find_graphs_old | R Documentation |
This function generates and evaluates admixture graphs in numgen
iterations across numrep
independent repeats
to find well fitting admixturegraphs. It uses the function future_map
to parallelize across the independent repeats. The function plan
can be called
to specify the details of the parallelization. This can be used to parallelize across cores or across nodes on
a compute cluster. Setting numadmix
to 0 will search for well fitting trees, which is much faster than searching
for admixture graphs with many admixture nodes.
find_graphs_old(
data,
pops = NULL,
outpop = NULL,
numrep = 1,
numgraphs = 50,
numgen = 5,
numsel = 5,
numadmix = 0,
numstart = 1,
keep = c("all", "best", "last"),
initgraphs = NULL,
mutfuns = namedList(spr_leaves, spr_all, swap_leaves, move_admixedge_once,
flipadmix_random, mutate_n),
mutprobs = NULL,
opt_worst_residual = FALSE,
store_intermediate = NULL,
parallel = TRUE,
stop_after = NULL,
verbose = TRUE,
...
)
data |
Input data in one of three forms:
|
pops |
Populations for which to fit admixture graphs (default all) |
outpop |
An outgroup population which will split at the root from all other populations in all tested graphs. If one of the populations is know to be an outgroup, designating it as |
numrep |
Number of independent repetitions (each repetition can be run in parallel) |
numgraphs |
Number of graphs in each generation |
numgen |
Number of generations |
numsel |
Number of graphs which are selected in each generation. Should be less than |
numadmix |
Number of admixture events within each graph |
numstart |
Number of random initializations in each call to |
keep |
Which models should be returned. One of
|
initgraphs |
Optional graph or list of igraphs to start with. If |
mutfuns |
Functions used to modify graphs. Defaults to the following:
See examples for how to make new mutation functions. |
mutprobs |
Relative frequencies of each mutation function.
|
opt_worst_residual |
Optimize for lowest worst residual instead of best score. |
store_intermediate |
Path and prefix of files for intermediate results to |
parallel |
Parallelize over repeats (if |
stop_after |
Stop optimization after |
verbose |
Print progress updates |
... |
Additional arguments passed to |
A nested data frame with one model per line
qpgraph
## Not run:
find_graphs_old(example_f2_blocks, numrep = 200, numgraphs = 100,
numgen = 20, numsel = 5, numadmix = 3)
## End(Not run)
## Not run:
# Making new mutation functions by modifying or combining existing ones:
newfun1 = function(graph, ...) mutate_n(graph, 3, ...)
newfun2 = function(graph, ...) flipadmix_random(spr_leaves(graph, ...), ...)
find_graphs_old(f2_blocks, mutfuns = namedList(spr_leaves, newfun1, newfun2), mutprobs = c(0.2, 0.3, 0.5))
## End(Not run)
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