add-my-pet / debtool_j.jl Goto Github PK

There is a lot of code here that can be heavily optimized for performance, and restructured a little (e.g. to remove globals)

But we really need tests for each function to be able to do that easily.

Are there any tests of the original MATLAB?

DifferentialEquations is a kitchen sink package, and blows out load and compilation time be a few minutes.

We should instead include just the packages directly needed here.

Matlab in DEBtool_M is running Perl (via select), C++ (via popDyn), Java (via NetLogo in popDyn), Latex/BibTex (to compose references) and outputs in HTML, JavaScript. If we finally master the DOI archiving, we can perhaps add R to the list as well. Moreover it runs a collection of functions, such as wget, in the shell and reads in HTML pages, e.g. to classify the species. I doubtlessly forgot some more. The list shows that we should not think in terms of either/or, but of and/and. If the Julia exercise shows us what parts is slowing down the procedure most, we can also think of replacing those modules directly by C++. We also might try to run Julia under Matlab.

Can Julia handle Matlab's concept "persistent"? We use it to avoid the need to re-load allStat, but also in DEBtool_M/animal/get_tjm to set s_M if v_H < v_Hj and use it if v_H > v_Hj.

Small remarks about the js pars_init file:

1. the zoom factor is dimless (does not have dim length)

2. DEBtool_M pars_init files use DEBtool_M/lib/pet/get_d_V and get_N_waste for default values for d_E, d_V and n_*N, based on the classification of the species. The user can overwrite the default values.