Get the output variables from an AEME object
Usage
get_output_vars(
aeme,
model,
ens_n = 1,
group = c("core", "diag", "sediment")[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 inaeme.- ens_n
numeric; ensemble number to allocate to model output which is loaded. Defaults to 1.
- group
character; which variables to list:
"core"(time and depth x time variables, default),"diag"(diagnostics and scalars), and/or"sediment"(sediment zone/layer variables). Diagnostic and sediment variables keep their raw model names.
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 [32ms]
#>
#> 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 CAR_doc: 15 replaced with 41.6285
#> ℹ CAR_poc: 15 replaced with 16.6514
#> ℹ CHM_oxy: 225 replaced with 312.5
#> ℹ NIT_amm: 2.25 replaced with 1.4279
#> ℹ NIT_don: 21 replaced with 21.4183
#> ℹ NIT_nit: 6.96 replaced with 1.0709
#> ℹ NIT_pon: 19.8 replaced with 7.1394
#> ℹ PHS_dop: 0.008 replaced with 0.3229
#> ℹ PHS_frp: 0.05 replaced with 0.3229
#> ℹ PHS_pop: 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 SIL_rsi: 100 replaced with 1
#> 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)
#> ℹ Running models... (Have you tried parallelizing?) [2026-10-14 00:25:44]
#> ℹ GLM-AED running... [2026-10-14 00:25:44]
#> ✔ GLM-AED running... [2026-10-14 00:25:47] [2.9s]
#>
#> ✔ Model run complete! [2026-10-14 00:25:47]
get_output_vars(aeme, model)
#> Water temperature
#> "HYD_temp"
#> Thermocline depth
#> "HYD_thmcln"
#> Dissolved oxygen
#> "CHM_oxy"
#> Total chlorophyll a
#> "PHY_tchla"
#> Total nitrogen
#> "NIT_tn"
#> Total phosphorus
#> "PHS_tp"
#> Water level
#> "LKE_lvlwtr"
#> Evaporative heat flux
#> "LKE_Qe"
#> Sensible heat flux
#> "LKE_Qh"
#> Longwave radiation
#> "LKE_Qlw"
#> Shortwave radiation
#> "LKE_Qsw"
#> Volume
#> "LKE_vol"
#> Evaporation
#> "LKE_evpvol"
#> Evaporation
#> "LKE_evpflx"
#> Surface area
#> "LKE_A0"
#> Evaporation
#> "LKE_evprte"
#> Inflow
#> "LKE_inflow"
#> Overflow
#> "LKE_overflow"
#> Outflow
#> "LKE_outflow"
#> Total outflow
#> "LKE_outftot"
#> Precipitation
#> "LKE_precip"
#> Precipitation
#> "LKE_pcpvol"
#> Surface temperature
#> "HYD_surft"
#> Lake depth
#> "LKE_depths"
#> z
#> "z"
#> Water density
#> "HYD_dens"
#> Stratified
#> "HYD_strat"
#> Salinity
#> "CHM_salt"
#> Phosphate
#> "PHS_frp"
#> Dissolved organic P
#> "PHS_dop"
#> Particulate organic P
