create_jaatha_model.coalmodel: Use a coala model in Jaatha

Description

This creates a Jaatha model from a coala model. Simulation for this model model are conducted via the simulate function for the coala model. The parameters that are estimated must be specified via par_range and the model must not have any other named parameters. Summary statistics present in the coala model are used in Jaatha.

Usage

## S3 method for class 'coalmodel':
create_jaatha_model(x, jsfs_summary = c("sums", "none",
  "smooth"), four_gamete_breaks = c(0.2, 0.5), mcmf_breaks = c(0.5, 0.7,
  0.9), jsfs_part = c(1, 3), jsfs_part_hi = c(1, 3), ...,
  scaling_factor = 1, test = TRUE)

Arguments

The coala model

jsfs_summary

The way the Joint Site Frquency Spectrum (JSFS) is further summarized. Can be sums (default), none or "smoothing". For sums, 23 different areas of the JSFS are summed up, and the sums are used as indep

four_gamete_breaks

Quantiles of the real data that will be used as breaks for binning the Four Gamete test based statistic if present in the model.

mcmf_breaks

Quantiles of the real data that will be used as breaks for binning the MCMF statistic if present in the model.

jsfs_part

Partitions used for the summarizing the JSFS. This is only used if jsfs_summary is "sums". Is used as the part argument of coarsen_jsfs. Please go there for an explanation.

jsfs_part_hi

Same as jsfs_part, but used as part_hi argument in coarsen_jsfs.

...

Additional parameters passed on to the dispatch function.

scaling_factor

If your model is a down-scaled version of your data, you can indicated this using this value. The estimated expectation values are multiplied with this factor before the likelihood is calculated.

test

A logical indicating whether a simulation is performed to test the model.