gadget3 (version 0.14-0)

init_val: 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)

Value

A new parameter template list/table containing modifications

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. If set to TRUE, any existing optimise/lower/upper/parscale values will be cleared. 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]

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