make-Rda/make_pars.R
In sashahafner/ATM99: Simulate Anaerobic Biodegradation
# Creates parameter objects
# best fit grp_pars2.0 based on multiple datasets using CP, RFd, starch and Cfat as inputs
grp_pars2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.0628, m1 = 0.0628, m2 = 0.0628, sr1 = 0.0628),
xa_init = c(all = 0.0628),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.693, m1 = 0.407, m2 = 1.65, m3 = 7.2, m4 = 8, m5 = 8, sr1 = 8.95),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 6.41, m2 = 6.41, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.3),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
mic_pars2.0 <- list(ks_SO4 = 0.00694,
km_urea = 0.913,
decay_rate_xa = 0.02)
man_pars2.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 3.17, sulfate = 0.2, TAN = 0.0, starch = 5.25,
VFA = 1.7, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 27.6, CPs = 21.1 * 0.55, CPf = 21.1 * 0.45,
RFd = 25.4, iNDF = 11.3, VSd = 0, VSd_A = 55, VSnd_A = 23.5, ash = 15),
pH = 7, dens = 1000)
wthr_pars2.0 <- list(temp_air_C = 20, RH = 90, rain = 1.9, pres_kpa = 101, rs = 10)
arrh_pars2.0 <- list(lnA = c(VSd_A = 31.3),
E_CH4 = c(VSd_A = 81000),
A = c(xa_dead= 3.61383 * 10^12, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 1.499476 * 10^12, VSd = 3.61383 * 10^12, urea = 4.38*10^15),
E = c(xa_dead= 81557, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 81052, VSd = 81557, urea = 81559),
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 1, notVSd = 1, CP = 1),
kl = c(NH3 = 64*8, NH3_floor = 36*8, H2S = 0.02),
scale_EF_NH3 = 1)
save(grp_pars2.0, file = '../data/grp_pars2.0.rda')
save(mic_pars2.0, file = '../data/mic_pars2.0.rda')
save(man_pars2.0, file = '../data/man_pars2.0.rda')
save(wthr_pars2.0, file = '../data/wthr_pars2.0.rda')
save(arrh_pars2.0, file = '../data/arrh_pars2.0.rda')
# best fit grp_pars for Dalby et al. 2023, EST using VSd as input
grp_pars1.0 <- list(grps = c('m0','m1','m2', 'sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.0628, m1 = 0.0628, m2 = 0.0628, sr1 = 0.0628),
xa_init = c(all = 0.0628),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.17071975112963, sr1 = 0.4682879),
qhat_opt = c(m0 = 0.4742862, m1 = 1.138287, m2 = 1.770668 , m3 = 7.2, m4 = 8, m5 = 8, sr1 = 2.529526),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 10, m2 = 10, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.13),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 4.8),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
man_pars1.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 3.17, sulfate = 0.2, TAN = 0.0, starch = 0,
VFA = 2, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 0, CPs = 0, CPf = 0, RFd = 0, iNDF = 0, VSd = 75,
VSd_A = 55, VSnd_A = 22, ash = 15), pH = 7, dens = 1000)
save(grp_pars1.0, file = '../data/grp_pars1.0.rda')
save(man_pars1.0, file = '../data/man_pars1.0.rda')
## set in progress 2.0
grp_pars_VS_pig2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.509, m1 = 0.255, m2 = 1.2701, m3 = 7.2, m4 = 8, m5 = 8, sr1 = 8.95),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 1.39, m2 = 1.39, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 5.37),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7.5),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_pig2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 2*0.2826429, m1 = 2.5*0.2826429, m2 = 3*0.2826429 , m3 = 4*0.2826429, m4 = 8*0.2826429, m5 = 8*0.2826429, sr1 = 8.95*0.2826429),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 10, m2 = 10, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 3.223),
