create_jaatha_model.coalmodel {jaatha} | R Documentation |
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", "folded_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
x |
The coala model |
jsfs_summary |
The way the Joint Site Frquency Spectrum (JSFS)
is further summarized. Can be |
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_part_hi |
Same as |
... |
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. |