graphmod_pavel: Return all graphs created from permuting a subclade

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Return all graphs created from permuting a subclade

Description

generates new graphs from basegraph as follows:

1. generates all possible trees using addpops (which are not in basegraph)

2. attaches trees to connection_edge, which is defined by two nodes in basegraph

3. adds edges originating above each edge in source_node, to each node above addpops

Usage

graphmod_pavel(basegraph, addpops, connection_edge, source_nodes)

Arguments

basegraph	an admixture graph as igraph object. (convert from edge list using igraph::graph_from_edgelist)
addpops	a vector of population labels which are not in basegraph. These populations should form a clade. All possible trees will be generated and those trees will be attached to basegraph.
connection_edge	edge in basegraph where the tree made from addpops should be attached
source_nodes	nodes in basegraph. edges above these nodes will be added and attached to all terminal edges leading to addpops

Examples

## Not run: 
graphlist = graphmod_pavel(example_igraph, addpops = c('pop1', 'pop2', 'pop3'),
                           connection_edge = c('N2N0', 'N1N'),
                           source_nodes = c('Denisova.DG', 'N2N2'))
results = tibble(graph = graphlist) %>%
  mutate(res = map(graph, ~qpgraph(example_f2_blocks, .))) %>%
  unnest_wider(res) %>%
  mutate(worstz = map_dbl(f3, ~max(abs(.$z))))

## End(Not run)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.