def construct_V0(
cpa :UnEstimatedParameters,
epa :EstimatedParameters,
) -> np.ndarray:
"""Construct the initial values for the forward simulation
from constant and evaluated parameters
param: cpa : constant parameeters
param: epa : estimated parameters
"""
# to make sure that we are in the right order we use the
# StateVariables namedtuple
X_0 = StateVariables(
C_leaf = epa.C_leaf_0,
C_wood = cpa.C_Veg_0 - epa.C_leaf_0 - cpa.C_root_0,
C_root=cpa.C_root_0,
C_abvstructural_lit = epa.C_abvstrlit_0_frac*cpa.C_litter_0,
C_abvmetabolic_lit = epa.C_abvmetlit_0_frac*cpa.C_litter_0,
C_belowstructual__lit = epa.C_blwstrlit_0_frac*cpa.C_litter_0,
C_belowmetabolic_lit = cpa.C_litter_0 - epa.C_abvstrlit_0_frac*cpa.C_litter_0 - epa.C_abvmetlit_0_frac*cpa.C_litter_0 - epa.C_blwstrlit_0_frac*cpa.C_litter_0,
C_surface_microbe = epa.C_surfacemic_0_frac*cpa.C_soil_0,
C_soil_microbe = epa.C_soilmic_0_frac*cpa.C_soil_0,
C_slow_soil = epa.C_slow_0_frac*cpa.C_soil_0,
C_passive_soil = cpa.C_soil_0 - epa.C_soilmic_0_frac*cpa.C_soil_0 - epa.C_slow_0_frac*cpa.C_soil_0 - epa.C_surfacemic_0_frac*cpa.C_soil_0
)
# add the respiration start value to the tuple
cpa = UnEstimatedParameters(
C_Veg_0 = cveg[0],
C_root_0 = croot[0],
C_litter_0 = clitter[0],
npp = npp,
number_of_months = tot_len,
C_soil_0 = csoil[0],
rh_0=rh[0]
)
V_0 = (*X_0,cpa.rh_0)
return np.array(V_0).reshape(11,1)
def main(client):
from model_specific_helpers import (get_example_site_vars,
make_param_filter_func,
make_weighted_cost_func,
make_param2res, make_param2res_2,
UnEstimatedParameters,
EstimatedParameters, Observables)
from general_helpers import (make_uniform_proposer,
make_multivariate_normal_proposer, mcmc,
make_feng_cost_func, plot_solutions)
# fixme:
# put the (relative or asolute) location of your data into a small file called 'config.json' and
# in my case the content looks like this:
# {"dataPath": "/home/data/yuanyuan"}
# DO NOT add the file to the repository. It is not only model- but also site specific.
# So you are likely to have one for every model on every computer
# you run this code on.
# (this example uses an absolute path starting with a '/'
with Path('config.json').open(mode='r') as f:
conf_dict = json.load(f)
dataPath = Path(conf_dict['dataPath'])
# fixme:
# Note that the function is imported from
# model_specific_helpers which means that you have to provide
# your version of this fuction which will most likely return different
# variables
npp, rh, clitter, csoil, cveg, cleaf, croot, cwood = get_example_site_vars(
dataPath)
# combine them to a single array which we will later use as input to the costfunction
#nyears=140
nyears = 10
tot_len = 12 * nyears
obs = np.stack([cleaf, croot, cwood, clitter, csoil, rh],
axis=1)[0:tot_len, :]
# leaf, root , wood, metabolic, structural, CWD, microbial, slow, passive
# fixme
c_min = np.array([
0.09, 0.09, 0.09, 0.01, 0.01, 1 / (2 * 365), 1 / (365 * 10),
1 / (60 * 365), 0.1 / (0.1 * 365), 0.06 / (0.137 * 365),
0.06 / (5 * 365), 0.06 / (222.22 * 365), clitter[0] / 100,
clitter[0] / 100, csoil[0] / 100, csoil[0] / 2
])
c_max = np.array([
