four_leaves_graphs: Four leaves graphs.

Description Usage Format See Also Examples

Description

Kind of obsolete since the introduction of all_graphs. A comprehensive listing of all the 37 admixture graphs with four leaves and at most two admixture events. Our convention is that the position of the root does not matter (as long as it's not after an admixture event) and that graphs that have eyes, two inner nodes with the property that all the paths between any two leaves visits both or neither of them, are excluded. The reason is that the f statistics can't detect the exact position of the root or distinguish between an eye and a simple branch. The position of the root can be moved later with the function make_an_outgroup.

Usage

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Format

A list of functions on four leaves and a parameter permutations which is FALSE by default. The outputs of these functions are either single agraph objects with the input vector as leaves, or if permutations is TRUE, lists of all the possible agraph objects with that leaf set up to symmetry.

See Also

all_graphs

make_permutations

fit_permutations_and_graphs

fit_graph_list

add_a_leaf

add_an_admixture

add_an_admixture2

make_an_outgroup

Other graphs: eight_leaves_trees, five_leaves_graphs, seven_leaves_graphs, six_leaves_graphs

Examples

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# While the usage of this function is pretty self-explanatory, let's plot all the graphs
# just for browsing.
for (i in seq(1, length(four_leaves_graphs))) {
  graph <- four_leaves_graphs[[i]](c("A", "B", "C", "D"))
  # This is how you include quotation marks in strings by the way:
  title <- paste("four_leaves_graphs[[", i, "]](c(\"A\", \"B\", \"C\", \"D\"))", sep = "")
  plot(graph, color = "tomato3", title = title)
}

mailund/admixture_graph documentation built on April 3, 2018, 9:28 p.m.