Get the output variables from an AEME object
get_output_vars.RdGet 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)
#> Building simulation for Wainamu [2024-11-18 05:19:13]
#> Missing state variables in inflows: PHY_crypt
#> Added default values for missing variables.
#> Using observed water level
#> Missing values in observed water level
#> Using constant water level
#> Correcting water balance using estimated outflows (method = 2).
#> Calculating lake level using lake depth and a sinisoidal function.
#> Warning: 'C:\Users\RUNNER~1\AppData\Local\Temp\RtmpmaQu5E\45819_wainamu' already exists
#> Building GLM3-AED2 model for lake wainamu
#> Copied in AED nml file
#> oxy_initial = 312.5 replaced with 312.5
#> frp_initial = 0.3229 replaced with 0.3229
#> dop_initial = 0.3229 replaced with 0.3229
#> pop_initial = 0.3229 replaced with 0.3229
#> amm_initial = 1.4279 replaced with 1.4279
#> nit_initial = 1.0709 replaced with 1.0709
#> don_initial = 21.4183 replaced with 21.4183
#> pon_initial = 7.1394 replaced with 7.1394
#> doc_initial = 41.6285 replaced with 41.6285
#> poc_initial = 16.6514 replaced with 16.6514
#> rsi_initial = 1 replaced with 1
#> PHY_cyano 0.24022 replaced with 0.24022
#> PHY_green 0.300275 replaced with 0.300275
#> PHY_crypt replaced with
#> PHY_diatom 0.300275 replaced with 0.300275
#> ss_initial = 3, replaced with 3,
#> Building GOTM-WET for lake wainamu
#> instances/abiotic_water/initialization/sO2W 10 replaced with 10
#> instances/abiotic_water/initialization/sPO4W 0.01 replaced with 0.01
#> instances/abiotic_water/initialization/sPDOMW 0.01 replaced with 0.01
#> instances/abiotic_water/initialization/sPPOMW 0.01 replaced with 0.01
#> instances/abiotic_water/initialization/sNH4W 0.02 replaced with 0.02
#> instances/abiotic_water/initialization/sNO3W 0.015 replaced with 0.015
#> instances/abiotic_water/initialization/sNDOMW 0.3 replaced with 0.3
#> instances/abiotic_water/initialization/sNPOMW 0.1 replaced with 0.1
#> instances/abiotic_water/initialization/sDDOMW 0.5 replaced with 0.5
#> instances/abiotic_water/initialization/sDPOMW 0.2 replaced with 0.2
#> instances/abiotic_water/initialization/sSiO2W 1 replaced with 1
#> instances/cyanobacteria/initialization/sDW 0.2 replaced with 0.2
#> instances/cyanobacteria/initialization/sNW 0.03 replaced with 0.03
#> instances/cyanobacteria/initialization/sPW 0.0019 replaced with 0.0019
#> instances/greens/initialization/sDW 0.1 replaced with 0.1
#> instances/greens/initialization/sNW 0.015 replaced with 0.015
#> instances/greens/initialization/sPW 0.00094 replaced with 0.00094
#> instances/diatoms/initialization/sDW 0.25 replaced with 0.25
#> instances/diatoms/initialization/sNW 0.038 replaced with 0.038
#> instances/diatoms/initialization/sPW 0.0024 replaced with 0.0024
#> instances/abiotic_water/initialization/sDIMW 3 replaced with 3
# Run models
aeme <- run_aeme(aeme = aeme, model = model, verbose = FALSE,
path = path, model_controls = model_controls,
parallel = TRUE, ncores = 2L)
#> Running models in parallel... [2024-11-18 05:19:17]
#> Model run complete![2024-11-18 05:19:22]
#> Reading models in parallel... [2024-11-18 05:19:22]
#> Model reading complete![2024-11-18 05:19:24]
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"
#> Water level Volume
#> "LKE_lvlwtr" "LKE_V"
#> Change in volume Surface area
#> "LKE_dV" "LKE_A0"
#> Evaporation Evaporation
#> "LKE_evprte" "LKE_evpflx"
#> Evaporative heat flux Sensible heat flux
#> "LKE_Qe" "LKE_Qh"
#> Longwave radiation Shortwave radiation
#> "LKE_Qlw" "LKE_Qsw"
#> Net surface heat flux Evaporation
#> "LKE_Qnet" "LKE_evpvol"
#> Precipitation Precipitation
#> "LKE_precip" "LKE_pcpvol"
#> Inflow Outflow
#> "LKE_inflow" "LKE_outflow"
#> Net water balance Lake layer
#> "LKE_netwbl" "LKE_layers"
#> Lake depth e-folding depth
#> "LKE_depths" "LKE_efold"
#> e-folding depth Euphotic depth
#> "LKE_efoldh" "LKE_photic"
#> Euphotic depth Remote sensed skin temperature
#> "LKE_photich" "HYD_surft"
#> Air temperature Water-air temperature difference
#> "MET_tmpair" "HYD_atdiff"
#> Salinity Phosphate
#> "CHM_salt" "PHS_frp"
#> Dissolved organic P Particulate organic P
#> "PHS_dop" "PHS_pop"
#> Particulate inorganic P Ammoniacal nitrogen
#> "PHS_pip" "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"
#> Suspended solids Remotely sensed total chlorophyll a
#> "NCS_ss1" "PHY_rstchla"
#> Centre of buoyancy Epilimnion depth
#> "HYD_ctrbuy" "HYD_epidep"
#> Hypolimnion depth Schmidt stability
#> "HYD_hypdep" "HYD_schstb"
#> Oxycline depth Epilimnetic oxygen
#> "CHM_oxycln" "CHM_oxyepi"
#> Hypolimnetic oxygen Metalimnetic oygen
#> "CHM_oxyhyp" "CHM_oxymet"
#> 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"