Finish plot_island_tbl on tree_plots branch

joshwlambert / DAISIEmainland

Simulate phylogenetic data on islands with a evolving mainland pool

https://joshwlambert.github.io/DAISIEmainland/

GNU General Public License v3.0

1 stars 1 forks source link

Closed richelbilderbeek closed 2 years ago

richelbilderbeek commented 2 years ago

Just make the tests in test-plot_island_tbl.R produce beautiful tables.

No need to separate between ideal and empircal data yet, this depends on #55.

richelbilderbeek commented 2 years ago

Current state:

Screenshot from 2022-01-11 06-13-12

richelbilderbeek commented 2 years ago

Some info from Josh:

The col_t given to each cladogenetic species (spec_type == “C”) is the same, it is the time clade colonised
- The branch_t of the first cladogenetic species in the clade is the same as the col_t, the branch_t of the other species in the clade is the time they branched
- The branch_code is different from mainland_clade, species that don’t speciate have branch_code == NA.
- A cladogenetic speciation event causes one new row to be added, unlike mainland_clade where two rows are added

richelbilderbeek commented 2 years ago

@joshwlambert:

is this picture correct? That is, the green lines should become the sketched orange lines, right?
Am I correct that no extinction events are present in island_tbl?

I'd enjoy to be corrected here :-)

current_state_annotated

joshwlambert commented 2 years ago

@richelbilderbeek the figure is correct. The two green lines should form the clade you have drawn on the left-hand side.

richelbilderbeek commented 2 years ago

@joshwlambert great that the figure is correct, with some luck I will finish it today.

AFAICS, I never get info on clades that went extinct before the present. Am I correct [1]?

[1] Whether they should be in is another question altogether. Let's talk after the next release :-)

joshwlambert commented 2 years ago

@richelbilderbeek the island_tbl only contains reconstructed information so no extinct species are kept.

richelbilderbeek commented 2 years ago

For now, this Issue is on hold until after the next release. I will close it for now.