#> "PHS_pop"
#> Ammoniacal nitrogen
#> "NIT_amm"
#> Nitrate
#> "NIT_nit"
#> Dissolved organic N
#> "NIT_don"
#> Particulate organic N
#> "NIT_pon"
#> Dissolved organic C
#> "CAR_doc"
#> Particulate organic C
#> "CAR_poc"
#> SIL_rsi
#> "SIL_rsi"
#> Cyanobacteria
#> "PHY_cyano"
#> Green algae
#> "PHY_green"
#> Diatoms freshwater
#> "PHY_diatom"
#> Suspended solids
#> "NCS_ss1"
#> Suspended solids
#> "NCS_ss2"
#> NS
#> "NS"
#> blue_ice_thickness
#> "blue_ice_thickness"
#> snow_thickness
#> "snow_thickness"
#> white_ice_thickness
#> "white_ice_thickness"
#> surface_layer
#> "surface_layer"
#> solar
#> "solar"
#> wind
#> "wind"
#> vol_snow
#> "vol_snow"
#> vol_blue_ice
#> "vol_blue_ice"
#> vol_white_ice
#> "vol_white_ice"
#> rain
#> "rain"
#> local_runoff
#> "local_runoff"
#> snowfall
#> "snowfall"
#> seepage_vol
#> "seepage_vol"
#> snow_density
#> "snow_density"
#> albedo
#> "albedo"
#> max_temp
#> "max_temp"
#> min_temp
#> "min_temp"
#> Qsw
#> "Qsw"
#> Qe
#> "Qe"
#> Qh
#> "Qh"
#> Qlw
#> "Qlw"
#> light
#> "light"
#> benthic_light
#> "benthic_light"
#> surface_wave_height
#> "surface_wave_height"
#> surface_wave_length
#> "surface_wave_length"
#> surface_wave_period
#> "surface_wave_period"
#> lake_number
#> "lake_number"
#> max_dT_dz
#> "max_dT_dz"
#> CD
#> "CD"
#> CHE
#> "CHE"
#> z_L
#> "z_L"
#> H
#> "H"
#> V
#> "V"
#> A
#> "A"
#> radn
#> "radn"
#> extc
#> "extc"
#> umean
#> "umean"
#> uorb
#> "uorb"
#> taub
#> "taub"
#> epsilon
#> "epsilon"
#> NCS_ss1_vvel
#> "NCS_ss1_vvel"
#> NCS_ss1_set
#> "NCS_ss1_set"
#> NCS_ss2_vvel
#> "NCS_ss2_vvel"
#> NCS_ss2_set
#> "NCS_ss2_set"
#> NCS_set
#> "NCS_set"
#> OXY_sat
#> "OXY_sat"
#> OXY_oxy_dsfv
#> "OXY_oxy_dsfv"
#> OXY_oxy_atmv
#> "OXY_oxy_atmv"
#> NIT_nitrif
#> "NIT_nitrif"
#> NIT_denit
#> "NIT_denit"
#> NIT_anammox
#> "NIT_anammox"
#> NIT_dnra
#> "NIT_dnra"
#> OGM_docr
#> "OGM_docr"
#> OGM_donr
#> "OGM_donr"
#> OGM_dopr
#> "OGM_dopr"
#> OGM_cpom
#> "OGM_cpom"
#> OGM_poc_set
#> "OGM_poc_set"
#> OGM_cpom_set
#> "OGM_cpom_set"
#> OGM_pon_set
#> "OGM_pon_set"
#> OGM_pop_set
#> "OGM_pop_set"
#> OGM_cdom
#> "OGM_cdom"
#> OGM_poc_hyd
#> "OGM_poc_hyd"
#> OGM_pon_hyd
#> "OGM_pon_hyd"
#> OGM_pop_hyd
#> "OGM_pop_hyd"
#> OGM_doc_min
#> "OGM_doc_min"
#> OGM_don_min
#> "OGM_don_min"
#> OGM_dop_min
#> "OGM_dop_min"
#> OGM_doc_anaerobic
#> "OGM_doc_anaerobic"
#> OGM_doc_denit
#> "OGM_doc_denit"
#> OGM_docr_min
