Apply IPCC manure-management losses to the collected manure streams.
Source:R/manure_management.R
apply_management_losses.RdNets the nitrogen surviving manure management onto the field, applying the
IPCC 2019 management-loss fractions to the collected/housed streams from
split_manure_management(): applied_n = n_stream * (1 - FracLossMS) where
FracLossMS = FracGasMS + FracLeachMS + EF3 + FracN2MS. The grazing
(pasture/range/paddock) stream is deposited in situ and keeps its full
nitrogen (its in-situ soil losses belong to the soil stage). Indirect N2O is
reported as a labelled sub-flux of the already-removed volatilized and leached
nitrogen (the same N is not removed twice). Carbon applied to the field is
c_stream * (1 - c_loss_fraction), the stream's carbon less what its
management system mineralises in storage, and the volatile solids are scaled
by the same ratio. The applied C:N is therefore a RESULT of that loss rather
than an imposed cap. Loss fractions and their sources are in
inst/extdata/manure/manure_storage_c_loss.csv: nothing for grazing or daily
spread, which have no storage stage; 0.420 of initial carbon for solid
storage and 0.424 for poultry litter (Pardo et al. 2015,
doi:10.1111/gcb.12806
); 0.110 (cattle) and 0.128 (pigs) for slurry,
derived from Kupper et al. 2020 (doi:10.1016/j.agee.2020.106963
) using
this package's own 0.47 kg C per kg volatile solids.
Until whep#1006 this was a cap, pmin(c_stream, applied_n * post-storage C:N), which produced a loss only as a side effect of holding the applied
C:N down. That made the loss depend on the excreted composition rather than
on the storage system: when excreted carbon moved, the reported loss for
cattle solid storage fell from 40.3% to 6.9% with no coefficient changing.
Usage
apply_management_losses(split, options = list())Arguments
- split
A tibble from
split_manure_management(), optionally with then_beddingandc_beddingcolumnsadd_manure_bedding()adds.- options
A named list.
methodselects the loss method ("ipcc_2019_tier2").bedding_c_lossselects how bedding carbon is treated in storage:"same_as_excreta"(default) or"none"; see the Bedding section.indirect_n2o_sourceselects the edition of indirect_n2o_ef the EF4 and EF5 of the indirect N2O are read from:"ipcc_2019"(default; EF5 0.011, Vol 4, Ch 11, Table 11.3 (Updated), p. 11.26 of the 2019 Refinement) or"ipcc_2006"(EF5 0.0075, Table 11.3, p. 11.24 of the 2006 Guidelines, the value shipped before whep#1245). EF4 is 0.010 in both, so only the leached share ofn2o_indirect_nmoves, by a factor of 1.467;applied_ndoes not.ef3_sourceselects the edition of ipcc_manure_ef3 the direct N2O of each stored stream is read from:"ipcc_2019"(default; Vol 4, Ch 10, Table 10.21 (Updated) of the 2019 Refinement) or"as_shipped"(the mixed table read before whep#601). It movesn2o_direct_nandn2_n, and soapplied_n, of the collected streams; the grazing stream carries no management N2O either way.slurry_crustsets the liquid-slurry crust share under the 2019 edition:"half"(default, EF3 0.0025),"none"(0) or"all"(0.005); see ipcc_manure_ef3.method_direct_n2orecords the choice (e.g."ipcc_2019; slurry_crust_half").
Value
The input rows with manure_type, applied_n, applied_c,
applied_vs, n_volatilized, n_leached, n2o_direct_n, n2_n,
n2o_indirect_n, c_lost, vs_destroyed, n_bedding, c_bedding,
method_losses, method_bedding_c, method_indirect_n2o and
method_direct_n2o.
Bedding
When the rows carry n_bedding and c_bedding (from
add_manure_bedding()), the straw bedded under housed animals is part of
the manure that reaches the field, and the applied C:N is the C:N of the
bedded farmyard manure rather than of the excreta alone. Without those
columns nothing changes: they default to zero and every number is the
excreta-only one.
Nitrogen follows IPCC 2019 Refinement Vol. 4 Ch. 10 Eq. 10.34 (p. 10.94)
exactly: NbeddingMS sits outside the (1 - FracLossMS) term, because
"mineralization of nitrogen compounds in beddings occurs more slowly
compared to manure and the concentration of ammonia fraction in organic
beddings is negligible", so "both volatilization and leaching losses during
storage of bedding are assumed to be zero" (p. 10.93). Bedding nitrogen
therefore raises applied_n one-for-one and raises none of the loss
side-streams.
Carbon has no IPCC rule at all – manure CO2 is out of scope there – so
bedding_c_loss selects it. "same_as_excreta" (default) applies the
stream's own storage carbon-loss fraction to the bedding carbon too: the
0.420 for solid storage comes from Pardo et al. 2015
(doi:10.1111/gcb.12806
, Table 2), a systematic review of whole manure
heaps, and a heap in solid storage in practice already contains its litter,
so the measured loss is a whole-heap loss. "none" keeps every gram of
bedding carbon, mirroring the zero storage loss IPCC gives bedding nitrogen;
it is the upper bound on applied carbon and raises the applied carbon of a
bedded solid-storage stream by 0.420 / (1 - 0.420) = 72% of the bedding
carbon relative to the default.
Volatile solids stay excreta-only under both, so the Tier 2 methane engine
in build_livestock_ghg_extension() is untouched. IPCC 2019 Ch. 10 does ask
for bedding to be combined with volatile solids when estimating manure
methane; that is a separate change to a separate engine and is not made
here.
Examples
excretion <- tibble::tribble(
~year, ~territory, ~sub_territory, ~livestock_category,
~n_excretion, ~c_excretion, ~vs_excretion,
2020L, "203", NA, "Cattle_milk", 100, 1900, 60
)
apply_management_losses(split_manure_management(excretion))
#> # A tibble: 5 × 24
#> year territory sub_territory livestock_category species_gen mms_type
#> <int> <chr> <lgl> <chr> <chr> <chr>
#> 1 2020 203 NA Cattle_milk Cattle Anaerobic Lagoon
#> 2 2020 203 NA Cattle_milk Cattle Daily Spread
#> 3 2020 203 NA Cattle_milk Cattle Liquid/Slurry
#> 4 2020 203 NA Cattle_milk Cattle Pasture/Range/Pa…
#> 5 2020 203 NA Cattle_milk Cattle Solid Storage
#> # ℹ 18 more variables: manure_type <chr>, stream <chr>, applied_n <dbl>,
#> # applied_c <dbl>, applied_vs <dbl>, n_volatilized <dbl>, n_leached <dbl>,
#> # n2o_direct_n <dbl>, n2_n <dbl>, n2o_indirect_n <dbl>, c_lost <dbl>,
#> # vs_destroyed <dbl>, n_bedding <dbl>, c_bedding <dbl>, method_losses <chr>,
#> # method_bedding_c <chr>, method_indirect_n2o <chr>, method_direct_n2o <chr>