS or "lme" with REML) may be suitable forreplicated, imbalanced, cross-over designed BE study. We have planned to add more functions later. At that moment, "lme" will be used.
Ref.:
❝ 4. Although Sums-of-Squares is pretty much a mine field, I think it would be wise to at least implement an option of getting type III SS. Some regulators seem unwilling to accept anything other than type III, while others couldn't care less (I have it on good account ).
Yes, we add "type III SS" in the next release. We're fixing bear right now. Hopefully it can be done before the end of July.
❝ ...I am no expert (neither in statistics nor in BE) I should add.
You certainly are an expert in BE . Thank you for your comments.
Edit: Link corrected for FDA’s new site. [Helmut]
All the best,
-- Yung-jin Lee
bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here
Complete thread:
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-12 20:53 [🇷 for BE/BA]
- bear v1.0.0 for R - first impressions Helmut 2008-07-14 04:12
- bear v1.0.0 for R - first impressions yjlee168 2008-07-14 10:26
- bear v1.0.0 for R - first impressions Helmut 2008-07-14 14:02
- bear v1.0.0 for R - first impressions yjlee168 2008-07-14 18:12
- bear v1.0.0 for R... Helmut 2008-07-14 18:56
- bear v1.0.0 for R... yjlee168 2008-07-14 19:30
- bear v1.0.0 for R... Helmut 2008-07-14 20:35
- bear v1.0.0 for R... yjlee168 2008-07-14 19:30
- bear v1.0.0 for R... Helmut 2008-07-14 18:56
- bear v1.0.0 for R - first impressions yjlee168 2008-07-15 09:44
- bear v1.0.0 for R - first impressions yjlee168 2008-07-14 18:12
- bear v1.0.0 for R - first impressions Helmut 2008-07-14 14:02
- bear v1.0.0 for R - first impressions yjlee168 2008-07-14 10:26
- bear v1.0.0 - a data analytical tool for ABE in R martin 2008-07-14 12:18
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-14 19:02
- bear v1.0.0 - a data analytical tool for ABE in R Aceto81 2008-07-15 10:07
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-16 07:22
- bear v1.0.0 - a data analytical tool for ABE in R Aceto81 2008-07-16 09:47
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-16 21:32
- bear v1.0.0 - a data analytical tool for ABE in R Aceto81 2008-07-16 09:47
- lambda_z estimation yjlee168 2008-09-23 12:13
- lambda_z estimation d_labes 2008-09-23 14:41
- lambda_z estimation yjlee168 2008-09-24 22:41
- lambda_z estimation Aceto81 2008-09-25 10:56
- lambda_z estimation yjlee168 2008-09-25 21:00
- lambda_z estimation yjlee168 2008-09-26 08:03
- lambda_z estimation Aceto81 2008-09-26 10:25
- lambda_z estimation yjlee168 2008-09-28 00:08
- lambda_z estimation yjlee168 2008-09-29 13:32
- WinNonlin 5.2.1 vs. 6 beta Helmut 2008-09-29 15:54
- WinNonlin 5.2.1 vs. 6 beta yjlee168 2008-09-29 18:45
- WinNonlin 5.2.1 vs. 6 beta --> new finding yjlee168 2008-09-30 08:10
- Example 4 in SASophylistic d_labes 2008-09-30 09:43
- Example 4 in SASophylistic yjlee168 2008-09-30 12:23
- Example 4 in SASophylistic d_labes 2008-09-30 09:43
- WinNonlin 5.2.1 vs. 6 beta Helmut 2008-09-29 15:54
- lambda_z estimation Aceto81 2008-09-26 10:25
- TTT method for lambda_z estimation yjlee168 2008-09-30 12:34
- TTT method for lambda_z estimation d_labes 2008-09-30 14:48
- TTT method for lambda_z estimation yjlee168 2008-09-30 20:28
- TTT method plus best fit combined d_labes 2008-10-01 08:43
- AIC or ARS as the best fit criterion? yjlee168 2008-10-02 12:40
- AIC or ARS as the best fit criterion? d_labes 2008-10-02 13:59
- AIC or ARS as the best fit criterion? yjlee168 2008-10-02 12:40
- TTT method plus best fit combined d_labes 2008-10-01 08:43
- TTT method for lambda_z estimation yjlee168 2008-09-30 20:28
