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Options

Source: vignettes/options.Rmd
options.Rmd

status

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" and macpan2_log_dir = tools::R_user_dir("macpan2") : Where to put log files generated by the engine. By default, the path to log files will be {macpan2_log_dir}/.macpan2/{macpan2_session_name}/log.txt. If you want to get access to the log file you should set the value of macpan2_log_dir. If you want to set macpan2_log_dir to the working directory at the time the model is created, you should set macpan2_log_dir = "".
  • 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().
  • macpan2_tol_singular_cov =1e-6` : Used to determine if estimated covariance matrices can be used to generate multivariate normal samples of parameter vectors.

Advanced

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

  • macpan2_traj_tmb_macro = "simulate" (valid values are "simulate" and "report") : What TMB macro should mp_trajectory() use to generate simulations. Before version 2.4.0 this was implicitly assumed to be "report", which does not respect the random seed set using set.seed. For reproducibility with earlier versions, please set options(macpan2_traj_tmb_macro = "report").
  • 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.
  • macpan2_saving_conflict_msg_fn = base::message : Function to use for reporting messages when conflicting information about saving or not saving a particular variable is received. This relates to must_save and must_not_save arguments in functions like mp_tmb_model_spec.

Deprecated

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()

No Longer or Not Yet Used

  • macpan2_tmb_type = "ADFun"
  • macpan2_tmb_check = TRUE