Get the variables that are both in the observation and model output
get_mod_obs_vars.RdGet the variables that are both in 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", "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 05:19:01]
#> 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.
#> Building GLM3-AED2 model for lake wainamu
#> Copied in GLM nml file
#> Copied in AED nml file
#> oxy_initial = 625 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 = 3,3 replaced with 3,
#> Building GOTM-WET for lake wainamu
#> Copied all GOTM configuration files
#> instances/abiotic_water/initialization/sO2W 13 replaced with 10
#> instances/abiotic_water/initialization/sPO4W 0.1 replaced with 0.01
#> instances/abiotic_water/initialization/sPDOMW 0.001 replaced with 0.01
#> instances/abiotic_water/initialization/sPPOMW 0.001 replaced with 0.01
#> instances/abiotic_water/initialization/sNH4W 0.05 replaced with 0.02
#> instances/abiotic_water/initialization/sNO3W 0.5 replaced with 0.015
#> instances/abiotic_water/initialization/sNDOMW 0.01 replaced with 0.3
#> instances/abiotic_water/initialization/sNPOMW 0.01 replaced with 0.1
#> instances/abiotic_water/initialization/sDDOMW 2.5 replaced with 0.5
#> instances/abiotic_water/initialization/sDPOMW 0.1 replaced with 0.2
#> instances/abiotic_water/initialization/sSiO2W 3.5 replaced with 1
#> instances/cyanobacteria/initialization/sDW 0.1 replaced with 0.2
#> instances/cyanobacteria/initialization/sNW 0.03 replaced with 0.03
#> instances/cyanobacteria/initialization/sPW 0.003 replaced with 0.0019
#> instances/greens/initialization/sDW 0.1 replaced with 0.1
#> instances/greens/initialization/sNW 0.05 replaced with 0.015
#> instances/greens/initialization/sPW 0.001 replaced with 0.00094
#> instances/diatoms/initialization/sDW 0.2 replaced with 0.25
#> instances/diatoms/initialization/sNW 0.05 replaced with 0.038
#> instances/diatoms/initialization/sPW 0.005 replaced with 0.0024
#> instances/abiotic_water/initialization/sDIMW 4 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 05:19:05]
#> Model run complete![2024-11-18 05:19:10]
#> Reading models in parallel... [2024-11-18 05:19:10]
#> Model reading complete![2024-11-18 05:19:12]
get_mod_obs_vars(aeme = aeme, model = model)
#> Cyanobacteria Dissolved oxygen
#> "PHY_cyano" "CHM_oxy"
#> Salinity Water temperature
#> "CHM_salt" "HYD_temp"
#> Total chlorophyll a Dissolved organic carbon
#> "PHY_tchla" "CAR_doc"
#> Phosphate Ammoniacal nitrogen
#> "PHS_frp" "NIT_amm"
#> Nitrate Total nitrogen
#> "NIT_nit" "NIT_tn"
#> Total phosphorus Thermocline depth
#> "PHS_tp" "HYD_thmcln"
#> 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"
#> Metalimnetic oygen Metalimnetic oxygen minima
#> "CHM_oxymet" "CHM_oxymom"
#> Number of anoxic layers Trophic Level Index 3
#> "CHM_oxynal" "LKE_tli3"
#> Trophic Level Index 4 Water level
#> "LKE_tli4" "LKE_lvlwtr"