Run GLM-AED diagnostics
Usage
run_glm_aed_diagnostics(
aeme,
model,
groups = NULL,
depth_collapse = "mean",
plot = FALSE,
use_bounds = TRUE,
print_table = TRUE
)Arguments
- aeme
Aeme object.
- model
Model name. One of "gotm_wet", "glm_aed", or "dy_cd".
- groups
character vector selecting catalogue entries. Accepts:
catalogue entry names (e.g. "nitrogen_state"),
element codes ("O","N","P","Phy"),
types ("state","process"). Default NULL = all entries.
- depth_collapse
"mean", "surface" or "max" – reduce 3D variables
- plot
draw combined plots, grouped by element
- use_bounds
add dashed lines to plots showing expected bounds (from catalogue)
- print_table
print the kable summary
Examples
aeme_dir <- system.file("extdata/lake/", package = "AEME")
# Copy files from package into tempdir
path <- tempdir()
aeme <- yaml_to_aeme(path = aeme_dir, "aeme.yaml")
vars_sim <- c("HYD_strat", "HYD_temp", "HYD_thmcln", "HYD_schstb",
"CHM_oxycln", "CHM_oxynal",
"NIT_tn", "PHS_tp", "PHY_tchla")
model_controls <- get_model_controls(use_bgc = TRUE)
model_controls <- set_vars_sim(model_controls = model_controls,
vars_sim = vars_sim)
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 [35ms]
#>
#> 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 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.
aeme <- run_aeme(aeme)
#> ℹ Running models... (Have you tried parallelizing?) [2026-10-14 00:27:33]
#> ℹ GLM-AED running... [2026-10-14 00:27:33]
#>
#> Reading configuration from C:\Users\runneradmin\AppData\Local\Temp\RtmpqAKjog/LID45819_wainamu/glm_aed/glm4.nml
#> No 'particles' config, assuming no particles
#> NOTE: value for base_elev is no longer used; H[1] is assumed.
#> VolAtCrest= 1946739.94960; MaxVol= 1946739.94960 (m3)
#> No 'snowice' section, setting defaults & assuming no snowfall
#> 'sediment' section present, simulating sediment heating
#>
#> -------------------------------------------------------
#> | General Lake Model (GLM) Version 4.0.0 |
#> -------------------------------------------------------
#>
#> glm built using gcc version 16.1.0
#>
#> nDays= 200; timestep= 3600.000000 (s)
#> Maximum lake depth is 18.070000
#> Depth where flow will occur over the crest is 18.070000
#> *sed_temp_mean[0] = 16.29600
#> aed_api built using gfortran version 16 . 1 . 0
#> libaed enabled.... aed_configure_models processing: aed/aed.nml
#> ---------- AED API config : start ----------
#> libaed-water version 3.0.0
#> libaed built using gfortran version 16 . 1 . 0
#> libaed-ben version 3.0.0
#> libaed built using gfortran version 16 . 1 . 0
#> libaed-demo version 3.0.0
#> libaed built using gfortran version 16 . 1 . 0
#> libaed-riparian version 3.0.0
#> libaed built using gfortran version 16 . 1 . 0
#> libaed-lighting version 3.0.0
#> libaed built using gfortran version 16 . 1 . 0
#> libaed-dev version 3.0.0
#> libaed built using gfortran version 16 . 1 . 0
#> Processing aed_models config from aed/aed.nml
#> aed_sedflux configuration
#> *******************************
#> module aed_sedflux : configured for zone_averaging
#> *******************************
#> aed_noncohesive configuration
#> *******************************
#> module aed_noncohesive : configured for zone_averaging
#> *******************************
#> aed_oxygen configuration
#> *******************************
#> module aed_oxygen : configured for zone_averaging
#> *******************************
#> aed_silica configuration
#> *******************************
#> module aed_silica : configured for zone_averaging
#> *******************************
#> aed_nitrogen configuration
#> *******************************
#> module aed_nitrogen : configured for zone_averaging
#> *******************************
#> aed_phosphorus configuration
#> *******************************
#> module aed_phosphorus : configured for zone_averaging
#> *******************************
#> aed_organic_matter configuration
#> *******************************
#> module aed_organic_matter : configured for zone_averaging
#> *******************************
#> aed_phytoplankton configuration
#> Solving temperature functions for phytoplankton -
#> using the form : f(T) = v^(T-20)-v^(k(T-a))+b
#> *******************************
#> module aed_phytoplankton : configured for zone_averaging
#> *******************************
#> aed_totals configuration
#> *******************************
#> module aed_totals : configured for zone_averaging
#> *******************************
#> ... nml file parsing completed.
