Search found 39 matches

by Tjalling
Mon Dec 26, 2022 2:20 pm
Forum: Toxicokinetic (TK) modelling
Topic: Fit data to an analytical solution?
Replies: 2
Views: 312

Re: Fit data to an analytical solution?

Yes, you can set up the code to use analytical solutions. The examples folder of BYOM shows you how. In the examples/logistic folder, there is a derivative in derivatives.m and an analytical solution in simplefun.m. In call_deri, one of these is used, depending on the setting of the global glo.useod...
by Tjalling
Thu Dec 15, 2022 10:35 am
Forum: Announcements
Topic: New version "Modelling essentials" e-book (and others as well!)
Replies: 1
Views: 454

Re: New version "Modelling essentials" e-book

My other e-books have now been updated end of 2022 as well. It has been a while, for most books, so it was time to include new publications, to correct broken links, and to clarify a few points. The DEBkiss e-book received a reworking of the chapters on toxicokinetics and toxicant effects. This mate...
by Tjalling
Thu Dec 15, 2022 10:29 am
Forum: Announcements
Topic: BYOM update v 6.4
Replies: 0
Views: 29

BYOM update v 6.4

At the end of the year, a nice new update of BYOM. Especially some new functionality for 'DEBtox' analyses. Also corrected a silly mistake in calc_proflik that meant that the parallel toolbox was not used for profiling the likelihood, where it should have been used. Full list of changes in the versi...
by Tjalling
Tue Dec 06, 2022 12:40 pm
Forum: Software for modelling (e.g., BYOM)
Topic: How do you choose among different data transformations(-1,0,0.5,1)?
Replies: 2
Views: 391

Re: How do you choose among different data transformations(-1,0,0.5,1)?

Whether or not to transform depends on the (expected) distribution of the residuals around the mean. If you have replicated data, you may get an idea from the data. With body-residue measurements, I think it is safe to assume that the residuals will increase with the mean measured value. In general,...
by Tjalling
Mon Dec 05, 2022 1:32 pm
Forum: Software for modelling (e.g., BYOM)
Topic: Sensitivity analysis function
Replies: 6
Views: 193

Re: Sensitivity analysis function

I expected the same line of argumentation you used for survival (i.e., GUTS e-book, Section 7.5 ) also applies to damage. However, this is not discussed in the book or the paper. Thus, I doubted if my expectation was wrong, i.e., due to the argument that the change of damage is important even at lo...
by Tjalling
Fri Dec 02, 2022 6:40 pm
Forum: Software for modelling (e.g., BYOM)
Topic: Sensitivity analysis function
Replies: 6
Views: 193

Re: Sensitivity analysis function

I think I wanted to avoid additional complexity in the paper, so I kept the relative sensitivity for survival. It does not become really problematic here as survival does not get very close to zero. What is your question on damage? Why I selected that endpoint for SA or why I did not go for absolute...
by Tjalling
Fri Dec 02, 2022 11:42 am
Forum: Software for modelling (e.g., BYOM)
Topic: Sensitivity analysis function
Replies: 6
Views: 193

Re: Sensitivity analysis function

Hi Annika, Perhaps I should have, but I haven't documented the BYOM functions, other than the lavish commenting of the code. Struggling with the interpretation of sensitivity analysis is normal, especially when it is a dynamic model that was fitted. I would say that such a sensitivity analysis is, i...
by Tjalling
Wed Nov 02, 2022 4:39 pm
Forum: Announcements
Topic: New version "Modelling essentials" e-book (and others as well!)
Replies: 1
Views: 454

New version "Modelling essentials" e-book (and others as well!)

Today, I released an update of the e-book "Mechanistic modelling essentials" that was also used for the 2021 course. Participants to the course should have received an email from Leanpub about this new version. If you have downloaded the e-book from Leanpub, you are also entitled to downlo...
by Tjalling
Fri Sep 16, 2022 9:56 am
Forum: Toxicokinetic (TK) modelling
Topic: How to retrieve simulation data
Replies: 12
Views: 1169

Re: How to retrieve simulation data

The reason I asked for acquiring simulation data is because I am wondering if the BYOM could do some reverse dosimetry work? For example, I could measure the concentration of a chemical in one-compartment (i.e. blood), then I could predict the external concentration (i.e. the chemical concentration...
by Tjalling
Thu Sep 15, 2022 1:16 pm
Forum: Toxicokinetic (TK) modelling
Topic: How to retrieve simulation data
Replies: 12
Views: 1169

Re: How to retrieve simulation data

Ah, you are using sim_and_plot ... then this does not work. There is no easy way to get the data out, as plotting is done ‘on the fly’ so that it’s kind of animated. You could use a regular script file (the ones that fit), and simply don’t fit anything. There’s an option for that ... I will have to ...