2023-02-09

This is Marco's daily open-notebook.

Today is 2023.02.09

Todo today

Have a look at the DBGI discussion forum

• https://github.com/orgs/digital-botanical-gardens-initiative/discussions

Doing

• comment code from https://github.com/anticipated-lotus/elotus-trees
  • prepare_pseudoabsence_tables.R
  • prettyStructuresTable.R
  • prettyTree.R

Paused

Done

Commented code from https://github.com/anticipated-lotus/elotus-trees :

• count_npclasses.R
• papers_taxa_correlation.R

Notes

Scripts descrition

I think the most important script for us is prepare_pseudoabsence_tables.R. It generates presence and absence tables of chemical compounds based on the Order. The Order could be changed to then have tables based on Family, Subfamily, Genus, etc...

This will have to be discussed:

• At what level of taxonomy do we want to work ?
• At what level of chemical taxonomy should we work ?
• Should we try all the levels ?

Links to look at

https://openmolecules.org/datawarrior/ https://www.dendron.so/

https://www.dbgi.org/dendron-dbgi/notes/tofizf0eb38rduuw6ffnzba/

LOTUS outputs https://zenodo.org/communities/the-lotus-initiative/?page=1&size=20

https://zenodo.org/record/7534071#.Y-S2QJOZP8Y

Some links https://www.dbgi.org/dendron-dbgi/notes/inakqagsydtih7ls65eh3nb/

https://www.sib.swiss/training/upcoming-training-courses

https://www.irradiatedsoftware.com/sizeup/

Todo tomorrow

Today I learned that