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USEPA / CompTox-ToxCast-tcplFit2

Performs basic concentration response curve fitting
https://cran.r-project.org/package=tcplfit2
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Update polynomial 2 model documentation (2023) #11

Closed sedavid01 closed 2 months ago

sedavid01 commented 10 months ago

The current parameterization of the polynomial 2 model diverges from that of BMDS and BMDExpress. It assumes that the background response is always at zero and also does not allow for fitting of biphasic responses (that is, an observed response which increases in the low dose region then changes directionality and decreases in higher doses, or vice versa).

Needs:

sedavid01 commented 10 months ago

Current blocker, does the optimization in tcplfit2 for the poly2 model allow for the "b" parameter to be negative? Does constOptim allow for any of the constraints to be negative for any of the parameters within a specified function?

gracezhihuizhao commented 10 months ago

The current implementation of poly2 in tcplfit2 will always have a lower limit of 1e^-8*conc_max constrain on the "b" parameter, it's a very small number so basically it's a positive boundary for "b". constOptim should allow for negative constraints for any of the parameters that we want to optimize.

sedavid01 commented 10 months ago

Thank you for looking into this, @gracezhihuizhao.

sedavid01 commented 3 months ago

@gracezhihuizhao, can you please follow-up on the poly2 updates to check whether the poly2 modeling function(s) had their documentation updated with https://github.com/USEPA/CompTox-ToxCast-tcplFit2/issues/69. If yes, please just make a comment here and I can close this ticket out. If no, then please work on updating the relevant modeling functions.

gracezhihuizhao commented 2 months ago

@gracezhihuizhao, can you please follow-up on the poly2 updates to check whether the poly2 modeling function(s) had their documentation updated with #69. If yes, please just make a comment here and I can close this ticket out. If no, then please work on updating the relevant modeling functions.

Yes, the documentations are updated in #69.

sedavid01 commented 2 months ago

Thanks, @gracezhihuizhao for following-up. Closing out this ticket as this has already been resolved.