abm: The ABM model

In sashahafner/ATM99: Simulate Anaerobic Biodegradation

The ABM model

Description

An implementation of the ABM model for simulation of anaerobic biodegradation of organic substrates.

Usage

abm(days = 365, 
    delta_t = 1,
    times = NULL,
    wthr_pars = ABM::wthr_pars2.0,
    evap_pars = list(evap = 0.5 * et(temp_C = ABM::wthr_pars2.0$temp_air_C, 
                                     pres_kpa = ABM::wthr_pars2.0$pres_kpa, 
                                     rs = ABM::wthr_pars2.0$rs)), 
    mng_pars = list(slurry_prod_rate = 5700, 
                    slurry_mass = 39000,     
                    storage_depth = 0.6,     
                    resid_depth = 0.05,      
                    floor_area = 650,        
                    area = 715,              
                    empty_int = 42,          
                    temp_C = 20,
                    wash_water = 75000,            
                    wash_int = NA,
                    rest_d = 5,
                    cover = 'none',
                    resid_enrich = 0.9,
                    slopes = c(urea = NA, slurry_prod_rate = NA),
                    graze = c(start = 'May', duration = 0, hours_day = 0),
                    scale = c(ks_coefficient = 1, qhat_opt = 1, 
                              xa_fresh = 1, yield = 1, alpha_opt = 1)),
    man_pars = ABM::man_pars2.0,
    init_pars = list(conc_init = man_pars$conc_fresh),
    grp_pars = ABM::grp_pars2.0,
    mic_pars = ABM::mic_pars2.0,
    chem_pars = ABM::chem_pars2.0,
    arrh_pars = ABM::arrh_pars2.0,
    resp = TRUE,
    add_pars = NULL,
    pars = NULL,
    startup = 0,
    starting = NULL,
    approx_method_temp = 'linear', 
    approx_method_pH = 'linear',
    approx_method_vent_air = 'linear',
    par_key = '\\.',
    value = 'ts',                 
    warn = TRUE)