1, 1, 0.21, 1, 1, 1 / (0.3 * 365), 1 / (0.8 * 365), 1 / 365,
1 / (365 * 0.1), 0.6 / (365 * 0.137), 0.6 / (365 * 5),
0.6 / (222.22 * 365), clitter[0], clitter[0], csoil[0] / 3, csoil[0]
])
# fixme
# this function is model specific: It discards parameter proposals
# where beta1 and beta2 add up to more than 0.99
isQualified = make_param_filter_func(c_max, c_min)
uniform_prop = make_uniform_proposer(
c_min,
c_max,
D=100.0, # this value
filter_func=isQualified)
cpa = UnEstimatedParameters(C_leaf_0=cleaf[0],
C_root_0=croot[0],
C_wood_0=cwood[0],
clitter_0=clitter[0],
csoil_0=csoil[0],
rh_0=rh[0],
npp=npp,
number_of_months=tot_len,
clay=0.2028,
silt=0.2808,
lig_wood=0.4,
f_wood2CWD=1,
f_metlit2mic=0.45)
param2res = make_param2res(cpa)
epa_0 = EstimatedParameters(
beta_leaf=0.15,
beta_root=0.2,
lig_leaf=0.15,
f_leaf2metlit=0.28,
f_root2metlit=0.6,
k_leaf=1 / 365,
k_root=1 / (365 * 5),
k_wood=1 / (365 * 40),
k_metlit=0.5 / (365 * 0.1),
k_mic=0.3 / (365 * 0.137),
k_slowsom=0.3 / (365 * 5),
k_passsom=0.3 / (222.22 * 365),
C_metlit_0=0.05,
CWD_0=0.1,
C_mic_0=1,
C_passom_0=5,
)
# it is sensible to use the same costfunction for both the demo and
# the formal run so we define it here for both
#costfunction=make_feng_cost_func(obs)
costfunction = make_weighted_cost_func(obs)
# Look for data from the demo run and use it to compute the covariance matrix if necessarry
demo_aa_path = dataPath.joinpath('cable_demo_da_aa.csv')
demo_aa_j_path = dataPath.joinpath('cable_demo_da_j_aa.csv')
if not demo_aa_path.exists():
print("Did not find demo run results. Will perform demo run")
C_demo, J_demo = mcmc(initial_parameters=epa_0,
proposer=uniform_prop,
param2res=param2res,
costfunction=costfunction,
nsimu=10000)
# save the parameters and costfunctionvalues for postprocessing
pd.DataFrame(C_demo).to_csv(demo_aa_path, sep=',')
pd.DataFrame(J_demo).to_csv(demo_aa_j_path, sep=',')
else:
print("""Found {p} from a previous demo run.
If you also want to recreate the demo output then move the file!
""".format(p=demo_aa_path))
C_demo = pd.read_csv(demo_aa_path).to_numpy()
J_demo = pd.read_csv(demo_aa_j_path).to_numpy()
# build a new proposer based on a multivariate_normal distribution using the
# estimated covariance of the previous run if available first we check how many
# accepted parameters we got
# and then use part of them to compute a covariance matrix for the
# formal run
covv = np.cov(C_demo[:, int(C_demo.shape[1] / 10):])
normal_prop = make_multivariate_normal_proposer(covv=covv,
filter_func=isQualified)
# Look for data from the formal run and use it for postprocessing
#formal_aa_path = dataPath.joinpath('cable_formal_da_aa.csv')
#formal_aa_j_path = dataPath.joinpath('cable_formal_da_j_aa.csv')
#if not formal_aa_path.exists():
# print("Did not find results. Will perform formal run")
# C_formal, J_formal = mcmc(
# initial_parameters=epa_0,
# proposer=normal_prop,
# param2res=param2res,
# costfunction=costfunction,
# nsimu=100
# )
# pd.DataFrame(C_formal).to_csv(formal_aa_path,sep=',')
# pd.DataFrame(J_formal).to_csv(formal_aa_j_path,sep=',')
#else:
