Options

Potentially Useful

macpan2_verbose = TRUE : Should the TMB computational engine used by macpan2 be verbose (default) or not. In particular, the silent argument of TMB::MakeADFun gets !getOption("macpan2_verbose").
macpan2_session_name = "default" : Where to put log files generated by the engine. By default this will be .macpan2/default.
macpan2_tol_hazard_div = 1e-8 : Used by the mp_hazard() function to generate an expression that calls the proportions() engine function. This option becomes the third tolerance argument to proportions().

You almost always want to leave these at their default values.

macpan2_time_dep_funcs = c("convolution", "rbind_lag", "rbind_time", "cbind_lag", "cbind_time") : List of engine functions that cannot be called unless their first argument has a saved simulation history.
macpan2_non_iterable_funcs = c("time_var", "rbinom", "rpois", "rnorm", "rnbinom", "reulermultinom") : List of functions that cannot be called repeatedly within a single time-step (as would happen for example with RK4 state updates). Randomness and time-variation are the only examples we have now.
macpan2_dll = "macpan2" : What C++ shared object should be used as the TMB engine. This is useful if you want to compare different versions of the engine. To use this feature you need to produce an alternative to src/macpan2.cpp, compile it using TMB::compile("path/to/alt.cpp"), load it using dyn.load(TMB::dynlib("alt")), and set the option as macpan2_dll = "alt" where "alt" is the name of the alternative C++ file without the extension. After this, simulation code will utilize this alternative engine as opposed to the built in src/macpan2.cpp engine.

These options should not be used unless an old and deprecated approach is used. They are present for back-compatibility only.

macpan2_default_loss = c("clamped_poisson", "poisson", "sum_of_squares", "neg_bin") : ## FIXME: macpan2_vec_by is old and not relevant i think
macpan2_vec_by = c(“state”, “flow_rates”, “trans_rates”) |> self_named_vector()