qpgraph_precompute_f3 | R Documentation |
Takes a 3d array of f2 block jackknife estimates and computes f3-statistics between the
first population p1
and all population pairs i, j
: f3(p1; p_i, p_j)
qpgraph_precompute_f3(
data,
pops,
f3basepop = NULL,
lambdascale = 1,
boot = FALSE,
seed = NULL,
diag_f3 = 1e-05,
lsqmode = FALSE
)
data |
Input data in one of three forms:
|
pops |
Populations for which to compute f3-statistics |
f3basepop |
f3-statistics base population. If |
lambdascale |
Scales f2-statistics. This has no effect on the fit, but is used in the original qpGraph program to display branch weights on a scale that corresponds to FST distances. |
boot |
If |
seed |
Random seed used if |
diag_f3 |
Regularization term added to the diagonal elements of the covariance matrix of estimated f3 statistics (after scaling by the matrix trace). In the original qpGraph program, this is fixed at 0.00001. |
lsqmode |
Least-squares mode. If |
A list with four items
f3_est
a matrix with f3-statistics for all population pairs with the output
ppinv
a matrix with the inverse of the f3-statistic covariance matrix
f2out
a data frame with f2 estimates
f3out
a data frame with f3 estimates
pops = get_leafnames(example_igraph)
qpgraph_precompute_f3(example_f2_blocks, pops)$f3_est
## Not run:
qpgraph_precompute_f3(f2_dir, pops)
## End(Not run)
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