-
Notifications
You must be signed in to change notification settings - Fork 2
/
input_parms.R
176 lines (137 loc) · 4.16 KB
/
input_parms.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
####################################################
################### CONSTANTS ######################
####################################################
Tref <- 20
K <- 8.617330350E-5
####################################################
############### DEFAULT PARAMETERS #################
####################################################
# --- phytoplankton ---
median_diatom_vol_um3 <- 1.16E5
median_sp_mass_ugC <- 1.4E-4
# Kremer et al. 2017
Ea_pp <- 0.42 #0.42
Ea <- 0.32 # 0.317
PCref_beta <- -0.14
PCref_beta_pp_mp1 <- 0.05
PCref_beta_diat <- -0.14
PCref_const_pp <- 17
PCref_const_mp1 <- 13.3
PCref_const_diaz <- 11
PCref_const_mp <- 11.5
PCref_const_diat <- 12.4
# Edwards et al. 2015
# alphaPI
alphaPI_beta <- -0.15 # range (-0.17, -0.09)
alphaPI_const <- 10^(-0.25) # range (-1.5, -1.22)
alphaPI_diat_beta <- -0.12
alphaPI_diat_const <- 10^(-0.17)
#alphaPI_pp_const <- 10^(-0.6)
# thetaN_max
# derive a relationship based on alpha, Geider et al. 1997
# maximum is 8 mg Chla / mmol N (graph from Edwards et al. 2015)
# minimum is 0.8 mg Chla / mmol N
#thetaC_alpha_beta <- -0.4
#thetaC_alpha_const <- 0.47
#thetaC_alpha_beta_diat <- -0.5
#thetaC_alpha_const_diat <- 0.55
thetaC_beta_lg <- 0.026
thetaC_const_lg <- 0.285
thetaC_pp <- 0.12 # Pro ranges from 0.008-0.011 mg chl-a/mg C
# nutrients
# units of micromol N or P per liter, equivalent to mmol N or P per cubic meter
# Edwards et al. 2012
#VN_beta <- 0.82
#VN_const <- 10^(-8.1)
#VP_beta <- 1.0
#VP_const <- 10^(-9.1)
nut_beta_generic <- 0.3 # these were 0.3 before accoring to edwards et al. 2013
nut_beta_diatoms <- 0.3 # 0.3
diatom_nut_lim_factor = 1
diaz_Fe_lim_factor = 1.5 # N-fixation machinery?
kNO3_beta <- nut_beta_generic
kNO3_const <- 10^(-0.65)
kNO3_beta_diat <- nut_beta_diatoms
kNO3_const_diat <- kNO3_const * diatom_nut_lim_factor
kNO3_diaz = 2
kNH4_diaz = 0.2
kPO4_beta <- nut_beta_generic
kPO4_const <- 10^(-2.2)
kPO4_beta_diat <- nut_beta_diatoms
kPO4_const_diat <- kPO4_const * diatom_nut_lim_factor
kFe_const = 0.6e-5
kFe_beta = nut_beta_generic
kFe_const_diat = kFe_const * diatom_nut_lim_factor
kFe_beta_diat = nut_beta_diatoms
Qp_beta = 0.1
Qp_const = 0.022
Qp_fixed_diaz = 1/300
Qp_fixed_pp = 0.004651163
#Qp_fixed = 1/117
gQfe_min = 2.5E-6
gQfe_0 = 42E-6
gQfe_0_diaz = 60E-6
kSiO3_const <- 0.035
kNH4_const <- 0.02
kNH4_const_diat <- kNH4_const * diatom_nut_lim_factor
kDOP_marbl <- 0.5
kDOP_const <- 0.08
kDOP_const_diat <- kDOP_const * diatom_nut_lim_factor
# mortality & aggregation
#mort_beta <- -0.1
#mort_const <- 0.06
mort_PCref_factor <- 0.03
mort_PCref_diat_factor <-0.02
mort2_beta <- 0
mort2_const <- 0.035
## attmepting to do mortality for pp to be 0, and increase their mort per day
agg_min_beta <- 0
agg_min_const <- 0.01
agg_max_beta <- 0
agg_max_const <- 0.5
diat_agg_rate_min_multiplier = 1
loss_poc_beta <- 0 #0.075
loss_poc_const <- 0 #0.02 / (median_sp_mass_ugC ^ loss_poc_beta)
phyto_PCref_modification = 2
# --- zooplankton ---
zoo_Ea = 0.55
# grazing parameters
# Hansen et al. 1997 converted to ESD_mm relationship
umax_beta = -0.25 # -0.21 +/- 0.02
umax_const = 4.5 # log a: -0.52+/- 0.29
km_beta <- 0#-0.03 # =-0.03 +/- 0.03
km_const <- 1.1 # log a: 0.35 +/- 0.58
opt_pred_prey_ratio_const = 12.5 # target 8:1 for ciliates, 18:1 for mesozooplankton
opt_pred_prey_ratio_beta = 0.15
#opt_pred_prey_sd_const = 9.5
#opt_pred_prey_sd_beta = 0.095
# assimilation and egestion parameters
AE = 0.65
graze_zoo_micro <- 0.3
graze_zoo_meso <- 0.3
graze_doc_frac <- 0.25
graze_poc_beta <- 0.3
graze_poc_const <- 0.2
graze_poc_diatom_scaling <- 1.2
# loss parameters
z_mort_beta <- -0.25 # McGurk et al. 1987 MEPS
z_mort_const <- 0.12 # it was 0.02 initially.
z_mort2_beta <- 0.2
z_mort2_const <- 0.2
lg_zoo_mort2_scaling = 4
zoo_loss_thres <- 0.075
# egestion
zoo_detr_const = 0.1
zoo_detr_beta = 0.1
zoo_detr_diatom_scaling = 1
# grazing scalings
diat_grazing_scaling <- 0.65
med_diat_grazing_scaling <-1
lg_diat_grazing_scaling <-0.75
calcifiers_grazing_scaling <- 1.5
zoo_grazing_scaling <- 0.45
microzoo_grazing_scaling = 0.85
microZ_diat_grazing = 0.45 # fraction relative to the feeding kernel-determined grazing rate
#mesoZ_diat_grazing = 2.3
microZ_pp_grazing_fixed = 0.35
#mesoZ_d2_grazing = 0.7