Notice: I decided to remove the
DEBtoxM packages from this web page. The last versions
were from 2015, and I no longer maintain or use them.
Please use the BYOM framework
instead. This page will remain here, along with the
version logs, an an archive. If you really want
to use DEBtoxM, please contact me.
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
|
|
