In richelbilderbeek/ggdaisie:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Goal

To recreate figure 1 from Valente el al., from DAISIE input data:

Here the same data in a table (simplified from Valente et al., 2015)

Lineage name|Galápagos species|Type|Stem age (Mya) ---|---|---|--- Vermilion flycatcher|Pyrocephalus rubinus|Non-endemic|10.28 Dark-billed cuckoo|Coccyzus melacoryphus|Non-endemic|7.456 Galápagos mockingbirds|Radiation (4 species)|Cladogenetic|3.958 Galápagos dove|Zenaida galapagoensis|Anagenetic|3.51 Darwin’s finches|Radiation (15 species)|Cladogenetic|3.028 Galápagos flycatcher|Myiarchus magnirostris|Anagenetic|0.855 Galápagos warbler|Dendroica petechia aureola|Non-endemic|0.34 Galápagos martin|Progne modesta|Anagenetic|0.086

Setup

library(DAISIE)
library(ggdaisie)

Load a DAISIE example input and order like the figure:

df <- get_daisie_data("Galapagos_datatable.RData")
fig_order <- c(2, 7, 5, 3, 6, 8, 1, 4)
testit::assert(fig_order == unique(fig_order))
df <- df[ order(fig_order), ]
rownames(df) <- NULL
knitr::kable(df)

Plot:

ggdaisie(df, island_age = 4)

Using DAISIE

DAISIE has an equivalent way to plot this:

DAISIE::DAISIE_plot_island(
  get_daisie_data("Galapagos_datatable.RData"),
  4
)

richelbilderbeek/ggdaisie documentation built on May 4, 2019, 8:42 a.m.