# print("""Found {p} from a previous demo run.
# If you also want recreate the output then move the file!
# """.format(p = formal_aa_path))
#C_formal = pd.read_csv(formal_aa_path).to_numpy()
#J_formal = pd.read_csv(formal_aa_j_path).to_numpy()
#define parallel mcmc wrapper
def parallel_mcmc(_):
return (mcmc(initial_parameters=epa_0,
proposer=normal_prop,
param2res=param2res,
costfunction=costfunction,
nsimu=20000))
print("before map")
print("Client: ", client)
#run 10 chains
[[c_form1, j_form1], [c_form2, j_form2], [c_form3, j_form3],
[c_form4, j_form4], [c_form5, j_form5], [c_form6, j_form6],
[c_form7, j_form7], [c_form8, j_form8], [c_form9, j_form9],
[c_form10,
j_form10]] = client.gather(client.map(parallel_mcmc, range(0, 10)))
print("after map")
print("Client: ", client)
#print chain5 output as test
formal_c_path = dataPath.joinpath('chain5_pmcmc_c.csv')
formal_j_path = dataPath.joinpath('chain5_pmcmc_j.csv')
pd.DataFrame(c_form5).to_csv(formal_c_path, sep=',')
pd.DataFrame(j_form5).to_csv(formal_j_path, sep=',')
#use output csv file for post processing
C_formal = pd.read_csv(formal_c_path).to_numpy()
J_formal = pd.read_csv(formal_j_path).to_numpy()
# POSTPROCESSING
#
# The 'solution' of the inverse problem is actually the (joint) posterior
# probability distribution of the parameters, which we approximate by the
# histogram consisting of the mcmc generated samples.
# This joint distribution contains as much information as all its (infinitly
# many) projections to curves through the parameter space combined.
# Unfortunately, for this very reason, a joint distribution of more than two
# parameters is very difficult to visualize in its entirity.
# to do:
# a) make a movie of color coded samples of the a priori distribution of the parameters.
# b) -"- of the a posteriory distribution -'-
# Therefore the following visualizations have to be considered with caution:
# 1.
# The (usual) histograms of the values of a SINGLE parameters can be very
# misleading since e.g. we can not see that certain parameter combination only
# occure together. In fact this decomposition is only appropriate for
# INDEPENDENT distributions of parameters in which case the joint distribution
# would be the product of the distributions of the single parameters. This is
# however not even to be expected if our prior probability distribution can be
# decomposed in this way. (Due to the fact that the Metropolis Hastings Alg. does not
# produce independent samples )
df = pd.DataFrame({
name: C_formal[:, i]
for i, name in enumerate(EstimatedParameters._fields)
})
subplots = df.hist()
fig = subplots[0, 0].figure
fig.set_figwidth(15)
fig.set_figheight(15)
fig.savefig('histograms.pdf')
# As the next best thing we can create a matrix of plots containing all
# projections to possible parameter tuples
# (like the pairs plot in the R package FME) but 16x16 plots are too much for one page..
# However the plot shows that we are dealing with a lot of colinearity for this parameter set
subplots = pd.plotting.scatter_matrix(df)
fig = subplots[0, 0].figure
fig.set_figwidth(15)
fig.set_figheight(15)
fig.savefig('scatter_matrix.pdf')
# 2.
# another way to get an idea of the quality of the parameter estimation is
# to plot trajectories.
# A possible aggregation of this histogram to a singe parameter
# vector is the mean which is an estimator of the expected value of the
# desired distribution.
sol_mean = param2res(np.mean(C_formal, axis=1))
fig = plt.figure()
plot_solutions(fig,
times=range(sol_mean.shape[0]),
var_names=Observables._fields,
tup=(sol_mean, obs),
names=('mean', 'obs'))
fig.savefig('solutions.pdf')
def setUp(self):
self.dataPath = dataPath
####################################################
# The estimated parameters include start values
# for some of the pools
epa0 = EstimatedParameters(
beta_leaf=0.15,
beta_root=0.2,
lig_leaf=0.15,
f_leaf2metlit=0.28,
f_root2metlit=0.6,
k_leaf=1 / 365,
k_root=1 / (365 * 5),
k_wood=1 / (365 * 40),
k_metlit=0.5 / (365 * 0.1),
k_mic=0.3 / (365 * 0.137),
k_slowsom=0.3 / (365 * 5),
k_passsom=0.3 / (222.22 * 365),
C_metlit_0=0.05,
C_CWD_0=0.1,
C_mic_0=1,
C_passom_0=5,
)
npp, rh, clitter, csoil, cveg, cleaf, croot, cwood = get_example_site_vars(
self.dataPath)
self.x_init = StateVariables(C_leaf=cleaf[0],
C_root=croot[0],
C_wood=cwood[0],
C_metlit=epa0[12],
C_stlit=epa0[13],
C_CWD=clitter[0] - epa0[12] - epa0[13],
C_mic=epa0[14],
C_slowsom=csoil[0] - epa0[14] - epa0[15],
C_passsom=epa0[15])
cpa = UnEstimatedParameters(
C_leaf_0=cleaf[0],
C_root_0=croot[0],
C_wood_0=cwood[0],
clitter_0=clitter[0],
csoil_0=csoil[0],
rh_0=rh[0],
clay=0.2028,
silt=0.2808,
lig_wood=0.4,
f_wood2CWD=1,
f_metlit2mic=0.45,
npp=npp, #array!!!
