Configure an ensemble of lake model simulations from basic set of inputs.
Usage
build_aeme(
aeme = NULL,
model = c("dy_cd", "glm_aed", "gotm_wet"),
path = ".",
model_controls = NULL,
inf_factor = NULL,
outf_factor = NULL,
ext_elev = 0,
use_bgc = FALSE,
calc_wbal = TRUE,
wb_method = 2,
calc_wlev = TRUE,
use_aeme = FALSE,
coeffs = NULL,
hum_type = 3,
est_swr_hr = TRUE,
config = NULL
)Arguments
- aeme
aeme; object.
- model
vector; of models to be used. Can be
dy_cd,glm_aed,gotm_wet.- path
filepath; where input files are located relative to the current working directory.
- model_controls
dataframe; of configuration loaded from "model_controls.csv".
- inf_factor
vector; containing numeric factor to multiple the inflows. Needs to be named according to the model.
- outf_factor
vector; containing numeric factor to multiple the outflows. Needs to be named according to the model.
- ext_elev
numeric; metres to extend the hypograph by.
- use_bgc
logical; switch to use the biogeochemical model.
- calc_wbal
logical; calculate water balance. Default = TRUE.
- wb_method
numeric; method to use for calculating water balance. Must be 1 (no inflows or outflows) or 2 (outflows calculated) or 3 (Any unexplained gain in lake storage is treated as an effective inflow; any unexplained loss is treated as an effective outflow). Default = 2
- calc_wlev
logical; calculate water level.
- use_aeme
logical; use AEME object to generate model confiuration files.
- coeffs
numeric vector of length two; to be used to estimate surface water temperature for estimating evaporation. Defaults to NULL. If water temperature observations are included in
aemeobject, then it will use those to build a linear relationship between air temperature and water temperature. Otherwise. it uses the simple estimation \(temp_water = 5 + 0.75 * temp_air\) from Stefan & Preud'homme, 2007: www.doi.org/10.1111/j.1752-1688.1993.tb01502.x- hum_type
numeric; GOTM humidity metric (1=relative humidity (%), 2=wet-bulb temperature, 3=dew point temperature, 4=specific humidity (kg/kg)) Default = 3.
- est_swr_hr
logical; estimate hourly shortwave radiation from daily values. Default = TRUE.
- config
list; loaded via
config <- yaml::read_yaml("aeme.yaml")
Examples
# Read in example AEME object and build model configuration files for GLM-AED
aeme_dir <- system.file("extdata/lake/", package = "AEME")
path <- "aeme" # subdirectory where model configuration files will be written
aeme <- yaml_to_aeme(path = aeme_dir, "aeme.yaml")
model_controls <- get_model_controls()
model <- c("glm_aed")
aeme <- aeme |>
build_aeme(path = path, model = model, model_controls = model_controls,
ext_elev = 5)
#> ✔ Created missing directory: D:\a\AEME\AEME\docs\reference\aeme
#> ℹ All columns already match AEME standard variable names, skipping name
#> guessing.
#> ℹ All columns already match AEME standard inflow variable names, skipping name
#> guessing.
#> Warning: ! `SIL_rsi`: SIL_rsi is constant across all rows — this may be a placeholder
#> value.
#> ℹ Check raw data or unit conversion for this variable.
#> ℹ Using observed water level.
#> ! Missing values in observed water level.
#> ℹ Correcting water balance using estimated outflows (method = 2).
#> ℹ Calculating lake level using lake depth and a sinisoidal function.
#> ℹ Building GLM-AED for lake wainamu
#> ℹ Copied in GLM nml file
#> ℹ Copied in AED nml file and supporting files
#> ✔ GLM nml validation completed - no issues detected.
# Switch on biogeochemistry and use default model controls
aeme <- aeme |>
build_aeme(path = path, model = model, model_controls = model_controls,
ext_elev = 5, use_bgc = TRUE)
#> ℹ All columns already match AEME standard variable names, skipping name
#> guessing.
#> ℹ All columns already match AEME standard inflow variable names, skipping name
#> guessing.
#> Warning: ! `SIL_rsi`: SIL_rsi is constant across all rows — this may be a placeholder
#> value.
#> ℹ Check raw data or unit conversion for this variable.
#> Warning: ! 1 missing state variable in `FWMT`:
#> ✖ `ZOO_zoo1 `
#> ℹ Filled 1 missing variable with default value from `model_controls`.
#> ℹ Using observed water level.
#> ! Missing values in observed water level.
#> ℹ Correcting water balance using estimated outflows (method = 2).
#> ℹ Calculating lake level using lake depth and a sinisoidal function.
#> ℹ Building GLM-AED for lake wainamu
#> ℹ 15 replaced with 41.6285
#> ℹ 15 replaced with 16.6514
#> ℹ 225 replaced with 312.5
#> ℹ 2.25 replaced with 1.4279
#> ℹ 21 replaced with 21.4183
#> ℹ 6.96 replaced with 1.0709
#> ℹ 19.8 replaced with 7.1394
#> ℹ 0.008 replaced with 0.3229
#> ℹ 0.05 replaced with 0.3229
#> ℹ 0.05 replaced with 0.3229
#> ℹ PHY_cyano 10 replaced with 0.24022
#> ℹ PHY_diatom 8.4 replaced with 0.300275
#> ℹ PHY_green 0.04 replaced with 0.300275
#> ℹ 100 replaced with 1
#> ℹ Using default zooplankton initialisation
#> ✔ Updated GLM-AED models from: aed_sedflux, aed_oxygen, aed_silica,
#> aed_nitrogen, aed_phosphorus, aed_organic_matter, aed_phytoplankton,
#> aed_zooplankton, aed_macrophyte, aed_totals to: aed_sedflux, aed_oxygen,
#> aed_silica, aed_nitrogen, aed_phosphorus, aed_organic_matter,
#> aed_phytoplankton, aed_totals
#> ℹ Setting up AED aed_sed_const2d sediment zones: 2
#>
#> Tier 2: zone-median summer concentrations used for adjustment:
#> oxy amm nit frp
#> Zone1 0.075 0.078 0.010 0.004
#> Zone2 7.160 0.005 0.001 0.002
#> Tier 2 adjustments applied: fsed_amm (2 zones, direct NH4); fsed_frp (2 zones, direct FRP)
#>
#> === Sediment zone flux estimates (obs_adjusted) ===
#> n_zones: 2 | max lake depth: 13.07 m | ref_depth: 5 m
#>
#> zone height_lower_m height_upper_m depth_upper_m depth_lower_m mean_depth_m
#> 1 0.00 3.07 10 13.1 11.5
#> 2 3.07 19.00 0 10.0 5.0
#> area_m2 area_frac fsed_oxy fsed_amm fsed_nit fsed_frp
#> 43957 0.289 -38.8 5.835 -0.4 0.1035
#> 108386 0.711 -19.4 0.512 0.1 0.0259
#>
#> Lake-wide area-weighted average fluxes (for sanity check):
#> oxy amm nit frp
#> -25.007 2.050 -0.044 0.048
#> ✔ GLM nml validation completed - no issues detected.