Create phylogeny figure graphics

[mmore500]

• [x] example perfect phylogenies for each evolutionary "regime"

df["regime"] = df.apply(
    lambda row: {
        (1, 1, 2, 3.0517578125e-08): "plain",
        (1, 1, 1, 3.0517578125e-08): "neutral selection",
        (1, 1, 8, 3.0517578125e-08): "strong selection",
        (1, 4, 2, 3.0517578125e-06): "weak 4 niche ecology",
        (1, 4, 2, 3.0517578125e-08): "4 niche ecology",
        (1, 8, 2, 3.0517578125e-08): "8 niche ecology",
        (1024, 1, 2, 3.0517578125e-08): "spatial structure",
    }.get(
        tuple(
            row[
                [
                    "num_islands",
                    "num_niches",
                    "tournament_size",
                    "p_niche_invasion",
                ]
            ]
        ),
        np.nan,  # default
    ),
    axis="columns",
)

Other (less important) regimes are

# [ "num_islands",  "num_niches",  "tournament_size", "p_niche_invasion"]
        (1024, 4, 2, 3.0517578125e-06): "weak 4 niche ecology with spatial structure",
        (1024, 4, 2, 3.0517578125e-08): "4 niche ecology with spatial structure",
        (1024, 8, 2, 3.0517578125e-08): "8 niche ecology with spatial structure",

• [x] example reconstruction phylogenies for "plain" regime, one for each "quality" level

  df["quality"] = df.apply(
  lambda row: {
      ("reconstructed-tree", 3.0): "33% resolution",
      ("reconstructed-tree", 10.0): "10% resolution",
      ("reconstructed-tree", 30.0): "3% resolution",
      ("reconstructed-tree", 100.0): "1% resolution",
      ("collapsed-phylogeny", 0): "perfect resolution",
  }.get(
      tuple(row[["a", "resolution"]].fillna(0)),
      np.nan,  # default
  ),
  axis="columns",
  )

we can just put these files directly in on the tex branch in the image folder