- TTT method for lambda_z estimation Aceto81 2008-09-30 15:11
- TTT method for lambda_z estimation yjlee168 2008-09-30 19:57
- TTT method for lambda_z estimation Aceto81 2008-10-01 14:18
- TTT method for lambda_z estimation yjlee168 2008-10-02 12:29
- TTT method for lambda_z estimation Aceto81 2008-10-03 15:33
- TTT method for lambda_z estimation yjlee168 2008-10-03 21:22
- TTT method for lambda_z estimation Aceto81 2008-10-03 15:33
- TTT method for lambda_z estimation yjlee168 2008-10-02 12:29
- TTT method for lambda_z estimation Aceto81 2008-10-01 14:18
- TTT method for lambda_z estimation yjlee168 2008-09-30 19:57
- TTT method for lambda_z estimation d_labes 2008-09-30 14:48
- lambda_z estimation d_labes 2008-09-23 14:41
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-16 07:22
- bear v1.0.0 - a data analytical tool for ABE in R Aceto81 2008-07-15 10:07
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-14 19:02
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-07-22 14:35
- bear v1.0.0 - a data analytical tool for ABE in Ryjlee168 2008-07-23 09:55
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-07-24 10:04
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-25 20:38
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-07-28 08:42
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-07-25 20:38
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-09-23 16:10
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-09-24 22:00
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-09-25 09:03
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-09-25 13:52
- bear v1.0.0 - a data analytical tool for ABE in R Helmut 2008-09-25 14:39
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-09-25 14:55
- bear v1.0.0 - a data analytical tool for ABE in R Helmut 2008-09-25 15:33
- GLM in R and the power to know d_labes 2008-09-25 16:45
- GLM in R and the power to know ElMaestro 2008-09-25 19:23
- nesting in R? yjlee168 2008-09-25 20:49
- nesting in R? ElMaestro 2008-09-25 22:01
- lm in R Helmut 2008-09-26 00:23
- nesting in R? yjlee168 2008-09-25 20:49
- GLM in R and the power to know ElMaestro 2008-09-25 19:23
- GLM in R and the power to know d_labes 2008-09-25 16:45
- bear v1.0.0 - a data analytical tool for ABE in R Helmut 2008-09-25 15:33
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-09-25 14:55
- bear v1.0.0 - a data analytical tool for ABE in R Helmut 2008-09-25 14:39
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-09-25 13:52
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-09-25 09:03
- bear v1.0.0 - a data analytical tool for ABE in R yjlee168 2008-09-24 22:00
- bear v1.0.0 - a data analytical tool for ABE in R ElMaestro 2008-07-24 10:04
- Type III SS in balanced, crossover BE studies? yjlee168 2008-10-18 21:03
- Type III SS in balanced, crossover BE studies? ElMaestro 2008-10-21 13:09
- Type III SS in balanced, crossover BE studies? yjlee168 2008-10-21 13:19
- Only balanced, crossover BE studies? d_labes 2008-10-21 14:31
- Only balanced, crossover BE studies? yjlee168 2008-10-21 19:01
- Only balanced, crossover BE studies? ElMaestro 2008-10-24 11:26
- Thread locked Helmut 2008-10-24 11:58
- Only balanced, crossover BE studies? ElMaestro 2008-10-24 11:26
- Only balanced, crossover BE studies? yjlee168 2008-10-21 19:01
- Only balanced, crossover BE studies? d_labes 2008-10-21 14:31
- Type III SS in balanced, crossover BE studies? yjlee168 2008-10-21 13:19
- Type III SS in balanced, crossover BE studies? ElMaestro 2008-10-21 13:09
- bear v1.0.0 - a data analytical tool for ABE in Ryjlee168 2008-07-23 09:55
- bear v1.0.0 for R - first impressions Helmut 2008-07-14 04:12