Get the output variables from an AEME object
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", "gotm_wet")
aeme <- build_aeme(path = path, aeme = aeme, 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 Copied in GLM nml file
#> ℹ Copied in AED nml file and supporting files
#> ℹ 15 replaced with 41.6285
#> ℹ Using default pH initialisation
#> 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
#> ℹ Building GOTM-WET model for lake wainamu
#> ℹ Copied in GOTM configuration files
#> ℹ instances/abiotic_water/initialization/sDDOMW 2.5 replaced with 0.5
#> ℹ instances/abiotic_water/initialization/sDPOMW 0.1 replaced with 0.2
#> ℹ instances/abiotic_water/initialization/sO2W 13 replaced with 10
#> ℹ instances/abiotic_water/initialization/sDIMW 4 replaced with 3
#> ℹ instances/abiotic_water/initialization/sNH4W 0.05 replaced with 0.02
#> ℹ instances/abiotic_water/initialization/sNDOMW 0.01 replaced with 0.3
#> ℹ instances/abiotic_water/initialization/sNO3W 0.5 replaced with 0.015
#> ℹ instances/abiotic_water/initialization/sNPOMW 0.01 replaced with 0.1
#> ℹ instances/abiotic_water/initialization/sPDOMW 0.001 replaced with 0.01
#> ℹ instances/abiotic_water/initialization/sPO4W 0.1 replaced with 0.01
#> ℹ instances/abiotic_water/initialization/sPPOMW 0.001 replaced with 0.01
#> ℹ Setting initial condition for instances/cyanobacteria/initialization/sDW: 0.1
#> replaced with 0.2
#> ℹ Setting initial condition for instances/cyanobacteria/initialization/sNW:
#> 0.03 replaced with 0.03
#> ℹ Setting initial condition for instances/cyanobacteria/initialization/sPW:
#> 0.003 replaced with 0.0019
#> ℹ Setting initial condition for instances/diatoms/initialization/sDW: 0.2
#> replaced with 0.25
#> ℹ Setting initial condition for instances/diatoms/initialization/sNW: 0.05
#> replaced with 0.038
#> ℹ Setting initial condition for instances/diatoms/initialization/sPW: 0.005
#> replaced with 0.0024
#> ℹ Setting initial condition for instances/greens/initialization/sDW: 0.1
#> replaced with 0.1
#> ℹ Setting initial condition for instances/greens/initialization/sNW: 0.05
#> replaced with 0.015
#> ℹ Setting initial condition for instances/greens/initialization/sPW: 0.001
#> replaced with 0.00094
#> ℹ instances/abiotic_water/initialization/sSiO2W 3.5 replaced with 1
#> ℹ instances/cladocerans/initialization/sD 0.05 replaced with 1
#> ℹ Setting initial condition forinstances/cladocerans/initialization/sN: 0.0035
#> replaced with 0.07
#> ℹ Setting initial condition forinstances/cladocerans/initialization/sP: 5e-04
#> replaced with 0.01
#> ✔ GOTM YAML validation completed - no issues detected.
#> ✔ 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... [2026-05-17 21:36:59]
#> ✔ Model run complete! [2026-05-17 21:37:03]
#> ℹ Reading models in parallel...[2026-05-17 21:37:03]
#> ✔ Model reading complete! [2026-05-17 21:37:05]
get_output_vars(aeme, model)
#> Water temperature Thermocline depth
#> "HYD_temp" "HYD_thmcln"
#> Dissolved oxygen Total chlorophyll a
#> "CHM_oxy" "PHY_tchla"
#> Total nitrogen Total phosphorus
#> "NIT_tn" "PHS_tp"
#> Evaporative heat flux Sensible heat flux
#> "LKE_Qe" "LKE_Qh"
#> Longwave radiation Shortwave radiation
#> "LKE_Qlw" "LKE_Qsw"
#> Volume Evaporation
#> "LKE_V" "LKE_evpvol"
#> Evaporation Surface area
#> "LKE_evpflx" "LKE_A0"
#> Evaporation Inflow
#> "LKE_evprte" "LKE_inflow"
#> Outflow Precipitation
#> "LKE_outflow" "LKE_precip"
#> Precipitation Remote sensed skin temperature
#> "LKE_pcpvol" "HYD_surft"
#> e-folding depth Euphotic depth
#> "LKE_efold" "LKE_photic"
#> Lake depth Water density
#> "LKE_depths" "HYD_dens"
#> Stratified Schmidt stability
#> "HYD_strat" "HYD_schstb"
#> Centre of buoyancy Epilimnion depth
#> "HYD_ctrbuy" "HYD_epidep"
#> Hypolimnion depth Salinity
#> "HYD_hypdep" "CHM_salt"
#> Oxycline depth Epilimnetic oxygen
#> "CHM_oxycln" "CHM_oxyepi"
#> Metalimnetic oygen Hypolimnetic oxygen
#> "CHM_oxymet" "CHM_oxyhyp"
#> Metalimnetic oxygen minima Number of anoxic layers
#> "CHM_oxymom" "CHM_oxynal"
#> Trophic Level Index Chlorophyll-a Trophic Level Index Total Nitrogen
#> "LKE_tlic" "LKE_tlin"
#> Trophic Level Index Total Phosphorus Trophic Level Index Secchi depth
#> "LKE_tlip" "LKE_tlise"
#> Trophic Level Index 3 Trophic Level Index 4
#> "LKE_tli3" "LKE_tli4"
#> Phosphate Dissolved organic P
#> "PHS_frp" "PHS_dop"
#> Particulate organic P Ammoniacal nitrogen
#> "PHS_pop" "NIT_amm"
#> Nitrate Dissolved organic N
#> "NIT_nit" "NIT_don"
#> Particulate organic N Dissolved organic carbon
#> "NIT_pon" "CAR_doc"
#> Particulate organic carbon Cyanobacteria
#> "CAR_poc" "PHY_cyano"
#> Green algae Diatoms freshwater
#> "PHY_green" "PHY_diatom"
#> Photosynthetically active radiation Particulate inorganic P
#> "RAD_par" "PHS_pip"
#> Suspended solids Zooplankton
#> "NCS_ss1" "ZOO_zoo1"
#> Air temperature Water-air temperature difference
#> "MET_tmpair" "HYD_atdiff"