Arguments

days	Total number of days in simulation.
delta_t	Time step in output (d).
times	Alternative to delta_t, use to return specific times only. Only available with variable slurry mass.
wthr_pars	Weather inputs. List with elements 'temp_air_C' in degree C, 'RH' relative humidity in percent, 'rain' is precipitation in kg/m2/day, 'pres_kpa' is ambient pressure in kPa, 'rs' is solar radiation in MJ/m2/d. See parameters.
evap_pars	Evaporation inputs.
mng_pars	List of management parameters including slurry production rate (kg/day) (slurry_prod_rate), initial slurry mass in the system (kg) (slurry_mass). If (slurry_mass) is a data.frame with column names "time", "slurry_mass", then (slurry_prod_rate), (resid_depth), (empty_int), (wash_water), (wash_int) are calculated from the (slurry_mass) data.frame. depth of slurry storage (m) (storage_depth), height of slurry in the system after being emptied (m) (resid_depth), surface area of the barn floor that is accesible by the animals (m^2) (floor_area), surface area of the slurry storage (m^2) (area), removal frequency of the slurry in the slurry storage (days), where a value of 0 = "never remove slurry" (empty_int), slurry temperature (deg. C) (temp_C). The model provides some datasets for outside slurry temperatures in Denmark temperatures, wash water used per washing event (kg) (wash_water), time between washing events (days), where NA = "washing not applied" (wash_int), time that the animal section is empty after a batch of animals has been finished (days) (rest_d), argument for setting the type of cover on an outside storage tank (cover). The type of cover only affects the ammonia emission factor, with emission factors and types of covers taken from Sommer et al. 2022, e.g. cover = none means no cover, cover = tent reduces ammonia emission by 80 percent, cover = straw reduces ammonia emission by 33 percent. Factor that determines the degree of enrichment of microbes and organic matter components in the residual slurry after emptying (resid_enrich), and slopes is an expert user argument for changing the excretion rate of urea or slurry production during a growth period of an animal. By default this argument is not used (slopes), (graze) is a list with parameters to adjust the grazing activity outdoor, which affects the amount of slurry excreted in the barn. duration is the number of days per year that the animals are allowed to graze and hours_day are the number of hours animals graze per day during the grazing period, the start argument is the month, where grazing starts, e.g. "May". When the (graze) arguments are not 0, then the model simulation is with time reference to 1. January 00:00:00. Effectively, if start = May, the model simulates grazing from time = 120. Therefore, when combined with variable temperature, temperature should also be with time = 0 referencing to 1 January 00:00:00. scale is a multiplier for adjusting some grp_pars parmeters for all microbes at the same time (scale). Each element may be a length-one vector or, in some cases, a list. See usage, examples, and vignette.
man_pars	List of manure parameters. The default and alternative parameter values are detailed in parameters. Elements are: conc_fresh, the concentration of slurry components in fresh slurry pH, pH of the slurry entering the system and in the slurry in the system The conc_fresh element is a list itself, with the following elements: sulfide (sulfide), urea (urea), sulfate (sulfate), TAN (ammonia nitrogen), starch (starch and sugars), VFA (volatile fatty acids), xa_dead (dead microbial populations), Cfat (crude fat), CP (crude protein), RFd (residual fiber that is degradable: defined as neutral detergent fiber - indigestible neutral detergent fiber), iNDF (indigestible neutral detergent fiber), VSd (degradable, volatile solids), VSd_A (degradable volatile solids for Arrhenius calculation), VSnd_A (non-degradable volatile solids for Arrhenius calcualtion), ash (ash content) Concentrations are on an elemental basis (N/kg wet manure and S/kg wet manure) or else gCOD/kg wet manure (organic components). However, for VSd_A, VSnd_A and ash the unit is g/kg wet manure.
init_pars	List of parameters that define the intial concentrations of organic matter components in the slurry. The elements are similar to the conc_fresh elements in 'man_pars'. By default the element values are the same as values in conc_fresh
grp_pars	List containing parameter values for the microbial groups included in the model. m designates methanogen and sr designates sulfate reducer. The default and alternative parameter values are detailed in parameters. Elements are: yield, Growth yield of microbial groups (g COD-biomass / g COD-substrate) ; xa_fresh, Concentration of microbial groups in the slurry entering the system (g COD-biomass/kg); xa_init, Initial concentration of microbial groups in the slurry (g COD-biomass/kg); decay_rate, Deacay rate of microbial groups (1/day); ks_coefficient, Coefficient used to tune the half saturation constant (g COD-substrate/kg); qhat_opt, Maximum specific substrate utilization rate of microbial groups at their optimum growth temperature (g COD-substrate/g COD-biomass/day); T_opt, Optimum growth temperature of microbial groups (K); T_min, Minimum viable growth temperature of microbial groups (K); T_max, Maximum vaible growth temperature of microbial groups (K); ki_NH3_min, NH3 concentration at which NH3 inhibition starts (g TAN-nitrogen/kg); ki_NH3_max, NH3 concentration wher microbial groups are 100 percent inhibited (g TAN-nitrogen/kg); ki_NH4_min, NH4 concentration at which NH3 inhibition starts (g TAN-nitrogen/kg); ki_NH4_max, NH4 concentration wher microbial groups are 100 percent inhibited (g TAN-nitrogen/kg); ki_H2S_slope, inhibition parameter1 for calculating H2S inhibition factor (g H2S-sulfur/(kg pr pH unit)); ki_H2S_int, inhibition parameter2 for calculating H2S inhibition factor (g H2S-sulfur/kg); ki_H2S_min, inhibition parameter3 for calculating H2S inhibition factor (g H2S-sulfur/kg); Each of these elements is a vector with a named element for each group. See usage, examples, and vignettes.
mic_pars	List of other microbial parameters. The default and alternative parameter values are detailed in parameters. Elements are: ks_SO4, Half sulfate saturation constant for sulfate reducers (g sulfate-sulfur/kg); km_urea, half urea-N saturation constant for Michaelis-Menten urea hydrolysis (g urea-N/kg).
chem_pars	List of other chemical parameters. The default parameter values are detailed in parameters. Elements are: COD_conv, conversion factors for using a COD mass basis with the following named elements: CH4, Methane productivity coefficient (g COD-substrate/g CH4) ; xa_dead, COD to g dry matter mass of dead microbial populations (g COD/g dry xa dead); RFd, COD to g RFd (g COD/g RFd); iNDF, COD to g iNDF (g COD/g iNDF); starch, COD to g starch (g COD/g starch); Cfat, COD to g Cfat (g COD/g Cfat); CP, COD to g CP (g COD/g CP); VFA, COD to g VFA (g COD/g VFA); RFd, COD to g RFd (g COD/g RFd); S, COD-substrate to sulfur (g sulfur/g COD-substrate) ; VS, COD to g volatile solids (g COD/g volatile solids); CO2_ureo, carbon dioxide productivity coefficient for urea hydrolysis (g CO2/g urea-N); CP_N, crude protein COD per g crude protein N (g CP-COD/g CP-N); C_N_urea, carbon to nitrogen (g C/g urea-N); Other conversion factors designated C_ are carbon to COD of the named substrate (gC/gCOD)
arrh_pars	List of hydrolysis parameters that are related to Arrhenius kinetics. The default parameter values are detailed in parameters. Elements are: lnA, frequency factor used in danish methane emission inventory calculations, only used for comparing to ABM model (g CH4/ (kgVS * hour)); E_CH4, Activation energy used in danish methane emission inventory calculations, only used for comparing to ABM model (J/mol); R, universal gas constant (J/(K * mol)); VS_CH4, volatile solids consumed per methane produced (g VS/g CH4); A, Arrhenius factor for calculating the temperature sensitive hydrolysis rate constants of organic matter components (1/day); E, Activation energy for calculating the temperature sensitive hydrolysis rate constant of organic matter components (J/mol); kl, mass transfer coefficient of ammonia from the slurry pit (m/day) and from the barn floor (m/day) and mass transfer coefficient of H2S from the slurry (m/day).
resp	Set to TRUE (default) to include surface respiration. Can be FALSE for e.g. anaerobic digestion simulation.
pH_inhib_overrule	Default is FALSE. Can be TRUE if the inhibition should be governed by a pH inhibition function, rather than the default where inhibition is governed by concentrations of NH3, NH4, H2S and protonated VFA.
add_pars	List of other additional parameters not set in other arguments, or to be modified from defaults. See vignette.
pars	Combined parameters, as an alternative to all the '*_pars' arguments. Used internally when startup > 0 and may be convenient to use in an abm call in some cases.
startup	Number of startup times the simulation should be run before running a final time. Results from one simulation become starting conditions for next. Used to spin up or stabilize microbial population and substrates so that initial conditions do not affect results. Length-one integer vector. Optional.
starting	Starting conditions. Output (value = 'ts') from a previous abm() call. Values here for microbial biomass and slurry mass override those set in other arguments. Used to start one simulation where another ended. Optional.
approx_method_temp	Sets type of interpolation when temperature is variable (temp_c is a data frame). Passed to approxfun through hidden (not exported) makeTimeFunc(). See vignette. Suggested temperature sets for outside slurry storage are provided in temperatures.
approx_method_pH	Sets type of interpolation when pH is variable (pH is a data frame). Passed to approxfun through hidden (not exported) makeTimeFunc(). See vignette.
approx_method_vent_air	Sets type of interpolation when ventilation flow rate is variable. Passed to approxfun through hidden (not exported) makeTimeFunc(). See vignette.
par_key	Special character used to set individual nested elements within some arguments. See vignette for examples.
value	Sets the type of output. Default ('ts') returns a data frame with the complete time series. For a summary, use 'summ' (or 'sum' or 'summary'). code'eff' will return only those rows where slurry was removed–this option is convenient for working with effluent slurry.
warn	Set to FALSE to suppress warnings.