ki_NH4_min = c(all = 2.714),
ki_NH4_max = c(all = 10),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_VS_cattle2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.0446, m1 = 0.01, m2 = 1.697, m3 = 8.0, m4 = 8, m5 = 8, sr1 = 8.95),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 0.001, m2 = 0.001, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 1.528),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_cattle2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 2 * 0.962509436301619, m1 = 2.5* 0.962509436301619, m2 = 3* 0.962509436301619 , m3 = 4* 0.962509436301619, m4 = 8* 0.962509436301619, m5 = 8* 0.962509436301619, sr1 = 8.95* 0.962509436301619),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 10, m2 = 10, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.465),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_VS_digestate2.0 <- list(grps = c('m0', 'm1', 'm2', 'm3', 'sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(all = 0.3),
xa_init = c(all = 0.3),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.11, m1 = 1.92, m2 = 1.46, m3 = 3.4, sr1 = 9),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, sr1 = 44),
T_min = c(m0 = 0, m1 = 11.36, m2 = 11.36, m3 = 15, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, sr1 = 51),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.194),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.11, sr1 = -0.15),
ki_H2S_int = c(default = 1.0, sr1 = 1.4),
ki_H2S_min = c(default = 0.080),
IC50_low = c(default = 0.21, sr1 = 0.28),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
man_pars_pig2.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 3.17, sulfate = 0.01, TAN = 0.0, starch = 5.25,
VFA = 1.7, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 27.6, CPs = 21.1 * 0.55, CPf = 21.1 * 0.45, RFd = 25.4, iNDF = 11.3, VSd = 0,
VSd_A = 55, VSnd_A = 23.5, ash = 15), pH = 7, dens = 1000)
man_pars_cattle2.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 2.116, sulfate = 0.01, TAN = 0.0, starch = 1.4864,
VFA = 2.54, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 16.04, CPs = 30*0.55, CPf = 30*0.45, RFd = 44.4, iNDF = 21.465, VSd = 0,
VSd_A = 32.86, VSnd_A = 45.4, ash = 15), pH = 7, dens = 1000)
man_pars_digestate2.0 <- list(conc_fresh = list(sulfide = 0, urea = 0, sulfate = 0, TAN = 3, starch = 0.29,
VFA = 0.5, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 3.18, CPs = 5.95, CPf = 0, RFd = 8.8, iNDF = 21.47, VSd = 0,
VSd_A = 12.6, VSnd_A = 18.13, ash = 15), pH = 8, dens = 1000)
man_pars_VS_pig2.0 <- man_pars_pig2.0
man_pars_VS_cattle2.0 <- man_pars_cattle2.0
man_pars_VS_digestate2.0 <- man_pars_digestate2.0
# pig
man_pars_VS_pig2.0$conc_fresh['VSd'] <- (man_pars_VS_pig2.0$conc_fresh[['starch']] + man_pars_VS_pig2.0$conc_fresh[['xa_dead']] +
man_pars_VS_pig2.0$conc_fresh[['Cfat']] + man_pars_VS_pig2.0$conc_fresh[['RFd']] + man_pars_VS_pig2.0$conc_fresh[['CPs']] +
man_pars_VS_pig2.0$conc_fresh[['CPf']] +
man_pars_VS_pig2.0$conc_fresh[['iNDF']]) * 0.7
for (i in c('starch', 'xa_dead','Cfat','RFd','CPs', 'CPf', 'iNDF')){
man_pars_VS_pig2.0$conc_fresh[i] <- 0
}
# cattle
man_pars_VS_cattle2.0$conc_fresh['VSd'] <- (man_pars_VS_cattle2.0$conc_fresh[['starch']] + man_pars_VS_cattle2.0$conc_fresh[['xa_dead']] +
