init_val: Gadget3 parameter value setter

In gadget-framework/gadget3: Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3

Gadget3 parameter value setter

Description

Helper for setting initial parameter value

Usage

g3_init_val(
        param_template,
        name_spec,
        value = NULL,
        spread = NULL,
        lower = if (!is.null(spread)) min(value * (1-spread), value * (1+spread)),
        upper = if (!is.null(spread)) max(value * (1-spread), value * (1+spread)),
        optimise = !is.null(lower) & !is.null(upper),
        parscale = if (is.null(lower) || is.null(upper)) NULL else 'auto',
        random = NULL,
        auto_exponentiate = TRUE)

Arguments

param_template	A parameter template generated by g3_to_r or g3_to_tmb
name_spec	A glob-like string to match parameter names, see Details
value	Numeric value / vector of values to set for value / 'value' column in template. Original value left if NULL
spread	Shortcut for setting lower & upper.
lower	Numeric value / vector of values to set for 'lower' column in template. Original value left if NULL
upper	Numeric value / vector of values to set for 'upper' column in template. Original value left if NULL
optimise	Boolean value to set for 'optimise' column in template. Default is true iff both lower and upper are non-NULL. Original value left if NULL
parscale	Numeric value / vector of values to set for 'parscale' column in template. Default (auto) is difference between lower & upper (or NULL if they're not set). Original value left if NULL
random	Boolean value to set for 'random' column in template. Original value left if NULL
auto_exponentiate	If TRUE, will implicitly match parameters ending with "_exp", and if this is the case log all value/lower/upper values

Details

name_spec is a glob (or wildcard) matching parameters. It is a string separated by ., where each part can be:

1. A wildcard matching anything (*), or a matching anything with a prefix, e.g. m*

2. A wildcard matching any number (#), or a matching a number with a prefix, e.g. age*

3. A range of numbers, e.g. [1979-1984]

4. A choice of options can be separated with |, e.g. init|rec or [1979-1984]|[2000-2003]

Value

A new parameter template list/table containing modifications

See Also

g3_parameterized

Examples

# A parameter template, would already be got via. attr(g3_to_tmb(...), "parameter_template")
pt <- data.frame(
    switch = c(
        paste0('fish.init.', 1:9),
        paste0('fish.rec.', 1990:2000),
        'fish.M'),
    value = NA,
    lower = NA,
    upper = NA,
    parscale = NA,
    optimise = FALSE,
    random = FALSE)

# Set all fish.init.# parameters to optimise
pt <- g3_init_val(pt, 'fish.init.#', 4, spread = 8)

# Set a fixed value for any .M
pt <- g3_init_val(pt, '*.M', value = 0.3, optimise = FALSE)

# Set a fixed value for a range of recruitment years, optimise the rest
pt |>
    g3_init_val('*.rec.#', value = 4, lower = 0, upper = 10) |>
    g3_init_val('*.rec.[1993-1996]', value = 0, optimise = FALSE) |>
    identity() -> pt

pt

gadget-framework/gadget3 documentation built on June 13, 2025, 5:06 a.m.