#>
#> AED : n_aed_vars = 218 ; n_vars = 26
#> AED : n_vars_ben = 0 ; n_ptm_vars = 0
#> AED : n_vars_diag = 115 ; n_vars_diag_sheet = 29
#>
#> ---------- AED API config : end ----------
#> DBG calling initialise_lake
#> DBG entered initialise_lake
#> DBG init_profiles: num_heights=0 num_depths=2 the_heights=0000000000000000 the_depths=000001669AB41740 lake_depth=13.070000
#> DBG initialise_lake returned
#> WQ plugin active: included Num_WQ_Vars = 26
#> Heat pump disabled (heat_pump_switch = 0)
#> Oxygenation disabled
#>
#> Wall clock start time : Wed Oct 14 00:27:33 2026
#>
#> Simulation begins...
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#>
#> Wall clock finish time : Wed Oct 14 00:27:36 2026
#> Wall clock runtime was 3 seconds : 00:00:03 [hh:mm:ss]
#>
#> Model Run Complete
#> -------------------------------------------------------
#>
#> ✔ GLM-AED running... [2026-10-14 00:27:36] [3.1s]
#>
#> ✔ Model run complete! [2026-10-14 00:27:36]
out <- run_glm_aed_diagnostics(aeme = aeme)
#> Requesting 86 variables from model output... (sediment zone _Z variables are
#> optional; missing ones are skipped)
#> (34 variables not in output: NIT_no2, NIT_n2o, NIT_n2oprod, NIT_n2o_dsf,
#> NIT_no2_dsf, NIT_n2o_atm , ...)
#> ── GLM-AED diagnostic summary ──────────────────────────────────────────────────
#> ! 1 flagged variable
#> ┌─────────────┬───────────┬───────────────────────┬─────┬──────┬────┬────┬────┬────────────┐
#> │ group │ variable │ label │ min │median│mean│ max│ sd │ flag │
#> ├─────────────┼───────────┼───────────────────────┼─────┼──────┼────┼────┼────┼────────────┤
#> │oxygen_fluxes│OXY_oxy_atm│Atm O2 flux (mmol/m2/d)│-19.9│ 3.4 │13.8│ 594│51.4│OUT OF RANGE│
#> └─────────────┴───────────┴───────────────────────┴─────┴──────┴────┴────┴────┴────────────┘
#> ── Full summary ────────────────────────────────────────────────────────────────
#> ┌────────────────────────┬───────────────┬───────────────────────┬────────┬────────┬────────┬─────────┬────────┬────────────┐
#> │ group │ variable │ label │ min │ median │ mean │ max │ sd │ flag │
#> ├────────────────────────┼───────────────┼───────────────────────┼────────┼────────┼────────┼─────────┼────────┼────────────┤
#> │ oxygen_state │ OXY_oxy │ O2 (mmol/m3) │ 93.1 │ 248 │ 258 │ 327 │ 45.8 │ ok │
#> │ oxygen_state │ OXY_sat │ O2 saturation (%) │ 25.3 │ 84.9 │ 85.5 │ 98.9 │ 10.3 │ ok │
