bear v1.0.0 - a data analytical tool for ABE in R [🇷 for BE/BA]

posted by yjlee168 Homepage – Kaohsiung, Taiwan, 2008-07-23 11:55 (5727 d 23:33 ago) – Posting: # 2072
Views: 56,263

(edited by yjlee168 on 2008-07-23 12:57)

Dear EM,

❝ 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 for
replicated, imbalanced, cross-over designed BE study. We have planned to add more functions later. At that moment, "lme" will be used.
Ref.: http://www.fda.gov/cder/guidance/3616fnl.pdf US FDA Guidance for Industry: Statistical approaches to establishing bioequivalence, Jan, 2001.

❝ 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 :-D).


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
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