#> "OGM_docr_min"
#> OGM_donr_min
#> "OGM_donr_min"
#> OGM_dopr_min
#> "OGM_dopr_min"
#> OGM_cpom_bdown
#> "OGM_cpom_bdown"
#> OGM_bod5
#> "OGM_bod5"
#> OGM_pom_vvel
#> "OGM_pom_vvel"
#> OGM_cpom_vvel
#> "OGM_cpom_vvel"
#> PHY_cyano_IN
#> "PHY_cyano_IN"
#> PHY_cyano_IP
#> "PHY_cyano_IP"
#> PHY_cyano_NtoP
#> "PHY_cyano_NtoP"
#> PHY_cyano_set_c
#> "PHY_cyano_set_c"
#> PHY_cyano_set_n
#> "PHY_cyano_set_n"
#> PHY_cyano_set_p
#> "PHY_cyano_set_p"
#> PHY_cyano_fI
#> "PHY_cyano_fI"
#> PHY_cyano_fNit
#> "PHY_cyano_fNit"
#> PHY_cyano_fPho
#> "PHY_cyano_fPho"
#> PHY_cyano_fSil
#> "PHY_cyano_fSil"
#> PHY_cyano_fT
#> "PHY_cyano_fT"
#> PHY_cyano_fSal
#> "PHY_cyano_fSal"
#> PHY_cyano_gpp_c
#> "PHY_cyano_gpp_c"
#> PHY_cyano_rsp_c
#> "PHY_cyano_rsp_c"
#> PHY_cyano_exc_c
#> "PHY_cyano_exc_c"
#> PHY_cyano_mor_c
#> "PHY_cyano_mor_c"
#> PHY_cyano_gpp_n
#> "PHY_cyano_gpp_n"
#> PHY_cyano_rsp_n
#> "PHY_cyano_rsp_n"
#> PHY_cyano_exc_n
#> "PHY_cyano_exc_n"
#> PHY_cyano_mor_n
#> "PHY_cyano_mor_n"
#> PHY_cyano_gpp_p
#> "PHY_cyano_gpp_p"
#> PHY_cyano_rsp_p
#> "PHY_cyano_rsp_p"
#> PHY_cyano_exc_p
#> "PHY_cyano_exc_p"
#> PHY_cyano_mor_p
#> "PHY_cyano_mor_p"
#> PHY_green_IN
#> "PHY_green_IN"
#> PHY_green_IP
#> "PHY_green_IP"
#> PHY_green_NtoP
#> "PHY_green_NtoP"
#> PHY_green_set_c
#> "PHY_green_set_c"
#> PHY_green_set_n
#> "PHY_green_set_n"
#> PHY_green_set_p
#> "PHY_green_set_p"
#> PHY_green_fI
#> "PHY_green_fI"
#> PHY_green_fNit
#> "PHY_green_fNit"
#> PHY_green_fPho
#> "PHY_green_fPho"
#> PHY_green_fSil
#> "PHY_green_fSil"
#> PHY_green_fT
#> "PHY_green_fT"
#> PHY_green_fSal
#> "PHY_green_fSal"
#> PHY_green_gpp_c
#> "PHY_green_gpp_c"
#> PHY_green_rsp_c
#> "PHY_green_rsp_c"
#> PHY_green_exc_c
#> "PHY_green_exc_c"
#> PHY_green_mor_c
#> "PHY_green_mor_c"
#> PHY_green_gpp_n
#> "PHY_green_gpp_n"
#> PHY_green_rsp_n
#> "PHY_green_rsp_n"
#> PHY_green_exc_n
#> "PHY_green_exc_n"
#> PHY_green_mor_n
#> "PHY_green_mor_n"
#> PHY_green_gpp_p
#> "PHY_green_gpp_p"
#> PHY_green_rsp_p
#> "PHY_green_rsp_p"
#> PHY_green_exc_p
#> "PHY_green_exc_p"
#> PHY_green_mor_p
#> "PHY_green_mor_p"
#> PHY_diatom_IN
#> "PHY_diatom_IN"
#> PHY_diatom_IP
#> "PHY_diatom_IP"
#> PHY_diatom_NtoP
#> "PHY_diatom_NtoP"
#> PHY_diatom_set_c
#> "PHY_diatom_set_c"
#> PHY_diatom_set_n
#> "PHY_diatom_set_n"
#> PHY_diatom_set_p
#> "PHY_diatom_set_p"
#> PHY_diatom_fI
#> "PHY_diatom_fI"
#> PHY_diatom_fNit
