Toolbox: fig_3

A collection of functions that produces the figures of the DEB-book third edition. These functions show the actual data, how the data have been fitted, and what parameters are used in the various specific applications of the DEB theory; the DEB book gives biological background of and conclusions from the figures. The files also illustrate the use of functions in the library of DEBtool and the subtleties of parameter identifiability. Make sure that the path to DEBtool and all its subdirectories is set; this large collection of scripts and functions not only uses DEBtool/lib/ but also other toolboxes. Subdirectory fig_3 has subdirectories ch1, ch2, ., ch11 for figures in 11 chapters.

The first lines in each source-script file gives the figure name, the bib-codes for data-sources and the names of the output files as used in the DEB-book. This info is used for maintenance purposes.

If you run several figures, you might need to clear previous plots with clf.


fig

All figures are run from a single function fig, which requires a character string as input, with a chapter and a figure number, separated by a dot. If this figure has code, it runs the code, which is in one of the subdirectories ch1, ch2, ., ch11 and gives the page number of the DEB book as output. Many routines give details on parameter values, standard deviations and produce output during the search for the best fitting parameters.

To view the code, first inspect function fig to learn the name of the source function in one of the subdirectories, then inspect that function. So the code for figure '1.7' can be found in KooyHoef89 in /fig_3/ch1. This code typically calls other functions, which are either in that subdirectory, or in sister directories of fig_3.

Support exists for the following figures

  1. 2, 6, 7, 8
  2. 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 15, 17, 19
  3. 1, 2
  4. 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 13, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30
  5. 1, 5, 6, 8, 9, 12
  6. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16
  7. 2, 6, 7, 8, 10, 11, 12, 15, 17, 18, 20, 21, 22, 23, 24, 25
  8. 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15
  9. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17
  10. 8, 11
  11. 1

Example of use: fig('1.7') to run figure 7 of chapter 1.


Back to the DEBtool page