Gadget3 actions into TMB code

Turn g3 actions into CPP code that can be compiled using TMB

g3_to_tmb(actions, trace = FALSE, strict = FALSE)

g3_tmb_adfun(
        cpp_code,
        parameters = attr(cpp_code, 'parameter_template'),
        compile_flags = getOption('gadget3.tmb.compile_flags', default =
if (.Platform$OS.type == "windows") c("-O1", "-march=native")
            else c("-O3", "-flto=auto", "-march=native") ),
        work_dir = getOption('gadget3.tmb.work_dir', default = tempdir()),
        output_script = FALSE,
        compile_args = list(
            framework = getOption("gadget3.tmb.framework", default = "TMBad") ),
        ...)

g3_tmb_par(parameters, include_random = TRUE)

g3_tmb_lower(parameters)

g3_tmb_upper(parameters)

g3_tmb_parscale(parameters)

g3_tmb_relist(parameters, par)

Arguments

actions

A list of actions (i.e. list of formula objects), as produced by g3a_* functions.

trace

If TRUE, turn all comments into print statements.

strict

If TRUE, enable extra sanity checking in actions. Any invalid conditions (e.g. more/less fish after growth) will result in a warning.

cpp_code

cpp_code as produced by g3_to_tmb.

parameters

Parameter table as produced by attr(g3_to_tmb(...), 'parameter_template'), modified to provide initial conditions, etc.

par

Parameter vector, as produced by one of

1. nlminb(...)$par

2. obj.fun$env$last.par

3. g3_tmb_par()

The first will not include random parameters by default, the others will.

include_random

Should random parameters assumed to be part of par? Should be TRUE if using obj.fun$fn, obj.fun$report directly, e.g. obj.fun$fn(g3_tmb_par(param_tbl)). In other cases, FALSE.

compile_flags

List of extra flags to compile with, use e.g. "-g" to enable debugging output. Can be set with an option, e.g. options(gadget3.tmb.compile_flags = c('-O0', '-g'))

compile_args

Any other arguments to pass to TMB::compile

work_dir

Directory to write and compile .cpp files in. Defaults to R's current temporary directory Set this to preserve compiled output and re-use between R sessions if possible. Can be set with an option, e.g. options(gadget3.tmb.work_dir = fs::path_abs('tmb-workdir'))

output_script

If TRUE, create a temporary R script that runs MakeADFun, and return the location. This can then be directly used with gdbsource or callr::rscript.

...

Any other options handed directly to MakeADFun

Details

g3_tmb_adfun

g3_tmb_adfun will do both the compile and MakeADFun steps of making a model. If the code is identical to an already-loaded model then it won't be recompiled, so repeated calls to g3_tmb_adfun to change parameters are fast.

If MakeADFun is crashing your R session, then you can use output_script to run in a separate R session. Use this with gdbsource to debug your model.

Value

g3_to_tmb

A string of C++ code that can be used as an input to g3_tmb_adfun, with the following attributes:

actions

The original actions list given to the function

model_data

An environment containing data attached to the model

parameter_template

A data.frame to be filled in and used as parameters in the other g3_tmb_* functions

Use e.g. attr(cpp_code, 'parameter_template') to retrieve them.

g3_tmb_adfun

An ADFun as produced by TMB's MakeADFun, or location of temporary script if output_script is TRUE

g3_tmb_par

Values extracted from parameters table converted into a vector of values for obj$fn(par) or nlminb

g3_tmb_lower

Lower bounds extracted from parameters table converted into a vector of values for nlminb. Random parameters are always excluded

g3_tmb_upper

Lower bounds extracted from parameters table converted into a vector of values for nlminb. Random parameters are always excluded

g3_tmb_parscale

Parscale extracted from parameters table, converted into a vector of values for nlminb. Random parameters are always excluded

g3_tmb_relist

The parameters table value column, but with optimised values replaced with contents of par vector. i.e. the inverse operation to g3_tmb_par. par can either include or discount random variables.

Examples