Description Usage Arguments Value See Also Examples

Given a table of observed *f* statistics and a graph, uses Nelder-Mead algorithm to
find the graph parameters (edge lengths and admixture proportions) that minimize the value
of `cost_function`

, *i. e.* maximizes the likelihood of a graph with
parameters given the observed data.
Like `fast_fit`

but outputs a more detailed analysis on the results.

1 2 3 4 5 6 | ```
fit_graph(data, graph, point = list(rep(1e-05,
length(extract_graph_parameters(graph)$admix_prop)), rep(1 - 1e-05,
length(extract_graph_parameters(graph)$admix_prop))), Z.value = TRUE,
concentration = calculate_concentration(data, Z.value),
optimisation_options = NULL, parameters = extract_graph_parameters(graph),
iteration_multiplier = 3, qr_tol = 1e-08)
``` |

`data` |
The data table, must contain columns |

`graph` |
The admixture graph (an |

`point` |
If the user wants to restrict the admixture proportions somehow, like to fix some of them. A list of two vectors: the lower and the upper bounds. As a default the bounds are just it little bit more than zero and less than one; this is because sometimes the infimum of the values of cost function is at a point of non-continuity, and zero and one have reasons to be problematic values in this respect. |

`Z.value` |
Whether we calculate the default concentration from |

`concentration` |
The Cholesky decomposition of the inverted covariance matrix.
Default matrix determined by the parameter |

`optimisation_options` |
Options to the Nelder-Mead algorithm. |

`parameters` |
In case one wants to tweak something in the graph. |

`iteration_multiplier` |
Given to |

`qr_tol` |
Given to |

A class `agraph_fit`

list containing a lot of information about the fit:

`data`

is the input data,

`graph`

is the input graph,

`matrix`

is the output of `build_edge_optimisation_matrix`

,
containing the `full`

matrix, the `column_reduced`

matrix without zero
columns, and graph `parameters`

,

`complaint`

coding wchich subsets of admixture proportions are trurly fitted,

`best_fit`

is the optimal admixture proportions (might not be unique if they
are not trurly fitted),

`best_edge_fit`

is an example of optimal edge lengths,

`homogeneous`

is the reduced row echelon form of the matrix describing when
a vector of edge lengths have no effect on the prediced statistics *F*,

`free_edges`

is one way to choose a subset of edge lengths in such a vector as
free variables,

`bounded_edges`

is how we calculate the reamining edge lengths from the free ones,

`best_error`

is the minimum value of the `cost_function`

,

`approximation`

is the predicted statistics *F* with the optimal graph parameters,

`parameters`

is jsut a shortcut for the graph parameters.

See `summary.agraph_fit`

for the interpretation of some of these results.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | ```
# For example, let's fit the following two admixture graph to an example data on bears:
data(bears)
print(bears)
leaves <- c("BLK", "PB", "Bar", "Chi1", "Chi2", "Adm1", "Adm2", "Denali", "Kenai", "Sweden")
inner_nodes <- c("R", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", "M", "N")
edges <- parent_edges(c(edge("BLK", "R"),
edge("PB", "v"),
edge("Bar", "x"),
edge("Chi1", "y"),
edge("Chi2", "y"),
edge("Adm1", "z"),
edge("Adm2", "z"),
edge("Denali", "t"),
edge("Kenai", "s"),
edge("Sweden", "r"),
edge("q", "R"),
edge("r", "q"),
edge("s", "r"),
edge("t", "s"),
edge("u", "q"),
edge("v", "u"),
edge("w", "M"),
edge("x", "N"),
edge("y", "x"),
edge("z", "w"),
admixture_edge("M", "u", "t"),
admixture_edge("N", "v", "w")))
admixtures <- admixture_proportions(c(admix_props("M", "u", "t", "a"),
admix_props("N", "v", "w", "b")))
bears_graph <- agraph(leaves, inner_nodes, edges, admixtures)
plot(bears_graph, show_admixture_labels = TRUE)
fit <- fit_graph(bears, bears_graph)
summary(fit)
# It turned out the values of admixture proportions had no effect on the cost function. This is not
# too surprising because the huge graph contains a lot of edge variables compared to the tiny
# amount of data we used! Note however that the mere existence of the admixture event with non-
# trivial (not zero or one) admixture proportion might still decrease the cost function.
``` |

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

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