Details

The function simulates anaerobic biodegradation.

Value

By default, a data frame with most input and all output variables in a time series. Each row is separated by the value set with delta_t. Typically the primary variable of interest is methane emission, which is returned as a total (g) and rate (g/d), overall or normalized to COD or VS loading. These columns all start with CH4. Microbial biomass (g) is given in columns with names that match those used for the names of the groups. For more details, see the Output section in the vignette.

Author(s)

Sasha D. Hafner and Frederik R. Dalby

References

Dalby, F.R., Hafner, S.D., Petersen, S.O., Vanderzaag, A., Habtewold, J., Dunfield, K., Chantigny, M.H., Sommer, S.G., 2021. A mechanistic model of methane emission from animal slurry with a focus on microbial groups. PLOS ONE 16, e0252881. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1371/journal.pone.0252881")}

Dalby, F.R., Hansen, M.J., Guldberg, L.B., Hafner, S.D., Feilberg, A., 2023. Simple Management Changes Drastically Reduce Pig House Methane Emission in Combined Experimental and Modeling Study. Environ. Sci. Technol. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.est.2c08891")}

Dalby, F.R., Ambrose, H.W., Poulsen, J.S., Nielsen, J.L., Adamsen, A.P.S., 2023. Pig slurry organic matter transformation and methanogenesis at ambient storage temperatures. JEQ. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/jeq2.20512")}

Dalby, F.R., Hafner, S.D., Ambrose, H.W., Adamsen, A.P.S., 2024. Pig manure degradation and carbon emission: Measuring and modeling combined aerobic–anaerobic transformations. JEQ. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/jeq2.20603")}

Sommer, S.G, Hafner S.D., Laubach, J., van der Weerden, T.J., Pacholski, A., 2022. Model for calculating ammonia emission from stored animal liquid manure. Biosyst Eng \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.biosystemseng.2022.08.007")}

Examples

# Simulation 1~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Run model with default parameter values and input variables
out1 <- abm()

# Plot cumulative CH4 emission (g) and emission rate (g/d)
plot(CH4_emis_cum ~ time, data = out1, type = 'l')
plot(CH4_emis_rate ~ time, data = out1, type = 'l')

# Plot microbial biomass
matplot(out1$time, out1[, nn <- c('m0', 'm1', 'm2', 'sr1')],
        type = 'l', lty = 1, xlab = 'Time (d)', ylab = 'Microbial biomass (g)')
legend('topleft', nn, col = 1:4, lty = 1)

sashahafner/ATM99 documentation built on June 14, 2025, 5:34 p.m.