#> │ oxygen_fluxes │ OXY_oxy_atm │Atm O2 flux (mmol/m2/d)│ -19.9 │ 3.4 │ 13.8 │ 594 │ 51.4 │OUT OF RANGE│
#> │ oxygen_fluxes │ OXY_oxy_atmv │ Atm O2 flux (vol) │ -2.47 │ 0.436 │ 1.72 │ 74.8 │ 6.62 │ ok │
#> │ oxygen_fluxes │ OXY_oxy_dsf │SWI O2 flux (mmol/m2/d)│ -20.9 │ -15.9 │ -16 │ -8.86 │ 2.03 │ ok │
#> │ oxygen_fluxes │ OXY_oxy_dsfv │ SOD (vol) │ -3.64 │ -2.27 │ -2.29 │ -1.26 │ 0.38 │ ok │
#> │ nitrogen_state │ NIT_amm │ NH4 (mmol N/m3) │ 0.00101│ 0.00883│ 0.026 │ 0.0994 │ 0.0296 │ ok │
#> │ nitrogen_state │ NIT_nit │ NO3 (mmol N/m3) │4.76e-06│ 0.00354│ 0.0032 │ 0.00487 │ 0.00108│ ok │
#> │ nitrogen_organic │ OGM_don │ DON (mmol N/m3) │ 0.00486│ 0.0698 │ 0.0964 │ 0.204 │ 0.0478 │ ok │
#> │ nitrogen_organic │ OGM_donr │ Refractory DON │ 0.544 │ 1.38 │ 1.85 │ 8.94 │ 1.53 │ ok │
#> │ nitrogen_organic │ OGM_pon │ PON (mmol N/m3) │ 0.00292│ 0.365 │ 0.571 │ 1.5 │ 0.482 │ ok │
#> │nitrogen_transformations│ NIT_anammox │ Anammox │ 0 │ 0 │1.54e-06│ 2.14e-05│2.97e-06│ ok │
#> │nitrogen_transformations│ NIT_denit │ Denitrification │ 0 │ 0.0239 │ 0.0306 │ 0.103 │ 0.0294 │ ok │
#> │nitrogen_transformations│ NIT_dnra │ DNRA │ 0 │ 0 │2.69e-05│ 0.000362│4.45e-05│ ok │
#> │nitrogen_transformations│ NIT_nitrif │ Nitrification │ 0.00357│ 0.0355 │ 0.0423 │ 0.314 │ 0.0324 │ ok │
#> │ nitrogen_sediment_flux │ NIT_amm_dsf │ NH4 SWI flux │ 0.134 │ 0.382 │ 0.552 │ 1.33 │ 0.411 │ ok │
#> │ nitrogen_sediment_flux │ NIT_nit_dsf │ NO3 SWI flux │ -0.0322│-0.00571│4.36e-05│ 0.0453 │ 0.0262 │ ok │
#> │ phosphorus_state │ OGM_dop │ DOP │ 0.00035│ 0.00866│ 0.011 │ 0.0231 │ 0.00492│ ok │
#> │ phosphorus_state │ OGM_dopr │ Refractory DOP │ 0.00902│ 0.023 │ 0.0309 │ 0.149 │ 0.0256 │ ok │
#> │ phosphorus_state │ OGM_pop │ POP │0.000407│ 0.0189 │ 0.0265 │ 0.0626 │ 0.021 │ ok │
#> │ phosphorus_state │ PHS_frp │ FRP (mmol P/m3) │4.76e-06│ 0.00026│0.000676│ 0.00267 │0.000669│ ok │
#> │ phosphorus_fluxes │ OGM_dop_min │ DOP mineralisation │ 0 │ 0.0001 │0.000125│ 0.000298│ 5.8e-05│ ok │
#> │ phosphorus_fluxes │ OGM_dop_swi │ DOP SWI flux │ 0 │ 0 │ 0 │ 0 │ 0 │ ok │
#> │ phosphorus_fluxes │ OGM_pop_res │ POP resuspension │ 0 │ 0 │ 0 │ 0 │ 0 │ ok │
#> │ phosphorus_fluxes │ OGM_pop_swi │ POP SWI flux │ -0.016 │-0.00384│-0.00576│-8.09e-05│ 0.00477│ ok │
#> │ phosphorus_fluxes │ PHS_frp_dsf │ FRP SWI flux │ 0.00064│ 0.00188│ 0.00386│ 0.0144 │ 0.0038 │ ok │
#> │ phyto_biomass │ PHY_cyano │ Cyanobacteria │ 0.03 │ 0.0311 │ 0.0904 │ 0.947 │ 0.135 │ ok │
