compare_fits4: Compare the fit of two qpgraph models

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Compare the fit of two qpgraph models

Description

Takes two data frames with model fits computed on two graphs for on the same populations and tests whether the scores of one graph are significantly better than the scores of the other.

Usage

compare_fits4(fit1, fit2, f2_blocks, f2_blocks_test, boot = FALSE, seed = NULL)

Arguments

fit1	The fit of the first graph
fit2	The fit of the second graph
f2_blocks	f2 blocks used for fitting fit1 and fit2. Used in combination with f2_blocks_test to compute f-statistics covariance matrix.
f2_blocks_test	f2 blocks which were not used for fitting fit1 and fit2
boot	If FALSE (the default), block-jackknife resampling will be used to compute standard errors. Otherwise, block-bootstrap resampling will be used to compute standard errors. If boot is an integer, that number will specify the number of bootstrap resamplings. If boot = TRUE, the number of bootstrap resamplings will be equal to the number of SNP blocks. If bootstrap resampling is enabled, empirical p-values (p_emp) and 95 confidence intervals (ci_low and ci_high) will be reported.
seed	Random seed used if boot is TRUE. Does not need to match a seed used in fitting the models

Examples

## Not run: 
nblocks = dim(example_f2_blocks)[3]
train = sample(1:nblocks, round(nblocks/2))
fit1 = qpgraph(example_f2_blocks[,,train], graph1)
fit2 = qpgraph(example_f2_blocks[,,train], graph2)
compare_fits4(fit1, fit2, example_f2_blocks[,,train], example_f2_blocks[,,-train])

## End(Not run)

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