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Estimate zone-specific sediment fluxes from hypsograph

Source: R/estimate_zone_fluxes.R
estimate_zone_fluxes.Rd

Estimates zone-specific sediment fluxes for aed_sed_const2d using up to two tiers of adjustment:

Usage

estimate_zone_fluxes(
  aeme,
  path,
  ref_depth = 5,
  baseline = c(fsed_oxy = -25, fsed_amm = 2, fsed_nit = 0.2, fsed_frp = 0.05),
  verbose = TRUE
)

Arguments

aeme

Aeme object.

path

character; directory where input files are located. Defaults to the path stored in aeme, or the current working directory if not set.

ref_depth

Numeric. Reference depth (m) for literature baseline fluxes. Default 5.

baseline

Named numeric vector of baseline fluxes at ref_depth. Must include fsed_oxy, fsed_amm, fsed_nit, fsed_frp.

verbose

Logical. Print zone summary and copy-paste config lines. Default TRUE.

Value

Invisibly returns a named list with the following elements:

fsed_oxy

Numeric vector of length n_zones. Sediment oxygen demand flux (mmol O2/m2/d, negative).

fsed_amm

Numeric vector of length n_zones. Ammonium flux (mmol N/m2/d).

fsed_nit

Numeric vector of length n_zones. Nitrate flux (mmol N/m2/d).

fsed_frp

Numeric vector of length n_zones. Filterable reactive phosphorus flux (mmol P/m2/d).

zone_summary

Data frame of zone geometry and final flux estimates.

method

Character string; either "baseline_scaled" or "obs_adjusted".

Details

Tier 1 (always) – area-weighted depth scaling. Each zone's flux is scaled from literature baseline values according to its mean depth and fractional bed area. Deep zones receive higher SOD and nutrient fluxes reflecting greater organic matter accumulation and more persistent anoxia.

Tier 2 (optional, when obs supplied) – observed data adjustment. Near-bed summer concentrations of NH4 and FRP are used to adjust the relative difference in fluxes between zones. After adjusting, the fluxes are re-normalised so the lake-wide area-weighted total is unchanged: only the inter-zone ratios move, not the absolute magnitude. Observed O2 and NO3 are read and summarised per zone, but are not currently used to adjust fsed_oxy or fsed_nit, because a concentration ratio is not a good proxy for the direction of change in those fluxes. The adjustment is a heuristic based on concentrations, not on rates of change.

Literature baselines at reference depth 5 m (temperate lakes):

  • fsed_oxy: -25 mmol O2/m2/d (Muller et al. 2012; Sondergaard et al. 2003)

  • fsed_amm: 2 mmol N/m2/d (Andersen 1982; Beutel 2006)

  • fsed_nit: 0.2 mmol N/m2/d (Seitzinger 1988)

  • fsed_frp: 0.05 mmol P/m2/d (Nurnberg 1984)

Depth scaling (Beutel 2006; Muller et al. 2012): SOD and NH4/FRP fluxes scale approximately linearly with mean zone depth divided by ref_depth, with the scale factor capped at 2. NO3 flux transitions from small positive values (shallow, oxic) to negative values (deep, anoxic denitrification) at approximately 0.6 * max_depth.

Zones are the GLM sediment zones, taken from zone_heights in the built glm_aed configuration, so aeme must have been built. Zone 1 is the deepest.

References

Beutel, M.W. (2006). doi:10.1016/j.ecoleng.2006.05.009

Muller, B., et al. (2012). doi:10.1021/es301422r

Nurnberg, G.K. (1984). doi:10.4319/lo.1984.29.1.0111

Seitzinger, S.P. (1988). doi:10.4319/lo.1988.33.4part2.0702

Sondergaard, M., et al. (2003). doi:10.1023/B:HYDR.0000008611.12704.dd

Examples

if (FALSE) { # \dontrun{
zone_heights <- estimate_sed_zones(hypsograph)

# Tier 1 only
fluxes <- estimate_zone_fluxes(zone_heights, hypsograph)

# Tier 2 with observations (Southern Hemisphere)
fluxes <- estimate_zone_fluxes(
  zone_heights,
  hypsograph,
  obs = obs_df,
  lat = -38
)
} # }