number_of_months=10)
pa = Parameters.from_EstimatedParametersAndUnEstimatedParameters(
epa0, cpa)
mpa = ModelParameters(**{
k: v
for k, v in pa._asdict().items() if k in ModelParameters._fields
})
self.npp = npp
self.epa0 = epa0
self.cpa = cpa
self.pa = pa
self.mpa = mpa
def setUp(self):
self.dataPath = dataPath
npp, rh, ra, csoil, cveg = get_example_site_vars(
Path(conf_dict['dataPath']))
print(list(map(lambda a: a.shape, (npp, rh, ra, csoil, cveg))))
#nyears = 320
nyears = 2
obs_tup = Observables(c_veg=cveg,
c_soil=csoil,
a_respiration=monthly_to_yearly(ra),
h_respiration=monthly_to_yearly(rh))
self.obs = np.stack(obs_tup, axis=1)[0:nyears, :]
self.epa0 = EstimatedParameters(
beta_leaf=0.15, # 0
beta_root=0.2, # 1
k_leaf=1 / 365, # 2
k_root=1 / (365 * 5), # 3
k_wood=1 / (365 * 40), # 4
k_cwd=1 / (365 * 5), # 5
k_samet=0.5 / (365 * 0.1), # 6
k_sastr=0.5 / (365 * 0.1), # 7
k_samic=0.3 / (365 * 0.137), # 8
k_slmet=0.3 / (365), # 9
k_slstr=0.3 / (365), # 10
k_slmic=0.3 / (365), # 11
k_slow=0.3 / (365 * 5), # 12
k_arm=0.3 / (222 * 365), # 13
f_samet_leaf=0.3, # 14
f_slmet_root=0.3, # 15
f_samic_cwd=0.3, # 16
C_leaf_0=cveg[0] / 5, # 17
C_root_0=cveg[0] / 5, # 18
C_cwd_0=cveg[0] / 50, # 19
C_samet_0=cveg[0] / 300, # 20
C_sastr_0=cveg[0] / 300, # 21
C_samic_0=cveg[0] / 500, # 22
C_slmet_0=csoil[0] / 10, # 23
C_slstr_0=csoil[0] / 10, # 24
C_slmic_0=csoil[0] / 10, # 25
C_slow_0=csoil[0] / 10 # 26
)
self.cpa = UnEstimatedParameters(C_soil_0=csoil[0],
C_veg_0=cveg[0],
rh_0=rh[0],
ra_0=ra[0],
npp=npp,
clay=0.2028,
silt=0.2808,
nyears=nyears)
self.pa = Parameters.from_EstimatedParametersAndUnEstimatedParameters(
self.epa0, self.cpa)
self.mpa = ModelParameters(
**{
k: v
for k, v in self.pa._asdict().items()
if k in ModelParameters._fields
})
self.epa0 = self.epa0
cpa = UnEstimatedParameters(
C_wood1_0=0.76, #C_wood1[0],
C_wood2_0=0.67, #C_wood2[0],
C_wood3_0=0.34, #C_wood3[0],
C_wood4_0=0.42, #C_wood4[0],
C_leaf_0=C_leaf[0],
C_root_0=C_root[0],
C_fruit_0=0.056, #C_fruit[0],
C_litter1_0=0.005, #C_litter1[0],
C_litter2_0=0.009, #C_litter2[0],
C_litter3_0=0.035, #C_litter3[0],
C_litter4_0=0.017, #C_litter4[0],
C_litter5_0=0.05, #C_litter5[0],
C_litter6_0=0.065, #C_litter6[0],
C_surface_som_0=0.0044, #C_surface_som[0],
C_fast_som_0=0.012, #C_fast_som[0],
C_slow_som_0=4, #C_slow_som[0],
C_pass_som_0=0.0125, #C_pass_som[0],
rh_0=rh[0],
ra_0=ra[0],
