Finish plot_island_tbl on tree_plots branch
richelbilderbeek opened this issue · comments
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.
Current state:
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
- 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 :-)
@richelbilderbeek the figure is correct. The two green lines should form the clade you have drawn on the left-hand side.
@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 :-)
@richelbilderbeek the island_tbl only contains reconstructed information so no extinct species are kept.
For now, this Issue is on hold until after the next release. I will close it for now.