When used for demographic inference, Jaatha supports using the package coala
as simulation engine. If these packages do not suit your needs, it is of course
also possible to use the normal interface described in the Introduction
vignette.
Jaatha automatically creates a simulation function, parameter ranges and
summary statistics from a coala
model. We can for example specify a simple
isolation-with-migration model using par_range
s to mark parameters we want
to estimate with Jaatha:
if(require("coala")) { model <- coal_model(c(10, 15), 100) + feat_mutation(par_range("theta", 1, 10)) + feat_migration(par_range("m", 0, 3), symmetric = TRUE) + feat_pop_merge(par_range("t_split", 0.1, 2), 2, 1) + feat_recombination(1) + sumstat_jsfs() }
We can now just pass this coala
model to the create_jaatha_model
function
to convert it into a Jaatha model:
if(requireNamespace("coala")) { library(jaatha) jaatha_model <- create_jaatha_model(model) }
This uses coala
for the simulations, gets the parameter ranges specified with
par_range
and uses summary statistics added to the model.
Coala supports a wide range of models. Please refer to its documentation for
more information.
You can use coala's calc_sumstats_form_data
function to calculate the summary
statistic for genetic data. The output of this function can be directly passed
on to create_jaatha_data
.
From here on, you can estimate parameters using the jaatha
as described in the
introduction vignette.
If you are using a simulator that is writing temporary
files to disk (e.g. ms
, msms
and seq-gen
), please make sure that there
is sufficient free space on your tempdir()
to store the output of sim
simulations per core that you use (arguments sim
and cores
in the jaatha
function). Also, please make sure that your machine does not run out of memory.
Both will lead to failtures during the estimation process. Reducing the number
of cores reduces both the required memory and disk space at the cost of a
longer runtime.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.