npp=npp,
number_of_months=tot_len,
mrso=mrso,
tsl=tsl,
# C_wood_0=C_wood[0],
# C_leaf_0=C_leaf[0],
# C_root_0=C_root[0],
# C_litter_0=C_litter[0],
# C_soil_0=C_soil[0],
# rh_0=rh[0],
# ra_0=ra[0],
# npp=npp,
# number_of_months=tot_len,
# mrso=mrso,
# tsl=tsl,
beta_fruit=0.1)
# this function is model specific: It discards parameter proposals
# where beta1 and beta2 add up to more than 0.99
isQualified = make_param_filter_func(c_max, c_min)
uniform_prop = make_uniform_proposer(
c_min,
c_max,
D=100.0, # this value
filter_func=isQualified)
cpa = UnEstimatedParameters(C_leaf_0=cleaf[0],
C_root_0=croot[0],
C_wood_0=cwood[0],
clitter_0=clitter[0],
csoil_0=csoil[0],
rh_0=rh[0],
npp=npp,
number_of_months=tot_len,
clay=0.2028,
silt=0.2808,
lig_wood=0.4,
f_wood2CWD=1,
f_metlit2mic=0.45)
param2res = make_param2res(cpa)
epa_0 = EstimatedParameters(
beta_leaf=0.15,
beta_root=0.2,
lig_leaf=0.15,
f_leaf2metlit=0.28,
f_root2metlit=0.6,
k_leaf=1 / 365,
k_root=1 / (365 * 5),
C_root_0=cveg[0] / 5, # 18
C_cwd_0=csoil[0] / 50, # 19
C_samet_0=csoil[0] / 300, # 20
C_sastr_0=csoil[0] / 300, # 21
C_samic_0=csoil[0] / 500, # 22
C_slmet_0=csoil[0] / 10, # 23
C_slstr_0=csoil[0] / 10, # 24
C_slmic_0=csoil[0] / 10, # 25
C_slow_0=csoil[0] / 10 # 26
)
#set fixed parameters
cpa = UnEstimatedParameters(npp=npp,
rh_0=monthly_to_yearly(rh)[0],
ra_0=monthly_to_yearly(ra)[0],
C_veg_0=cveg[0],
C_soil_0=csoil[0],
clay=0.2028,
silt=0.2808,
nyears=320)
#make model function
param2res = make_param2res(cpa)
# set max/min parameters limits
c_min = np.array(epa0) * 0.001
c_max = np.array(epa0) * 1000
c_max[0] = 1
c_max[1] = 1
c_max[14] = 1
c_max[15] = 1
c_max[16] = 1
c_max[17] = cveg[0]
k_wood =(1/(60*365) + 1/365)/2, #7
k_root =(1/(10*365) + 1/(365*0.8))/2, #8
C_leaf_0 =((cveg[0]-croot[0])*0.1 + (cveg[0]-croot[0])*0.9)/2, #9
C_abvstrlit_0_frac = 0.3, #10
C_abvmetlit_0_frac = 0.3, #11
C_blwstrlit_0_frac = 0.3, #12
C_surfacemic_0_frac = 0.3, #13
C_soilmic_0_frac = 0.3, #14
C_slow_0_frac = 0.3 #15
)
cpa = UnEstimatedParameters(
C_Veg_0 = cveg[0],
C_root_0 = croot[0],
C_litter_0 = clitter[0],
npp = npp,
number_of_months = 120,
C_soil_0 = csoil[0],
rh_0=rh[0]
)
# -
StateVariables._fields
construct_V0(cpa,epa_0)
# +
def make_daily_iterator_sym(
def test_mcmc(self):
dataPath = self.dataPath
npp, rh, clitter, csoil, cveg, cleaf, croot, cwood = get_example_site_vars(
dataPath)
nyears = 10
