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Making sense of ecotoxicity test results



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DEBtox information

Software / DEBtoxM flavours

DEBtoxM flavours in Matlab


On this page, I present my Matlab scripts and functions to analyse toxicity data in a DEB framework. I call this collection "DEBtoxM", where the M stands for "multi", as it allows for the simultaneous analysis of multiple data sets with common parameters. These files are first and foremost to support my own research. However, I have attempted to structure and comment them in such a way that they can be useful to other people. For the basic idea behind DEBtox, I would like to refer to the DEBtox about. For a more elaborate introduction, please read my e-book. If you're new to Matlab, check out tutorial from Udemy, or the tutorial that the MathWorks offers.

The files are prepared with care, but not extensively tested (and I adapt them all the time), so I cannot give any guarantees as to their correctness (in fact, I am pretty sure that they will contain errors). I do not accept liability or responsibility for any damage or costs incurred as a result of these errors. If you spot an error or want to comment on these files, please contact me. If there is an update I will also notify that on the home page.

Note: I have not been able to work on these packages much over the last couple of years. I spent most of my coding time on the BYOM framework, which better suits the projects I am running now (BYOM is more appropriate for one-off analyses). I may return to DEBtoxM at some point, but it may take some time ... I advice the BYOM famework for most cases, although the DEBtoxM scripts are better suited for analyses with multiple datasets sharing some (but not all) common parameters.

There are at this moment three different flavours: Surv, GUTS and DEBtox. The DEB3 flavour is no longer offered as there are too many things in there that need a closer look (and furthermore, I focus on applications of DEBkiss now for). I also have a DEBkiss version of DEBtoxM, which I also not put here for download as it needs a closer look. However, if you want to use a beta version at your own risk, contact me. All flavours share several features, and many of the functions are common (the files in the folders 'common' and 'utils'). Read the manual for a full overview of the possibilities (all flavours share this manual, which also needs a revision):

---> Download the DEBtoxM manual. (9 May 2015)






 
Available DEBtoxM flavours
Flavour
Description
Types of data
Version and date
Download
Surv
Basic survival modelling, but very fast. Choice between stochastic death and individual tolerance. External concentration must be constant. This is a simplification of the GUTS flavour, and a good place to start getting acquainted with the DEBtoxM implementations.
Body residues, survival
1.04
17 Apr. 2015
DEBtoxM_surv.zip
version log.txt
GUTS
Flexible survival modelling, following the General Unified Threshold model for Survival (GUTS), as described in Jager et al. (2011). Allows time-varying external concentration. You have a choice of dose metrics (including scaled internal concentration, damage and receptor kinetics), and a choice between stochastic death and individual tolerance (or a combination of both).
External concentrations, body residues, survival
1.07b
6 May 2015
DEBtoxM_guts.zip
version log.txt
Basic DEBtox
Basic simplified DEB model, assuming that length at puberty and egg costs are constant (also under stress). This model is published by Jager & Zimmer (2012). The parameters are easy-to-interpret compound parameters such as "maximum reproduction rate" and "length at puberty". Only a limited number of parameters can be affected by a toxicant in this simplification; other "modes of action" will lead to inconsistencies and are thus not included.
Body residues, survival, body size, reproduction
1.04b
6 May 2015
DEBtoxM_debtox.zip
version log.txt
Full DEB3
Full DEB3 model; full flexibility, but also full complexity. This flavour implements the scaled DEB model as described in Kooijman et al. (2008), with toxicant effects as discussed in Jager et al. (2010). Applying these files succesfully requires a THOROUGH background in DEB theory!
Body residues, survival, body size, reproduction

No longer offered
DEBkiss
The DEBkiss model with explicit mass balance, and with toxicant effects.
Body residues, survival, body size, reproduction

No longer offered


The DEBtox information site, www.debtox.info, since July 2011