man_pars_VS_cattle2.0$conc_fresh[['Cfat']] + man_pars_VS_cattle2.0$conc_fresh[['RFd']] + man_pars_VS_cattle2.0$conc_fresh[['CPs']] +
man_pars_VS_cattle2.0$conc_fresh[['CPf']] +
man_pars_VS_cattle2.0$conc_fresh[['iNDF']]) * 0.42
for (i in c('starch', 'xa_dead','Cfat','RFd','CPs', 'CPf', 'iNDF')){
man_pars_VS_cattle2.0$conc_fresh[i] <- 0
}
# digestate
man_pars_VS_digestate2.0$conc_fresh['VSd'] <- (man_pars_VS_digestate2.0$conc_fresh[['starch']] + man_pars_VS_digestate2.0$conc_fresh[['xa_dead']] +
man_pars_VS_digestate2.0$conc_fresh[['Cfat']] + man_pars_VS_digestate2.0$conc_fresh[['RFd']] + man_pars_VS_digestate2.0$conc_fresh[['CPs']] +
man_pars_VS_digestate2.0$conc_fresh[['CPf']])
for (i in c('starch', 'xa_dead','Cfat','RFd','CPs', 'CPf', 'iNDF')){
man_pars_VS_digestate2.0$conc_fresh[i] <- 0
}
wthr_pars2.0 <- list(temp_air_C = 20, RH = 90, rain = 1.9, pres_kpa = 101, rs = 10)
chem_pars2.0 <- list(COD_conv = c(CH4 = 1/0.2507, xa = 1/0.7069561, RFd = 1/0.8444792, iNDF = 1/0.8444792, starch = 1/0.8444792,
Cfat = 1/0.3117844, CP = 1/0.6541602, VFA = 1/0.9383125, S = 1/0.5015, VS = 1/0.69, CO2_aer = 1/0.436, CO2_sr = 1/1.2, CO2_ureo = 1/1.57,
CP_N = 1/0.1014, C_xa = 1/0.3753125, C_RFd = 1/0.376, C_iNDF = 1/0.358, N_xa = 1/0.08754375,
C_starch = 1/0.377, C_Cfat = 1/0.265, C_CP = 1/0.359 , C_VFA = 1/0.374, C_VSd = 1/0.344, C_N_urea = 1/0.429,
frac_CP_xa = 0.835, C_xa_aer = 1/0.3753125, C_xa_bac = 1/0.3753125, C_xa_dead = 1/0.3753125))
arrh_pars_pig2.0 <- list(lnA = c(VSd_A = 28.717),
E_CH4 = c(VSd_A = 78479.55),
A = c(xa_dead= 3.61383 * 10^12, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 1.499476 * 10^12, VSd = 3.61383 * 10^12, urea = 4.38*10^15),
E = c(xa_dead= 81557, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 81052, VSd = 81557, urea = 81559),
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 0.26, notVSd = 0.55, CP = 6.84),
kl = c(NH3 = 375, NH3_floor = 0.36*375, H2S = 0.02),
scale_EF_NH3 = 0.0000048)
arrh_pars_cattle2.0 <- list(lnA = c(VSd_A = 31.2),
E_CH4 = c(VSd_A = 81000),
A = c(xa_dead= 22497134.8, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 2.567944 * 10^8, VSd = 22497134.8, urea = 4.38*10^15),
E = c(xa_dead= 55609, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 57867, VSd = 55609, urea = 81559), # CP is for GRA treatment in MILK project
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 2.4156, notVSd = 0.294, CP = 0.25),
kl = c(NH3 = 1000, NH3_floor = 0.36*1000, H2S = 0.02),
scale_EF_NH3 = 0.0000048)
arrh_pars_digestate2.0 <- list(lnA = c(VSd_A = 31.2),
E_CH4 = c(VSd_A = 81000),
A = c(xa_dead= 22497134.8, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 2.567944 * 10^8, VSd = 22497134.8, urea = 4.38*10^15),
E = c(xa_dead= 55609, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 57867, VSd = 55609, urea = 81559),
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 2.95, notVSd = 1, CP = 1),
kl = c(NH3 = 64*8, NH3_floor = 36*8, H2S = 0.02),
scale_EF_NH3 = 0.0000048)
pig_pars2.0 <- c(grp_pars_pig2.0, arrh_pars_pig2.0, man_pars_pig2.0)
cattle_pars2.0 <- c(grp_pars_cattle2.0, arrh_pars_cattle2.0, man_pars_cattle2.0)
pig_parsVS2.0 <- c(grp_pars_VS_pig2.0, arrh_pars_pig2.0, man_pars_VS_pig2.0)
cattle_parsVS2.0 <- c(grp_pars_VS_cattle2.0, arrh_pars_cattle2.0, man_pars_VS_cattle2.0)
digestate_parsVS2.0 <- c(grp_pars_VS_digestate2.0, arrh_pars_digestate2.0, man_pars_VS_digestate2.0)