tot_len = 12 * nyears
obs = np.stack([cleaf, croot, cwood, clitter, csoil, rh],
axis=1)[0:tot_len, :]
c_min = np.array([
0.09, 0.09, 0.09, 0.01, 0.01, 1 / (2 * 365), 1 / (365 * 10),
1 / (60 * 365), 0.1 / (0.1 * 365), 0.06 / (0.137 * 365),
0.06 / (5 * 365), 0.06 / (222.22 * 365), clitter[0] / 100,
clitter[0] / 100, csoil[0] / 100, csoil[0] / 2
])
c_max = np.array([
1, 1, 0.21, 1, 1, 1 / (0.3 * 365), 1 / (0.8 * 365), 1 / 365,
1 / (365 * 0.1), 0.6 / (365 * 0.137), 0.6 / (365 * 5),
0.6 / (222.22 * 365), clitter[0], clitter[0], csoil[0] / 3,
csoil[0]
])
isQualified = make_param_filter_func(c_max, c_min)
uniform_prop = make_uniform_proposer(
c_min,
c_max,
#D=10.0,
D=20.0,
filter_func=isQualified)
cpa = UnEstimatedParameters(C_leaf_0=cleaf[0],
C_root_0=croot[0],
C_wood_0=cwood[0],
clitter_0=clitter[0],
csoil_0=csoil[0],
rh_0=rh[0],
npp=npp,
number_of_months=tot_len,
clay=0.2028,
silt=0.2808,
lig_wood=0.4,
f_wood2CWD=1,
f_metlit2mic=0.45)
param2res = make_param2res(
cpa
) #pa=[beta1,beta2, lig_leaf, f41,f42, kleaf,kroot,kwood,kmet,kmic, kslow,kpass, cmet_init, cstr_init, cmic_init, cpassive_init ]
# pa= [0.15, 0.2,0.15,0.28, 0.6, 1/365, 1/(365*5), 1/(365*40), 0.5/(365*0.1), 0.3/(365*0.137), 0.3/(365*5), 0.3/(222.22*365), 0.05, 0.1, 1, 5]
epa_0 = EstimatedParameters(
beta_leaf=0.15,
beta_root=0.2,
lig_leaf=0.15,
f_leaf2metlit=0.28,
f_root2metlit=0.6,
k_leaf=1 / 365,
k_root=1 / (365 * 5),
k_wood=1 / (365 * 40),
k_metlit=0.5 / (365 * 0.1),
k_mic=0.3 / (365 * 0.137),
k_slowsom=0.3 / (365 * 5),
k_passsom=0.3 / (222.22 * 365),
C_metlit_0=0.05,
C_CWD_0=0.1,
C_mic_0=1,
C_passom_0=5,
)
# save the parameters and costfunctionvalues for postprocessing
demo_aa_path = Path('cable_demo_da_aa.csv')
demo_aa_j_path = Path('cable_demo_da_j_aa.csv')
if not demo_aa_path.exists():
print("did not find demo run results. Will perform demo run")
nsimu_demo = 200
C_demo, J_demo = mcmc(
initial_parameters=epa_0,
proposer=uniform_prop,
param2res=param2res,
#costfunction=make_weighted_cost_func(obs)
#costfunction=make_feng_cost_func(obs),
costfunction=make_jon_cost_func(obs),
nsimu=nsimu_demo)
# save the parameters and costfunctionvalues for postprocessing
pd.DataFrame(C_demo).to_csv(demo_aa_path, sep=',')
pd.DataFrame(J_demo).to_csv(demo_aa_j_path, sep=',')
else:
print("""Found {p} from a previous demo run.
If you also want to recreate the demo output move the file!
