Run aquatic model ensemble

Usage

run_aeme(
  aeme,
  model,
  return = TRUE,
  ens_n = 1,
  model_controls = NULL,
  nlev = NULL,
  verbose = FALSE,
  debug = FALSE,
  timeout = 0,
  parallel = FALSE,
  ncores,
  check_output = FALSE,
  path = "."
)

Arguments

aeme: aeme; object.
model: vector; of models to be used. Can be `dy_cd`, `glm_aed`, `gotm_wet`.
return: logical; return model output within an `aeme` object? Defaults to TRUE.
ens_n: numeric; ensemble number to allocate to model output which is loaded. Defaults to 1.
model_controls: dataframe; of configuration loaded from "model_controls.csv".
nlev: numeric; number of levels to return in model output. If NULL, calculates number of levels based on the `model_layer_structure`.
verbose: logical; print model output to console. Defaults to FALSE.
debug: logical; write debug log (Only DYRESM). Defaults to FALSE.
timeout: timeout in seconds, ignored if 0. This is a limit for the elapsed time running command in a separate process. Fractions of seconds are ignored.
parallel: logical; run models in parallel. Defaults to FALSE.
ncores: integer; number of cores to use for parallelization. Defaults to `min(c(detectCores() - 1, length(model)))`.
check_output: logical; check model output after running? Defaults to FALSE.
path: filepath; where input files are located relative to `config`.

Value

an `aeme` object with model output loaded.

Examples

aeme_file <- system.file("extdata/aeme.rds", package = "AEME")
aeme <- readRDS(aeme_file)
path <- tempdir()
model_controls <- get_model_controls()
model <- c("glm_aed")
aeme <- build_aeme(path = path, aeme = aeme, model = model,
model_controls = model_controls, ext_elev = 5)
#> Building simulation for Wainamu [2024-11-18 05:19:52]
#> Using observed water level
#> Missing values in observed water level
#> Using constant water level
#> Correcting water balance using estimated outflows (method = 2).
#> Calculating lake level using lake depth and a sinisoidal function.
#> Warning: 'C:\Users\RUNNER~1\AppData\Local\Temp\RtmpmaQu5E\45819_wainamu' already exists
#> Building GLM3-AED2 model for lake wainamu
aeme <- run_aeme(aeme = aeme, model = model, path = path)
#> Running models... (Have you tried parallelizing?) [2024-11-18 05:19:53]
#> GLM-AED running... [2024-11-18 05:19:53]
#> GLM-AED run successful! [2024-11-18 05:19:54]
#> Model run complete![2024-11-18 05:19:54]
#> Retrieving and formatting temp for model glm_aed
#> Retrieving and formatting salt for model glm_aed
plot_output(aeme, model = model)
#> Warning: Removed 82 rows containing missing values or values outside the scale range
#> (`geom_col()`).