Comments (7)
@richelbilderbeek the island_tbl only contains reconstructed information so no extinct species are kept.
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Current state:
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Some info from Josh:
- The col_t given to each cladogenetic species (spec_type == βCβ) 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 donβt speciate have branch_code == NA.
- A cladogenetic speciation event causes one new row to be added, unlike mainland_clade where two rows are added
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- 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 :-)
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@richelbilderbeek the figure is correct. The two green lines should form the clade you have drawn on the left-hand side.
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@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 :-)
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For now, this Issue is on hold until after the next release. I will close it for now.
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Related Issues (20)
- Remove link to Tidyverse coding standard? HOT 1
- Write read_results function
- change plotting functions to use results and not read the results in the plotting function
- fix the build on fix_check branch HOT 1
- Check whether island_to_table, ideal_island_to_table and empirical_island_to_table can be deleted
- add labels argument to plots
- Write function to create `ideal_island_tbl` and `emperical_island_tbl` from `island_tbl` HOT 6
- Resurrect island_to_tables and daisie_data_to_tables for V2? HOT 3
- add tidyverse style check to tests HOT 1
- Add `plot_daisie_mainland_data` HOT 4
- Color clades based on stac_str HOT 1
- Use time before present + plot recolonisations HOT 7
- Changing `plot_mainland` x-axis to time before present HOT 8
- plot_daisie_mainland_data: reverse time axis HOT 5
- Plot all recolonisations in 'plot_daisie_mainland_data' HOT 23
- Plot branches connected correctly by `plot_daisie_data` HOT 5
- No branching for colonist that underwent anagenesis? HOT 2
- Numerical integrator use HOT 1
- Island plot legend HOT 1
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