""".format(p=demo_aa_path))
C_demo = pd.read_csv(demo_aa_path).to_numpy()
J_demo = pd.read_csv(demo_aa_j_path).to_numpy()
# build a new proposer based on a multivariate_normal distribution using the estimated covariance of the previous run if available
# parameter values of the previous run
# first we check how many accepted parameters we got
n_accept = C_demo.shape[1]
# and then use part of them to compute a covariance matrix for the
# formal run
covv = np.cov(C_demo[:, int(n_accept / 10):])
normal_prop = make_multivariate_normal_proposer(
covv=covv, filter_func=isQualified)
C_formal, J_formal = mcmc(
initial_parameters=epa_0,
proposer=normal_prop,
param2res=param2res,
#costfunction=make_weighted_cost_func(obs)
#costfunction=make_feng_cost_func(obs),
costfunction=make_jon_cost_func(obs),
nsimu=200)
# save the parameters and costfunctionvalues for postprocessing
formal_aa_path = Path('cable_formal_da_aa.csv')
formal_aa_j_path = Path('cable_formal_da_j_aa.csv')
pd.DataFrame(C_formal).to_csv(formal_aa_path, sep=',')
pd.DataFrame(J_formal).to_csv(formal_aa_j_path, sep=',')
sol_mean = param2res(np.mean(C_formal, axis=1))
fig = plt.figure()
plot_solutions(fig,
times=range(sol_mean.shape[0]),
var_names=Observables._fields,
tup=(sol_mean, obs),
names=('mean', 'obs'))
fig.savefig('solutions.pdf')
csoil[0] / 3,
csoil[0] / 3,
csoil[0] / 5,
csoil[0],
csoil[0]
])
# fixme
# this function is model specific: It discards parameter proposals
# where beta1 and beta2 add up to more than 0.99
# change by zhoujian
cpa = UnEstimatedParameters(
cveg_0=cveg[0],
clitter_0=clitter[0],
csoil_0=csoil[0],
rh_0=rh[0],
npp=npp,
lig_frac=0.5,
number_of_months=tot_len,
)
isQualified = make_param_filter_func(c_max, c_min, cpa)
uniform_prop = make_uniform_proposer(
c_min,
c_max,
D=100.0, # this value
filter_func=isQualified)
# cpa = UnEstimatedParameters(
# cveg_0 = cveg[0],
# clitter_0=clitter[0],
# csoil_0=csoil[0],
def test_forward_simulation(self):
# compare stored monthly timesteps (although the computation happens in daily steps)
t0 = time()
npp, rh, ra, csoil, cveg = get_example_site_vars(
Path(conf_dict['dataPath']))
print("data_loaded after", time() - t0)
print(list(map(lambda a: a.shape, (npp, rh, ra, csoil, cveg))))
nyears = 320
#nyears = 2
obs_tup = Observables(c_veg=cveg,
c_soil=csoil,
a_respiration=monthly_to_yearly(ra),
h_respiration=monthly_to_yearly(rh))
obs = np.stack(obs_tup, axis=1)[0:nyears, :]
epa0 = EstimatedParameters(
beta_leaf=0.15, # 0
beta_root=0.2, # 1
k_leaf=1 / 365, # 2
k_root=1 / (365 * 5), # 3
k_wood=1 / (365 * 40), # 4
k_cwd=1 / (365 * 5), # 5
k_samet=0.5 / (365 * 0.1), # 6
k_sastr=0.5 / (365 * 0.1), # 7
k_samic=0.3 / (365 * 0.137), # 8
k_slmet=0.3 / (365), # 9
k_slstr=0.3 / (365), # 10
k_slmic=0.3 / (365), # 11
k_slow=0.3 / (365 * 5), # 12
k_arm=0.3 / (222 * 365), # 13
f_samet_leaf=0.3, # 14
f_slmet_root=0.3, # 15
f_samic_cwd=0.3, # 16
C_leaf_0=cveg[0] / 5, # 17
C_root_0=cveg[0] / 5, # 18
C_cwd_0=cveg[0] / 50, # 19
C_samet_0=cveg[0] / 300, # 20
C_sastr_0=cveg[0] / 300, # 21
