How can I estimate PD parameters for two - compartment model?

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I have a two compartment model with two types of dosing: PK dose and PD dose (scheduled).
I have mapped the data correctly, but my estimate is far off from the reference paper I was using as a prototype. I know thet fit program is for parameter estimate, however I dont know how to assign the baseline dose. Note, the model has no variant.
I do not know what excatly I am doing wrong, and i really do need help with this; been stuck with it for more than a week.
  2 Comments
BLESSING AKAH
BLESSING AKAH on 12 Apr 2022
The drug potency (k2), transient rate (k1) and initial tumor growth (wo) were estimated to be 13.8, 0.130, 0.0386 respectively.
I have tried all I could to get same paramter estimate using the build in model, but my estmate were all far from the actual estimate.
I do not know what exactly I am not doing well.
Please, I will apprecaite any help on how to get the exact estimated values given above.
Thanks,
Blessing.

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Accepted Answer

Arthur Goldsipe
Arthur Goldsipe on 12 Apr 2022
I looked at the project you attached in the comments. I didn't see any obvious problems. Your parameter estimates are within a factor of 2 of the ones you're trying to match. Do you have any reason to believe you should be able to reproduce the reported values more closely? If so, you will likely need to get more details from the author to make sure you are reproducing their model and their estimation methods. In fact, before you try to reproduce their estimation results, I recommend making sure you can reproduce their simulation results for a specific condition. For example, do the authors provide simulation results of tumor weight at the estimated parameter values? If so, can you simulate the same conditions and compare your simulation results? If those don't agree, then you may have a problem with your model. If those do agree, then I recommend double-checking that you're using the correct data and the same fitting approach (for example, the same error model).

More Answers (1)

BLESSING AKAH
BLESSING AKAH on 13 Apr 2022
Hi Arthur, thanks for the detailed information.
Yes, the author did provide the fit results for the estimated parameters: w0, k1 and k2. The initial values used by the author for the estimates were 0.04, 0.5 and 10 for the w0, k1, k2 respectively. The error model used by the author was exponential error model. I did replicate the model, but my estimates didn’t match with the values given by the author. Even when I tried estimating using the author built in model, I was unable to get the estimates for the parameters. I don’t know what I’m doing wrong. PS: I am currently using the author model as a reference on my project. Hence, I needed to get the exact parameter estimates to continue with my project. I am new to using sim biology, hence might be doing something wrong. Please, would you mind running the fit program with the same error model and initial parameters and see if you could get the exact values given by the author. I have been stuck on it for the past few weeks, and I really need my way out of it.
Please let me know if you need more clarification on that. Thanks so much for your help.
Best, Blessing.
  8 Comments
BLESSING AKAH
BLESSING AKAH on 15 Apr 2022
Thanks Arthur for your response; it does help solve my issue with the estimate. I greatly appreciate the consistency in your response. Sure, I will contact you directly if need be.

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