Gadget3 parameter value setter

Helper for setting initial parameter value

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:

A wildcard matching anything (*), or a matching anything with a prefix, e.g. m*
A wildcard matching any number (#), or a matching a number with a prefix, e.g. age*
A range of numbers, e.g. [1979-1984]
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

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
#>           switch value lower upper parscale optimise random
#> 1    fish.init.1   4.0   -28    36       64     TRUE  FALSE
#> 2    fish.init.2   4.0   -28    36       64     TRUE  FALSE
#> 3    fish.init.3   4.0   -28    36       64     TRUE  FALSE
#> 4    fish.init.4   4.0   -28    36       64     TRUE  FALSE
#> 5    fish.init.5   4.0   -28    36       64     TRUE  FALSE
#> 6    fish.init.6   4.0   -28    36       64     TRUE  FALSE
#> 7    fish.init.7   4.0   -28    36       64     TRUE  FALSE
#> 8    fish.init.8   4.0   -28    36       64     TRUE  FALSE
#> 9    fish.init.9   4.0   -28    36       64     TRUE  FALSE
#> 10 fish.rec.1990   4.0     0    10       10     TRUE  FALSE
#> 11 fish.rec.1991   4.0     0    10       10     TRUE  FALSE
#> 12 fish.rec.1992   4.0     0    10       10     TRUE  FALSE
#> 13 fish.rec.1993   0.0     0    10       10    FALSE  FALSE
#> 14 fish.rec.1994   0.0     0    10       10    FALSE  FALSE
#> 15 fish.rec.1995   0.0     0    10       10    FALSE  FALSE
#> 16 fish.rec.1996   0.0     0    10       10    FALSE  FALSE
#> 17 fish.rec.1997   4.0     0    10       10     TRUE  FALSE
#> 18 fish.rec.1998   4.0     0    10       10     TRUE  FALSE
#> 19 fish.rec.1999   4.0     0    10       10     TRUE  FALSE
#> 20 fish.rec.2000   4.0     0    10       10     TRUE  FALSE
#> 21        fish.M   0.3    NA    NA       NA    FALSE  FALSE

Arguments

Details

Value

See also

Examples