save(grp_pars_pig2.0, file = '../data/grp_pars_pig2.0.rda')
save(grp_pars_cattle2.0, file = '../data/grp_pars_cattle2.0.rda')
save(grp_pars_VS_pig2.0, file = '../data/grp_pars_VS_pig2.0.rda')
save(grp_pars_VS_cattle2.0, file = '../data/grp_pars_VS_cattle2.0.rda')
save(grp_pars_VS_digestate2.0, file = '../data/grp_pars_VS_digestate2.0.rda')
save(arrh_pars_pig2.0, file = '../data/arrh_pars_pig2.0.rda')
save(arrh_pars_cattle2.0, file = '../data/arrh_pars_cattle2.0.rda')
save(arrh_pars_digestate2.0, file = '../data/arrh_pars_digestate2.0.rda')
save(mic_pars2.0, file = '../data/mic_pars2.0.rda')
save(man_pars_pig2.0, file = '../data/man_pars_pig2.0.rda')
save(man_pars_VS_pig2.0, file = '../data/man_pars_VS_pig2.0.rda')
save(man_pars_cattle2.0, file = '../data/man_pars_cattle2.0.rda')
save(man_pars_VS_cattle2.0, file = '../data/man_pars_VS_cattle2.0.rda')
save(man_pars_VS_digestate2.0, file = '../data/man_pars_VS_digestate2.0.rda')
save(wthr_pars2.0, file = '../data/wthr_pars2.0.rda')
save(chem_pars2.0, file = '../data/chem_pars2.0.rda')
save(pig_pars2.0, file = '../data/pig_pars2.0.rda')
save(pig_parsVS2.0, file = '../data/pig_parsVS2.0.rda')
save(cattle_pars2.0, file = '../data/cattle_pars2.0.rda')
save(cattle_parsVS2.0, file = '../data/cattle_parsVS2.0.rda')
save(digestate_parsVS2.0, file = '../data/digestate_parsVS2.0.rda')
sashahafner/ATM99 documentation built on June 14, 2025, 5:34 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# Creates parameter objects
# best fit grp_pars2.0 based on multiple datasets using CP, RFd, starch and Cfat as inputs
grp_pars2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.0628, m1 = 0.0628, m2 = 0.0628, sr1 = 0.0628),
xa_init = c(all = 0.0628),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.693, m1 = 0.407, m2 = 1.65, m3 = 7.2, m4 = 8, m5 = 8, sr1 = 8.95),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 6.41, m2 = 6.41, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.3),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
mic_pars2.0 <- list(ks_SO4 = 0.00694,
km_urea = 0.913,
decay_rate_xa = 0.02)
man_pars2.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 3.17, sulfate = 0.2, TAN = 0.0, starch = 5.25,
VFA = 1.7, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 27.6, CPs = 21.1 * 0.55, CPf = 21.1 * 0.45,
RFd = 25.4, iNDF = 11.3, VSd = 0, VSd_A = 55, VSnd_A = 23.5, ash = 15),
pH = 7, dens = 1000)
wthr_pars2.0 <- list(temp_air_C = 20, RH = 90, rain = 1.9, pres_kpa = 101, rs = 10)
arrh_pars2.0 <- list(lnA = c(VSd_A = 31.3),
E_CH4 = c(VSd_A = 81000),
A = c(xa_dead= 3.61383 * 10^12, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 1.499476 * 10^12, VSd = 3.61383 * 10^12, urea = 4.38*10^15),
E = c(xa_dead= 81557, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 81052, VSd = 81557, urea = 81559),
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 1, notVSd = 1, CP = 1),
kl = c(NH3 = 64*8, NH3_floor = 36*8, H2S = 0.02),
scale_EF_NH3 = 1)
save(grp_pars2.0, file = '../data/grp_pars2.0.rda')
save(mic_pars2.0, file = '../data/mic_pars2.0.rda')
save(man_pars2.0, file = '../data/man_pars2.0.rda')
save(wthr_pars2.0, file = '../data/wthr_pars2.0.rda')
save(arrh_pars2.0, file = '../data/arrh_pars2.0.rda')
# best fit grp_pars for Dalby et al. 2023, EST using VSd as input
grp_pars1.0 <- list(grps = c('m0','m1','m2', 'sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.0628, m1 = 0.0628, m2 = 0.0628, sr1 = 0.0628),
