465b nemf issues - Githubissues

465b / nemf

A novel three step network-based general ecosystem modeling framework

BSD 3-Clause "New" or "Revised" License

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integrate more sophisticated, third party IVP(ODE)-solver

#45 465b closed 4 years ago
1
integrate more sophisticated, third party non-linear programming solvers

#44 465b closed 4 years ago
1
add documentation for debugging the typical problems

#43 465b opened 4 years ago
0
shall "optimisation" flag in yaml be optional?

#42 465b closed 4 years ago
1
add sanity check for: shape(reference data)==shape(defined optimisations)

#41 465b closed 4 years ago
2
redirect automated data output

#40 465b closed 4 years ago
1
add documentation for writing and using interaction functions

#39 465b closed 4 years ago
1
add a directed loop representatin to the graph plot

#38 465b closed 4 years ago
1
add dependencies to module package

#37 465b closed 4 years ago
0
add comments to exemplary configuration files

#36 465b closed 4 years ago
0
test and potentially remove the soft barrier enforcement

#35 465b closed 4 years ago
2
package library

#34 465b closed 4 years ago
0
restructure user-faced functions

#33 465b closed 4 years ago
0
Add sensitivity analysis?

#32 465b closed 4 years ago
1
add feature to fit non-steady-state solutions

#31 465b closed 4 years ago
3
Update documentation

#30 465b closed 4 years ago
1
The functionality of sources and sinks got lost

#29 465b closed 4 years ago
1
Potential bug if interaction function does not require parameters

#28 465b closed 4 years ago
1
add sanity checks to test to the model_config input

#27 465b closed 4 years ago
1
make network plot configuration dump pretty

#26 465b closed 4 years ago
0
remove the hardcoding of the interaction model

#25 465b closed 4 years ago
0
Bug in parameter selection during the optimisation

#24 465b closed 4 years ago
0
add decent default output plotting

#23 465b closed 4 years ago
0
make it possible to optimise coupled function parameters

#22 465b closed 4 years ago
2
add verbose option at runtime

#21 465b closed 4 years ago
0
write unit tests

#20 465b closed 4 years ago
0
write yaml documentation

#19 465b closed 4 years ago
0
remove compartments from yaml config

#18 465b closed 4 years ago
0
gradient descent calculates "center " prediction/cost twice

#17 465b closed 4 years ago
1
use of model_configuration in function is inconsistant

#16 465b closed 4 years ago
2
rewrite run_time_evo to be "model_configuration" independant

#15 465b closed 4 years ago
1
add a visualisation tool of the interaction graph

#14 465b closed 4 years ago
1
rewrite/design gradient_descent such that it only takes the position on the costfunction as input

#13 465b closed 4 years ago
2
sanity check algorithm for flows

#12 465b closed 4 years ago
2
add a function to contain the 'differential operator'

#11 465b closed 4 years ago
1
add a method that checks if everything has a flow into a detritus compartment

#10 465b closed 4 years ago
1
column normalisation in the coefficient matrix does not consider set constrains

#9 465b closed 4 years ago
1
stability checks fails or is imprecise if absolute value is close to zero

#8 465b closed 4 years ago
1
iteration step counter in barrier_hard_enforcement() is wrongly implemented

#7 465b closed 4 years ago
1
some object share the same name, even though they differ in dimension

#6 465b closed 4 years ago
2
add 'natural' stop in optimization if sufficiently converged

#5 465b closed 4 years ago
0
Create LICENSE

#4 465b closed 5 years ago
0
barrier_function returns "inf" if on boarder - breaks gradient method

#3 465b closed 5 years ago
0
add feature that enforces positive masses

#2 465b closed 5 years ago
1
unify integration schemes and time evolution schemes

#1 465b closed 5 years ago
1