Create plot_daisie_data

[richelbilderbeek]

Currently, we can plot the mainland and the island, i.e. data types mainland and island. However, the daisie_data cannot be plotted yet, which would be useful to verify the format_to_daisie_data function works nice.

It is easy to get a daisy_data from a daisie_mainland_data:

  daisie_mainland_data <- sim_island_with_mainland(
    total_time = 1,
    m = 10,
    island_pars = c(1, 1, 10, 0.1, 1),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "undiscovered",
    replicates = 10,
    verbose = FALSE
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]] # a daisie_data
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]] # a daisie_data

Plot each of these using plot_daisie_data

[joshwlambert]

@richelbilderbeek given the function format_to_data_data is not longer in the package, that we stop development of plot_daisie_data. What do you think?

[richelbilderbeek]

[edit: removed my confused comment]
Hmmm, I am getting confused here. I understood the structure called daisie_data contains the info to make nice plots of the islands, for both the observed and ideal data.

What is the name of data structure I can use to plot the history of the island histories, for the observed and ideal data?

[joshwlambert]

I thought the new plan was:

• island_tbl to ideal_island_tbl and empirical_island_tbl
• ideal_island_tbl is plotted by plot_ideal_island_tbl
• empirical_island_tbl is plotted by plot_empirical_island_tbl

Would be the only plotting functions for the plotting the island?

[richelbilderbeek]

Hi @joshwlambert, thanks for clearing that one up!

I still would enjoy plotting the DAISIE data: it allows one to verify that the conversion from DAISIEmainland data to DAISIE has gone

However, I will focus on plotting the ideal_island_tbl and empirical_island_tblfirst (i.e. #51)

[richelbilderbeek]

This is something for after the next release. I will ruthlessly close it for now.

[richelbilderbeek]

Nope, it appears this is what #59 actually depends on; to be able to plot a daisie_data, so I reopen this one, as I am now working on it :-)

[richelbilderbeek]

[richelbilderbeek]

Beautiful in a base-functionality-appreciated way:

[richelbilderbeek]

More clades works great too:

[richelbilderbeek]

An example when the two data sets differ:

test_that("much branching", {
  set.seed(
    1018,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )
  daisie_mainland_data <- sim_island_with_mainland(
    total_time = 1,
    m = 10,
    island_pars = c(1, 1, 10, 0.1, 1),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "complete",
    replicates = 1,
    verbose = FALSE
  )
  plot_daisie_mainland_data(daisie_mainland_data, replicate_index = 1)
})

[richelbilderbeek]

Done!