nlmixr2, NONMEM and lag time

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mattfidler commented 1 year ago

@kestrel99 ready to review and/or edit or commit

kestrel99 commented 1 year ago

@kestrel99 ready to review and/or edit or commit

Hi! What is the full citation for Gill, Murray, Saunders, and Wright (1983)?

mattfidler commented 1 year ago

P. E. Gill, W. Murray, M. A. Saunders, and M. H. Wright, Computing forward-difference intervals for numerical optimization, SIAM Journal on Scientific and Statistical Comput- ing, 4 (1983), pp. 310–321.

mattfidler commented 1 year ago

I couldnt find it when I wrote it but it was cited in the shi 2021 paper too

mattfidler commented 1 year ago

You need to use blogdown

I always use blogdown::check_site() and it tella me what to do.

On Sat, Nov 12, 2022, 8:02 AM Bill Denney @.***> wrote:

@.**** commented on this pull request.

In content/blog/2022-11-10-nlmixr2-nonmem/index.Rmd https://github.com/nlmixr2/blog/pull/11#discussion_r1020764677:

+These are types of gradients are undetermined by pure forward +sensitivities. The last few releases of nlmixr2 took the first +observation and tried to figure out the best step-size to calculate +the gradients for the whole individual based on the Gill, Murray, +Saunders, and Wright (1983) method. + +## New method for handling dose-based sensitivities + +Now in nlmixr2, we use the method proposed in Shi 2021 +(https://doi.org/10.48550/arXiv.2110.06380). This method is extended +so that instead of optimizing the gradient of one rate, we take the +harmonic mean of all the calculated rates for each observation and +optimize the best step size for that value (which is the same method +we use for the Hessian calculation in the generalized log-likelihood). + +In our limited testing of lag-times, this seems to perform better than

I made that change, but when I tried to regenerate the html everything changed. I think that someone else (or automation) will need to update the html.

— Reply to this email directly, view it on GitHub https://github.com/nlmixr2/blog/pull/11#discussion_r1020764677, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAD5VWRG7EMVOMDXBRZX7WTWH6POXANCNFSM6AAAAAAR5EJC5U . You are receiving this because you authored the thread.Message ID: @.***>

nlmixr2 / blog