#> "PHY_diatom_fNit"
#> PHY_diatom_fPho
#> "PHY_diatom_fPho"
#> PHY_diatom_fSil
#> "PHY_diatom_fSil"
#> PHY_diatom_fT
#> "PHY_diatom_fT"
#> PHY_diatom_fSal
#> "PHY_diatom_fSal"
#> PHY_diatom_gpp_c
#> "PHY_diatom_gpp_c"
#> PHY_diatom_rsp_c
#> "PHY_diatom_rsp_c"
#> PHY_diatom_exc_c
#> "PHY_diatom_exc_c"
#> PHY_diatom_mor_c
#> "PHY_diatom_mor_c"
#> PHY_diatom_gpp_n
#> "PHY_diatom_gpp_n"
#> PHY_diatom_rsp_n
#> "PHY_diatom_rsp_n"
#> PHY_diatom_exc_n
#> "PHY_diatom_exc_n"
#> PHY_diatom_mor_n
#> "PHY_diatom_mor_n"
#> PHY_diatom_gpp_p
#> "PHY_diatom_gpp_p"
#> PHY_diatom_rsp_p
#> "PHY_diatom_rsp_p"
#> PHY_diatom_exc_p
#> "PHY_diatom_exc_p"
#> PHY_diatom_mor_p
#> "PHY_diatom_mor_p"
#> PHY_tphy
#> "PHY_tphy"
#> PHY_in
#> "PHY_in"
#> PHY_ip
#> "PHY_ip"
#> PHY_gpp
#> "PHY_gpp"
#> PHY_ncp
#> "PHY_ncp"
#> PHY_upt_no3
#> "PHY_upt_no3"
#> PHY_upt_nh4
#> "PHY_upt_nh4"
#> PHY_upt_n2
#> "PHY_upt_n2"
#> PHY_upt_po4
#> "PHY_upt_po4"
#> PHY_upt_dic
#> "PHY_upt_dic"
#> PHY_set
#> "PHY_set"
#> PHY_par
#> "PHY_par"
#> Total organic C
#> "CAR_toc"
#> TOT_tss
#> "TOT_tss"
#> flux rate of oxygen across the swi
#> "SDF_Fsed_oxy"
#> flux rate of amm across the swi
#> "SDF_Fsed_amm"
#> flux rate of nit across the swi
#> "SDF_Fsed_nit"
#> flux rate of frp across the swi
#> "SDF_Fsed_frp"
#> net flux across the sediment-water interface
#> "NCS_swi"
#> NCS_swi_dz
#> "NCS_swi_dz"
#> NCS_resus
#> "NCS_resus"
#> NCS_d_taub
#> "NCS_d_taub"
#> O2 exchange across sed/water interface
#> "OXY_oxy_dsf"
#> O2 exchange across atm/water interface
#> "OXY_oxy_atm"
#> Si exchange across sed/water interface
#> "SIL_dsf_rsi"
#> ammonium sediment flux
#> "NIT_amm_dsf"
#> nitrate sediment flux
#> "NIT_nit_dsf"
#> PO4 exchange across sed/water interface
#> "PHS_frp_dsf"
#> Sediment TOC mass
#> "OGM_toc_sed"
#> Sediment TON mass
#> "OGM_ton_sed"
#> Sediment TOP mass
#> "OGM_top_sed"
#> Net POC flux @ the SWI
#> "OGM_poc_swi"
#> Net DOC flux @ the SWI
#> "OGM_doc_swi"
#> Net PON flux @ the SWI
#> "OGM_pon_swi"
#> Net DON flux @ the SWI
#> "OGM_don_swi"
#> Net POP flux @ the SWI
#> "OGM_pop_swi"
#> Net DOP flux @ the SWI
#> "OGM_dop_swi"
#> POC resuspenion rate
#> "OGM_poc_res"
#> PON resuspenion rate
#> "OGM_pon_res"
#> POP resuspenion rate
#> "OGM_pop_res"
#> PHY_phy_swi_c
#> "PHY_phy_swi_c"
#> PHY_phy_swi_n
#> "PHY_phy_swi_n"
#> PHY_phy_swi_p
#> "PHY_phy_swi_p"
#> ok
#> "ok"