Although DEBtool continues to expand, many implications of DEB theory will remain beyond the capacities of this package.
DEBtool and AmPtool are freely available via GitHub, see the DEB laboratory.
This release focuses on
- relationships between variables, as modified by parameter values
- extracting parameter values from data and testing model predictions
Basic-level useOctave and Matlab have a very similar syntax, but small differences do exist. The first steps in Octave are explained in separate notes . A useful short introduction to Matlab is: Knight, A. 2000 Basics of Matlab and Beyond, Chapman & Hall/CRC, 202 pp. A full manual of Octave is: Eaton, J. W., Batemen, D. and Hauberg, S. 2008 GNU Octave Manual, Version 3, Network Theory Limited, 555 pp. An electronic manual is on the web.
Don't work in DEBtool, but set a path to itIt is best to work in the subdirectory that has your own data and routines, and make a path to DEBtool. If you have this just besides DEBtool you set the path to DEBtool and all its subdirectories by
addpath(genpath('../DEBtool_O/'))in Octave or in the menu-bar in Matlab. Use
pwdunder Octave or Matlab for getting the current prosition in to directory-tree, and
lsfor the list of files in the current directory. Use
cdfor changing directories, where
..means the parent-directory. Example if you are in a sister-directory of DEBtool_M:
cd ../DEBtool_M/animal/will bring you to toolbox animal.
The routines in each subdirectory can call other routines from that subdirectory, or from the library DEBtool/lib, which has three subdirectories.
Erase variablesDo not forget to type
clear allafter switching toolboxes. No error messages are given if you do it otherwise, but the effect is not what you want it to be. So if you are in
cd ../plant, continue with
clear all; plant, for instance.
The plot ranges of DEBtools' plotting routines are set without notice, when you use the routines for the first time.
Clear them by either use
clear, or the 'default' option in the
See under the manual under
Recalculate optimisation results from different start valuesAlways remember that optimization results contain local extremes at best, and that a local extreme might differ from the global extreme. Try different starting values, and check the results by making plots. See instructions under
- mydata_*.m The practical application of many DEBtool functions is illustrated with mydata-files, i.e. script files with the name mydata_filename.m. This information is supplementary to that in this manual. You can change these files according to your own needs.
- sh*.m Routines that produce and show plots are called shfilename.m files.
- d*.m Routines that specify differential equations are called d*.m; they are frequently subroutines of *.
- pars_*.m Parameter values that are use in de demo's are specified in pars.m files; the notation follows the DEB-book, and explanations are given in the file. A demo is a script-file with a name equal to its toolbox (i.e. directory).