#> │ phyto_biomass │ PHY_diatom │ Diatoms │ 0.03 │ 0.0303 │ 0.057 │ 0.911 │ 0.102 │ ok │
#> │ phyto_biomass │ PHY_green │ Greens │ 0.515 │ 10 │ 18.2 │ 47.6 │ 15.2 │ ok │
#> │ phyto_biomass │ PHY_tchla │ Total chl-a (ug/L) │ 0.241 │ 3.05 │ 5.52 │ 14.3 │ 4.57 │ ok │
#> │ phyto_biomass │ PHY_tphy │Total phyto (mmol C/m3)│ 0.85 │ 10.2 │ 18.4 │ 47.8 │ 15.2 │ ok │
#> │ phyto_stoichiometry │ PHY_cyano_NtoP│ Cyano N:P │ 6.41 │ 18.2 │ 19.1 │ 34.2 │ 7.26 │ ok │
#> │ phyto_stoichiometry │PHY_diatom_NtoP│ Diatom N:P │ 9.79 │ 20.9 │ 20.5 │ 32.7 │ 4.03 │ ok │
#> │ phyto_stoichiometry │ PHY_green_NtoP│ Green N:P │ 6.22 │ 18.6 │ 22.6 │ 40 │ 9.74 │ ok │
#> │ phyto_limitation │ PHY_cyano_fI │ Cyano fI │ 0.0418 │ 0.168 │ 0.158 │ 0.226 │ 0.0442 │ ok │
#> │ phyto_limitation │ PHY_cyano_fNit│ Cyano fN │ 0 │ 0.194 │ 0.212 │ 0.606 │ 0.141 │ ok │
#> │ phyto_limitation │ PHY_cyano_fPho│ Cyano fP │ 0 │ 0.313 │ 0.348 │ 0.901 │ 0.278 │ ok │
#> │ phyto_limitation │ PHY_cyano_fT │ Cyano fT │ 0.561 │ 0.895 │ 0.862 │ 1.06 │ 0.142 │ ok │
#> │ phyto_limitation │ PHY_diatom_fI │ Diatom fI │ 0.0866 │ 0.246 │ 0.236 │ 0.312 │ 0.0514 │ ok │
#> │ phyto_limitation │PHY_diatom_fNit│ Diatom fN │ 0 │ 0.149 │ 0.147 │ 0.445 │ 0.106 │ ok │
#> │ phyto_limitation │PHY_diatom_fPho│ Diatom fP │ 0 │ 0.0814 │ 0.159 │ 0.906 │ 0.243 │ ok │
#> │ phyto_limitation │ PHY_diatom_fT │ Diatom fT │ 1 │ 1 │ 1 │ 1 │ 0 │ ok │
#> │ phyto_limitation │ PHY_green_fI │ Green fI │ 0.0418 │ 0.168 │ 0.158 │ 0.226 │ 0.0442 │ ok │
#> │ phyto_limitation │ PHY_green_fNit│ Green fN │ 0 │ 0.506 │ 0.52 │ 0.772 │ 0.159 │ ok │
#> │ phyto_limitation │ PHY_green_fPho│ Green fP │ 0 │ 0.49 │ 0.435 │ 0.931 │ 0.26 │ ok │
#> │ phyto_limitation │ PHY_green_fT │ Green fT │ 1 │ 1 │ 1 │ 1 │ 0 │ ok │
#> │ phyto_fluxes │ PHY_gpp │ GPP │ 0 │ 0.243 │ 0.396 │ 1.88 │ 0.408 │ ok │
#> │ phyto_fluxes │ PHY_ncp │ NCP │ -0.0661│ 0.142 │ 0.275 │ 1.74 │ 0.363 │ ok │
#> │ phyto_fluxes │ PHY_set │ Sedimentation │ -1.56 │ -0.273 │ -0.503 │ -0.0584 │ 0.398 │ ok │
#> │ phyto_fluxes │ PHY_upt_nh4 │ NH4 uptake │ 0 │ 0.00534│ 0.00768│ 0.129 │ 0.0114 │ ok │
#> │ phyto_fluxes │ PHY_upt_no3 │ NO3 uptake │ 0 │ 0.003 │ 0.0101 │ 0.362 │ 0.029 │ ok │
#> │ phyto_fluxes │ PHY_upt_po4 │ PO4 uptake │ 0 │0.000319│0.000489│ 0.0171 │ 0.0011 │ ok │
#> └────────────────────────┴───────────────┴───────────────────────┴────────┴────────┴────────┴─────────┴────────┴────────────┘