Simon Merkt

Improve sampling visualizations

1

- [ ] make trace & correlation plots transparent as default - [x] invert CIs light to dark default setting

Implement Copula interface/functionality

3

https://www.groups.ma.tum.de/en/statistics/research/vine-copula-models/packageslibraries/

Add verbose mode

2

It might be good to have the option to show some kind of progress in case of longer simulation loops

**Feature description** Use ipopt with gradient approximation. **Motivation/Application** Ipopt supports approximation of Jacobian/Gradients (https://coin-or.github.io/Ipopt/OPTIONS.html). However using ipopt in pypesto only with objective function yields the error: `ValueError: This Objective cannot...

Recover history and result object/file from unfinished optimizations

8

**Feature description** * Merge separate trace files into history file/object * convert history file/object to result file/object. **Motivation/Application** In case you reach wall time limit on a cluster or some...

Additional Model: D’Alessandro LA, Samaga R, Maiwald T et al. PLoS CB 2015

2

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004192

Visualization files for all models (list)

9

This issue serves as an overview of which models already have the visualization file. During the work on each model this model's issue should be re-opened. Once all models have...