sweepLink tasks¶
If you are starting out, work through the tutorial first — this section is for looking things up.
SweepLink performs several tasks. The task is the first argument on the command line, and each one accepts its own options:
$ ./sweeplink <task> --option value ...
Task |
What it does |
|---|---|
Infer locus-specific selection coefficients and population size from time-series data. This is the main task. |
|
Simulate time-series allele count data under the model. |
|
Evaluate the log-likelihood of each locus for a given set of parameters, without running an MCMC. |
|
Evaluate the log-likelihood of each locus at every value on the grid of selection coefficients. |
|
As above, over every combination of selection and dominance. |
|
Evaluate the log-likelihood over a grid of population sizes, per locus or summed across loci. |
The four calculateLL* tasks are for inspecting the likelihood surface
directly rather than sampling from the posterior; they are an advanced tool and
most analyses never need them.
Instead of flags, any task also accepts a .parameters file — the complete,
re-runnable record every run writes:
$ ./sweeplink myrun.parameters
Everything around the inference — converting a VCF, extracting results, plotting — lives in companion scripts instead.