Comments (7)
Feel free to write some plotting code, if you feel that the code is useful for the package once it is finished please make a pull request and if I agree it is useful it can be kept on the package. 😄
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Thank you for the idea of having these scenarios be made with a plotting functions in R. The picture pasted above is made using Tikz (latex). I have not attempted to write a plotting function for these in the past, and the I feel the pay-off of having them be produced in R is not worth the time input required to write what I believe would be a substantial amount of code.
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Thanks for the clear answer!
Would you mind to have some experimental plotting added if I do it? It will not be clean and it can well be non-exported
, it is just that I could use it.
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Done!
Here is my favorite test:
test_that("interesting picture, with recolonisation", {
set.seed(
9,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
mainland <- sim_mainland(
total_time = 10,
m = 10,
mainland_ex = 1.0
)
# Clade goes extinct, but after island age
mainland_clade <- mainland[[1]]
plot_mainland_clade(mainland_clade)
island <- sim_island(
total_time = 1,
island_pars = c(1, 1, 10, 12, 1),
mainland = mainland_clade,
mainland_sample_prob = 1,
mainland_sample_type = "complete")
plot_island(island)
})
The mainland clade (note that only until t = 1 is used):
The island:
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I am happy the pictures visualize all the info produced by sim_mainland
and sim_island
. Sure, they can be made more intuitive, but I need a closer look for that. Still, it is helpful that all information is visualized :-)
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Thanks for the new plotting functions. Can this issue be closed once the new code reaches main?
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Thanks for accepting! Sure, this Issue can be closed when it reaches main
, or 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
- Finish plot_island_tbl on tree_plots branch HOT 7
- 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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