xa_init = c(all = 0.0628),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.17071975112963, sr1 = 0.4682879),
qhat_opt = c(m0 = 0.4742862, m1 = 1.138287, m2 = 1.770668 , m3 = 7.2, m4 = 8, m5 = 8, sr1 = 2.529526),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 10, m2 = 10, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.13),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 4.8),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
man_pars1.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 3.17, sulfate = 0.2, TAN = 0.0, starch = 0,
VFA = 2, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 0, CPs = 0, CPf = 0, RFd = 0, iNDF = 0, VSd = 75,
VSd_A = 55, VSnd_A = 22, ash = 15), pH = 7, dens = 1000)
save(grp_pars1.0, file = '../data/grp_pars1.0.rda')
save(man_pars1.0, file = '../data/man_pars1.0.rda')
## set in progress 2.0
grp_pars_VS_pig2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.509, m1 = 0.255, m2 = 1.2701, m3 = 7.2, m4 = 8, m5 = 8, sr1 = 8.95),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 1.39, m2 = 1.39, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 5.37),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7.5),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_pig2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 2*0.2826429, m1 = 2.5*0.2826429, m2 = 3*0.2826429 , m3 = 4*0.2826429, m4 = 8*0.2826429, m5 = 8*0.2826429, sr1 = 8.95*0.2826429),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 10, m2 = 10, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 3.223),
ki_NH4_min = c(all = 2.714),
ki_NH4_max = c(all = 10),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_VS_cattle2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.0446, m1 = 0.01, m2 = 1.697, m3 = 8.0, m4 = 8, m5 = 8, sr1 = 8.95),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 0.001, m2 = 0.001, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 1.528),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_cattle2.0 <- list(grps = c('m0', 'm1', 'm2','sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(m0 = 0.06, m1 = 0.06, m2 = 0.06, sr1 = 0.06),
xa_init = c(all = 0.06),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 2 * 0.962509436301619, m1 = 2.5* 0.962509436301619, m2 = 3* 0.962509436301619 , m3 = 4* 0.962509436301619, m4 = 8* 0.962509436301619, m5 = 8* 0.962509436301619, sr1 = 8.95* 0.962509436301619),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, m4 = 43.75, m5 = 55, sr1 = 43.75),
T_min = c(m0 = 0, m1 = 10, m2 = 10, m3 = 15, m4 = 26.25, m5 = 30, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, m4 = 51.25, m5 = 60, sr1 = 51.25),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.465),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.10623, sr1 = -0.1495),
ki_H2S_int = c(default = 1.02, sr1 = 1.42),
ki_H2S_min = c(default = 0.08),
IC50_low = c(default = 0.20854, sr1 = 0.2772),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
grp_pars_VS_digestate2.0 <- list(grps = c('m0', 'm1', 'm2', 'm3', 'sr1'),
yield = c(default = 0.05, sr1 = 0.065),
xa_fresh = c(all = 0.3),
xa_init = c(all = 0.3),
decay_rate = c(all = 0.02),
ks_coefficient = c(default = 1.153337, sr1 = 0.461335),
qhat_opt = c(m0 = 0.11, m1 = 1.92, m2 = 1.46, m3 = 3.4, sr1 = 9),
T_opt = c(m0 = 18, m1 = 18, m2 = 28, m3 = 36, sr1 = 44),
T_min = c(m0 = 0, m1 = 11.36, m2 = 11.36, m3 = 15, sr1 = 0),
T_max = c(m0 = 25, m1 = 25, m2 = 38, m3 = 45, sr1 = 51),
