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)
#> ! Missing state variables in inflows:
#> ! ZOO_zoo1
#> ℹ Added default values for missing variables.
#> 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 2 replaced with 0.24022
#> ℹ PHY_diatom 10 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
#> 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... [2026-03-31 00:51:03]
#> ✔ Model run complete! [2026-03-31 00:51:06]
#> ℹ Reading models in parallel...[2026-03-31 00:51:06]
#> ✔ Model reading complete! [2026-03-31 00:51:08]
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"
#> Salinity Phosphate
#> "CHM_salt" "PHS_frp"
#> Dissolved organic P Particulate organic P
#> "PHS_dop" "PHS_pop"
#> Ammoniacal nitrogen Nitrate
#> "NIT_amm" "NIT_nit"
#> Dissolved organic N Particulate organic N
#> "NIT_don" "NIT_pon"
#> Dissolved organic carbon Particulate organic carbon
#> "CAR_doc" "CAR_poc"
#> Cyanobacteria Green algae
#> "PHY_cyano" "PHY_green"
#> Diatoms freshwater Stratified
#> "PHY_diatom" "HYD_strat"
#> Schmidt stability Centre of buoyancy
#> "HYD_schstb" "HYD_ctrbuy"
#> Epilimnion depth Hypolimnion depth
#> "HYD_epidep" "HYD_hypdep"
#> 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"
#> 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"
#> 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"