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Set initial conditions for AEME models

Source: R/set_initial_conditions.R
set_initial_conditions.Rd

Configure the initial state - water depth, temperature and salinity profile, and biogeochemical water-column pools - that build_aeme() writes into each model's configuration. Values can be supplied once for every model (depth, profile, wq) and/or overridden per model via model_init (for example a GLM-AED-specific temperature profile).

Usage

set_initial_conditions(
  aeme,
  depth = NULL,
  profile = NULL,
  wq = NULL,
  model_init = NULL,
  model_controls = NULL,
  from_obs = FALSE,
  reset = FALSE
)

Arguments

aeme

Aeme object.

depth

numeric(1); initial water depth (m), i.e. the height of the lake surface above the lowest point of the hypsograph. NULL (default) leaves it unchanged.

profile

data.frame; initial profile with a depth column (positive-down, 0 = surface) and a temperature column (degC); a salt column (ppt) is optional and defaults to 0. NULL (default) leaves the profile unchanged.

wq

named list; initial water-column values keyed by AEME variable name (e.g. list(CHM_oxy = 300, NIT_amm = 0.5)). Each element is either a single number (constant with depth) or a data.frame with depth and value columns. Names must be present in model_controls$var_aeme. NULL (default) leaves water-quality initial values unchanged.

model_init

named list; per-model overrides keyed by model name ("dy_cd", "glm_aed", "gotm_wet", "simstrat_aed2", "simstrat_aed"). Each element is itself a list with any of depth, profile and wq, following the same rules as the generic arguments. These are merged over the generic specification when that model is built. NULL (default) leaves per-model overrides unchanged.

model_controls

data.frame; model configuration, typically loaded via get_model_controls().

from_obs

logical; if TRUE, seed the generic profile and water-quality values from lake observations via update_init() before the explicit arguments are applied (the explicit arguments take precedence). Default FALSE.

reset

logical; if TRUE, discard any existing configuration(aeme)$initial_conditions before applying the arguments. Default FALSE, i.e. new values are merged into the existing specification.

Value

The aeme object with initial conditions set.

Details

The structured specification is stored in configuration(aeme)$initial_conditions as a list with a default entry plus an optional entry per model, and is resolved at build time by merging each model's overrides over the defaults. For backwards compatibility the generic depth/profile are also written to input(aeme)$init_depth / input(aeme)$init_profile, and scalar generic wq values into configuration(aeme)$model_controls$initial_wc, so the generic controls take effect immediately.

See also

get_initial_conditions(), update_init(), set_glm_init(), set_gotm_init(), set_simstrat_init()

Examples

aeme_file <- system.file("extdata/aeme.rds", package = "AEME")
aeme <- readRDS(aeme_file)

# Generic profile for all models
prof <- data.frame(depth = c(0, 5, 10), temperature = c(18, 14, 11))
aeme <- set_initial_conditions(aeme, depth = 10, profile = prof)
#> ℹ `profile` has no salt column; using 0.
#> ✔ Initial conditions updated.

# GLM-AED-specific override
aeme <- set_initial_conditions(
  aeme,
  model_init = list(
    glm_aed = list(profile = data.frame(depth = c(0, 10),
                                        temperature = c(20, 12)))
  )
)
#> ℹ `model_init$glm_aed$profile` has no salt column; using 0.
#> ✔ Initial conditions updated (1 model-specific override).