ki_NH3_min = c(all = 0.015),
ki_NH3_max = c(all = 0.194),
ki_NH4_min = c(all = 2.7),
ki_NH4_max = c(all = 7),
ki_H2S_slope = c(default = -0.11, sr1 = -0.15),
ki_H2S_int = c(default = 1.0, sr1 = 1.4),
ki_H2S_min = c(default = 0.080),
IC50_low = c(default = 0.21, sr1 = 0.28),
ki_HAC = c(default = 0.31),
pH_UL = c(default = 8.0),
pH_LL = c(default = 6.5, sr1 = 5.5))
man_pars_pig2.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 3.17, sulfate = 0.01, TAN = 0.0, starch = 5.25,
VFA = 1.7, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 27.6, CPs = 21.1 * 0.55, CPf = 21.1 * 0.45, RFd = 25.4, iNDF = 11.3, VSd = 0,
VSd_A = 55, VSnd_A = 23.5, ash = 15), pH = 7, dens = 1000)
man_pars_cattle2.0 <- list(conc_fresh = list(sulfide = 0.01, urea = 2.116, sulfate = 0.01, TAN = 0.0, starch = 1.4864,
VFA = 2.54, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 16.04, CPs = 30*0.55, CPf = 30*0.45, RFd = 44.4, iNDF = 21.465, VSd = 0,
VSd_A = 32.86, VSnd_A = 45.4, ash = 15), pH = 7, dens = 1000)
man_pars_digestate2.0 <- list(conc_fresh = list(sulfide = 0, urea = 0, sulfate = 0, TAN = 3, starch = 0.29,
VFA = 0.5, xa_aer = 0, xa_bac = 0, xa_dead = 0, Cfat = 3.18, CPs = 5.95, CPf = 0, RFd = 8.8, iNDF = 21.47, VSd = 0,
VSd_A = 12.6, VSnd_A = 18.13, ash = 15), pH = 8, dens = 1000)
man_pars_VS_pig2.0 <- man_pars_pig2.0
man_pars_VS_cattle2.0 <- man_pars_cattle2.0
man_pars_VS_digestate2.0 <- man_pars_digestate2.0
# pig
man_pars_VS_pig2.0$conc_fresh['VSd'] <- (man_pars_VS_pig2.0$conc_fresh[['starch']] + man_pars_VS_pig2.0$conc_fresh[['xa_dead']] +
man_pars_VS_pig2.0$conc_fresh[['Cfat']] + man_pars_VS_pig2.0$conc_fresh[['RFd']] + man_pars_VS_pig2.0$conc_fresh[['CPs']] +
man_pars_VS_pig2.0$conc_fresh[['CPf']] +
man_pars_VS_pig2.0$conc_fresh[['iNDF']]) * 0.7
for (i in c('starch', 'xa_dead','Cfat','RFd','CPs', 'CPf', 'iNDF')){
man_pars_VS_pig2.0$conc_fresh[i] <- 0
}
# cattle
man_pars_VS_cattle2.0$conc_fresh['VSd'] <- (man_pars_VS_cattle2.0$conc_fresh[['starch']] + man_pars_VS_cattle2.0$conc_fresh[['xa_dead']] +
man_pars_VS_cattle2.0$conc_fresh[['Cfat']] + man_pars_VS_cattle2.0$conc_fresh[['RFd']] + man_pars_VS_cattle2.0$conc_fresh[['CPs']] +
man_pars_VS_cattle2.0$conc_fresh[['CPf']] +
man_pars_VS_cattle2.0$conc_fresh[['iNDF']]) * 0.42
for (i in c('starch', 'xa_dead','Cfat','RFd','CPs', 'CPf', 'iNDF')){
man_pars_VS_cattle2.0$conc_fresh[i] <- 0
}
# digestate
man_pars_VS_digestate2.0$conc_fresh['VSd'] <- (man_pars_VS_digestate2.0$conc_fresh[['starch']] + man_pars_VS_digestate2.0$conc_fresh[['xa_dead']] +
man_pars_VS_digestate2.0$conc_fresh[['Cfat']] + man_pars_VS_digestate2.0$conc_fresh[['RFd']] + man_pars_VS_digestate2.0$conc_fresh[['CPs']] +
man_pars_VS_digestate2.0$conc_fresh[['CPf']])
for (i in c('starch', 'xa_dead','Cfat','RFd','CPs', 'CPf', 'iNDF')){
man_pars_VS_digestate2.0$conc_fresh[i] <- 0
}
wthr_pars2.0 <- list(temp_air_C = 20, RH = 90, rain = 1.9, pres_kpa = 101, rs = 10)
chem_pars2.0 <- list(COD_conv = c(CH4 = 1/0.2507, xa = 1/0.7069561, RFd = 1/0.8444792, iNDF = 1/0.8444792, starch = 1/0.8444792,
Cfat = 1/0.3117844, CP = 1/0.6541602, VFA = 1/0.9383125, S = 1/0.5015, VS = 1/0.69, CO2_aer = 1/0.436, CO2_sr = 1/1.2, CO2_ureo = 1/1.57,
CP_N = 1/0.1014, C_xa = 1/0.3753125, C_RFd = 1/0.376, C_iNDF = 1/0.358, N_xa = 1/0.08754375,
C_starch = 1/0.377, C_Cfat = 1/0.265, C_CP = 1/0.359 , C_VFA = 1/0.374, C_VSd = 1/0.344, C_N_urea = 1/0.429,