C_samic_0=cveg[0] / 500, # 22
C_slmet_0=csoil[0] / 10, # 23
C_slstr_0=csoil[0] / 10, # 24
C_slmic_0=csoil[0] / 10, # 25
C_slow_0=csoil[0] / 10 # 26
)
cpa = UnEstimatedParameters(C_soil_0=csoil[0],
C_veg_0=cveg[0],
rh_0=rh[0],
ra_0=ra[0],
npp=npp,
clay=0.2028,
silt=0.2808,
nyears=320)
param2res = make_param2res(cpa)
t1 = time()
res = param2res(epa0)
print(time() - t1)
#from IPython import embed; embed()
# the times have to be computed in days
fig = plt.figure()
plot_solutions(fig,
times=np.array(range(nyears)),
var_names=Observables._fields,
tup=(res, obs),
names=["solution with initial params", "observations"])
fig.savefig('solutions.pdf')
def setUp(self):
self.dataPath = dataPath
####################################################
# The estimated parameters include start values
# for some of the pools
epa0 = EstimatedParameters(
beta_leaf=0.6, # 0 (parameters used in original code)
beta_wood=0.25, # 1
k_leaf_litter_2_soil_fast=0.41 / (365 * 3.3), # 2
k_leaf_litter_2_soil_slow=0.07 / (365 * 3.3), # 3
k_leaf_litter_2_soil_passive=0.02 / (365 * 3.3), # 4
k_wood_litter_2_soil_fast=0.30 / (365 * 11), # 5
k_wood_litter_2_soil_slow=0.12 / (365 * 11), # 6
k_wood_litter_2_soil_passive=0.08 / (365 * 11), # 7
k_root_litter_2_soil_fast=0.30 / (365 * 11), # 8
k_root_litter_2_soil_slow=0.14 / (365 * 11), # 9
k_root_litter_2_soil_passive=0.07 / (365 * 11), # 10
k_leaf_2_leaf_litter=1 / (60 * 2), # 11
k_wood_2_wood_litter=1 / (365 * 30), # 12
k_root_2_root_litter=1 / (365 * 22), # 13
k_leaf_litter_rh=1 - (.41 + .07 + .02) / (365 * 3.3), # 14
k_wood_litter_rh=1 - (.3 + .12 + .08) / (365 * 11), # 15
k_root_litter_rh=1 - (.3 + .14 + .07) / (365 * 11), # 16
k_soil_fast_rh=1 / (365 * 18), # 17
k_soil_slow_rh=1 / (365 * 100), # 18
k_soil_passive_rh=1 / (365 * 350), # 19
C_leaf_lit_0=0.3, # 20
T_0=2, # 21
E=4, # 22
KM=10 # 23
)
nyears = 150 # reduced time span for testing purposes
tot_len = 12 * nyears
npp, C_leaf, C_wood, C_root, C_litter_above, C_litter_below, C_fast_som, C_slow_som, C_pass_som, \
rh, F_veg2litter, F_litter2som, mrso, tsl = get_example_site_vars(dataPath)
cpa = UnEstimatedParameters(C_leaf_0=C_leaf[0],
C_wood_0=C_wood[0],
C_root_0=C_root[0],
C_litter_above_0=C_litter_above[0],
C_litter_below_0=C_litter_below[0],
C_soil_fast_0=C_fast_som[0],
C_soil_slow_0=C_slow_som[0],
C_soil_passive_0=C_pass_som[0],
rh_0=rh[0],
F_veg_lit_0=F_veg2litter[0],
F_lit_soil_0=F_litter2som[0],
npp=npp,
number_of_months=tot_len,
mrso=mrso,
tsl=tsl)
self.x_init = StateVariables(C_leaf=cpa.C_leaf_0,
C_wood=cpa.C_wood_0,
C_root=cpa.C_root_0,
C_leaf_litter=epa0.C_leaf_lit_0,
C_wood_litter=cpa.C_litter_above_0 -
epa0.C_leaf_lit_0,
C_root_litter=cpa.C_litter_below_0,
C_soil_fast=cpa.C_soil_fast_0,
C_soil_slow=cpa.C_soil_slow_0,
C_soil_passive=cpa.C_soil_passive_0)
pa = Parameters.from_EstimatedParametersAndUnEstimatedParameters(
epa0, cpa)
mpa = ModelParameters(**{
k: v
for k, v in pa._asdict().items() if k in ModelParameters._fields
})
self.npp = npp
self.epa0 = epa0
self.cpa = cpa
self.pa = pa
self.mpa = mpa