Get the variables that are both in the observation and model output

Usage

list_mod_obs_vars(aeme, model, ens_n = 1)

Arguments

aeme: Aeme object.
model: character vector; models to use. One or more of "dy_cd", "glm_aed", "gotm_wet", "simstrat_aed2". Defaults to all models if not found in aeme.
ens_n: numeric; ensemble number to allocate to model output which is loaded. Defaults to 1.

Value

A character vector of variables that are in both the observation and model output

Examples

aeme_file <- system.file("extdata/aeme.rds", package = "AEME")
aeme <- readRDS(aeme_file)
path <- tempdir()
model_controls <- get_model_controls(use_bgc = TRUE)
model <- c("glm_aed")
aeme <- build_aeme(path = path, aeme = aeme, model = model,
                   model_controls = model_controls,
                   ext_elev = 5, use_bgc = TRUE)
#> 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.
#> 
#> ── Calculating water balance ──
#> 
#> Resolving water level
#>   ℹ Using observed water level
#> ! Missing values in observed water level
#> ℹ Estimating surface water temperature
#> ✔ Estimating surface water temperature [27ms]
#> 
#> Estimating lake water levels for glm_aed
#>   ℹ Optimizing parameters for water balance
#>   ✔ Optimization Complete: C = 0.3343, h_inv = 23.4915, Final RMSE = 0.1431
#> ℹ Correcting water balance using estimated outflows (method = 2).
#> 
#> ── Building GLM-AED for lake wainamu ──
#> 
#> ℹ Aligned AED sediment zones to GLM: 2 zones (all active).
#> ℹ Setting up AED aed_sed_const2d sediment zones: 2
#> ℹ Tier 2: zone-median summer concentrations used for adjustment:
#> ┌─────┬───────────┬────────────┬────────────┬────────────┐
#> │ zone│ O2 (mg/L) │ NH4 (mg/L) │ NO3 (mg/L) │ FRP (mg/L) │
#> ├─────┼───────────┼────────────┼────────────┼────────────┤
#> │Zone1│ 0.075     │ 0.078      │ 0.01       │ 0.004      │
#> │Zone2│ 7.16      │ 0.005      │ 0.001      │ 0.002      │
#> └─────┴───────────┴────────────┴────────────┴────────────┘
#> ℹ 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│H lower (m)│H upper (m)│D upper (m)│D lower (m)│Mean D (m)│Area (m2)│Area frac│ O2  │ NH4│ NO3│ FRP  │
#> ├────┼───────────┼───────────┼───────────┼───────────┼──────────┼─────────┼─────────┼─────┼────┼────┼──────┤
#> │   1│    0      │ 3.07      │   10      │ 13.1      │ 11.5     │ 4.4e+04 │ 0.289   │-38.8│ 5.7│-0.4│ 0.107│
#> │   2│ 3.07      │   19      │    0      │   10      │    5     │ 1.08e+05│ 0.711   │-19.4│ 0.5│ 0.1│0.0268│
#> └────┴───────────┴───────────┴───────────┴───────────┴──────────┴─────────┴─────────┴─────┴────┴────┴──────┘
#> 
#> ── Lake-wide area-weighted average fluxes (mmol/m2/d) ──────────────────────────
#> ┌──────────────┬───────────────┬───────────────┬───────────────┐
#> │O2 (mmol/m2/d)│NH4 (mmol/m2/d)│NO3 (mmol/m2/d)│FRP (mmol/m2/d)│
#> ├──────────────┼───────────────┼───────────────┼───────────────┤
#> │ -25.007      │ 2.002         │ -0.044        │ 0.05          │
#> └──────────────┴───────────────┴───────────────┴───────────────┘
#> ✔ GLM nml validation completed - no issues detected.
# Run models
aeme <- run_aeme(aeme = aeme, model = model, verbose = FALSE,
path = path, model_controls = model_controls,
parallel = TRUE, ncores = 2L)
#> ℹ Running models in parallel... [2026-10-14 00:26:25]
#> ✔ Model run complete! [2026-10-14 00:26:28]
#> ℹ Reading models in parallel...[2026-10-14 00:26:28]
#> ✔ Model reading complete! [2026-10-14 00:26:35]
aeme |> 
  list_mod_obs_vars()
#>       Cyanobacteria    Dissolved oxygen            Salinity   Water temperature 
#>         "PHY_cyano"           "CHM_oxy"          "CHM_salt"          "HYD_temp" 
#> Total chlorophyll a Dissolved organic C           Phosphate Ammoniacal nitrogen 
#>         "PHY_tchla"           "CAR_doc"           "PHS_frp"           "NIT_amm" 
#>             Nitrate      Total nitrogen    Total phosphorus   Thermocline depth 
#>           "NIT_nit"            "NIT_tn"            "PHS_tp"        "HYD_thmcln" 
#>          Stratified              Volume         Water level 
#>         "HYD_strat"           "LKE_vol"        "LKE_lvlwtr"