frac_CP_xa = 0.835, C_xa_aer = 1/0.3753125, C_xa_bac = 1/0.3753125, C_xa_dead = 1/0.3753125))
arrh_pars_pig2.0 <- list(lnA = c(VSd_A = 28.717),
E_CH4 = c(VSd_A = 78479.55),
A = c(xa_dead= 3.61383 * 10^12, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 1.499476 * 10^12, VSd = 3.61383 * 10^12, urea = 4.38*10^15),
E = c(xa_dead= 81557, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 81052, VSd = 81557, urea = 81559),
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 0.26, notVSd = 0.55, CP = 6.84),
kl = c(NH3 = 375, NH3_floor = 0.36*375, H2S = 0.02),
scale_EF_NH3 = 0.0000048)
arrh_pars_cattle2.0 <- list(lnA = c(VSd_A = 31.2),
E_CH4 = c(VSd_A = 81000),
A = c(xa_dead= 22497134.8, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 2.567944 * 10^8, VSd = 22497134.8, urea = 4.38*10^15),
E = c(xa_dead= 55609, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 57867, VSd = 55609, urea = 81559), # CP is for GRA treatment in MILK project
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 2.4156, notVSd = 0.294, CP = 0.25),
kl = c(NH3 = 1000, NH3_floor = 0.36*1000, H2S = 0.02),
scale_EF_NH3 = 0.0000048)
arrh_pars_digestate2.0 <- list(lnA = c(VSd_A = 31.2),
E_CH4 = c(VSd_A = 81000),
A = c(xa_dead= 22497134.8, starch = 5.86*10^18, Cfat = 0, CPs = 1.763612 * 10^12, CPf = 4.10669 * 10^11, RFd = 2.567944 * 10^8, VSd = 22497134.8, urea = 4.38*10^15),
E = c(xa_dead= 55609, starch = 109400, Cfat = 0, CPs = 87515.5450, CPf = 69361.3, RFd = 57867, VSd = 55609, urea = 81559),
R = 8.314,
VS_CH4 = 6.67,
scale_alpha_opt = list(VSd = 2.95, notVSd = 1, CP = 1),
kl = c(NH3 = 64*8, NH3_floor = 36*8, H2S = 0.02),
scale_EF_NH3 = 0.0000048)
pig_pars2.0 <- c(grp_pars_pig2.0, arrh_pars_pig2.0, man_pars_pig2.0)
cattle_pars2.0 <- c(grp_pars_cattle2.0, arrh_pars_cattle2.0, man_pars_cattle2.0)
pig_parsVS2.0 <- c(grp_pars_VS_pig2.0, arrh_pars_pig2.0, man_pars_VS_pig2.0)
cattle_parsVS2.0 <- c(grp_pars_VS_cattle2.0, arrh_pars_cattle2.0, man_pars_VS_cattle2.0)
digestate_parsVS2.0 <- c(grp_pars_VS_digestate2.0, arrh_pars_digestate2.0, man_pars_VS_digestate2.0)
save(grp_pars_pig2.0, file = '../data/grp_pars_pig2.0.rda')
save(grp_pars_cattle2.0, file = '../data/grp_pars_cattle2.0.rda')
save(grp_pars_VS_pig2.0, file = '../data/grp_pars_VS_pig2.0.rda')
save(grp_pars_VS_cattle2.0, file = '../data/grp_pars_VS_cattle2.0.rda')
save(grp_pars_VS_digestate2.0, file = '../data/grp_pars_VS_digestate2.0.rda')
save(arrh_pars_pig2.0, file = '../data/arrh_pars_pig2.0.rda')
save(arrh_pars_cattle2.0, file = '../data/arrh_pars_cattle2.0.rda')
save(arrh_pars_digestate2.0, file = '../data/arrh_pars_digestate2.0.rda')
save(mic_pars2.0, file = '../data/mic_pars2.0.rda')
save(man_pars_pig2.0, file = '../data/man_pars_pig2.0.rda')
save(man_pars_VS_pig2.0, file = '../data/man_pars_VS_pig2.0.rda')
save(man_pars_cattle2.0, file = '../data/man_pars_cattle2.0.rda')
save(man_pars_VS_cattle2.0, file = '../data/man_pars_VS_cattle2.0.rda')
save(man_pars_VS_digestate2.0, file = '../data/man_pars_VS_digestate2.0.rda')
save(wthr_pars2.0, file = '../data/wthr_pars2.0.rda')
save(chem_pars2.0, file = '../data/chem_pars2.0.rda')
save(pig_pars2.0, file = '../data/pig_pars2.0.rda')
save(pig_parsVS2.0, file = '../data/pig_parsVS2.0.rda')
save(cattle_pars2.0, file = '../data/cattle_pars2.0.rda')
save(cattle_parsVS2.0, file = '../data/cattle_parsVS2.0.rda')
save(digestate_parsVS2.0, file = '../data/digestate_parsVS2.0.rda')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.