def run_sensitivity(site="fall creek", year="2016"):
elev, area = util.select_rows("tests/data/bathymetry.csv",
"elevation (m)",
"2d_area (m2)",
site=site)
bathymetry = InterpolatedFunction(elev, area)
k_results = []
w_results = []
ld_results = []
ad_results = []
for month in [4, 5, 6, 7, 8, 9]:
print(month)
values = get_values(site, year, month)
daphnia_density, daphnia_size, light_extinction = values
daphnia = get_daphnia_dist(site, month, year, daphnia_density,
daphnia_size)
temp_fn = get_temp_fn(site, month, year)
starting_mass = 10
for k in np.geomspace(0.01, 10, 15):
batch = Model(
starting_mass,
daphnia,
temp_fn,
bathymetry,
daylengths[month],
k,
day_light=39350,
allow_dvm=True,
allow_functional_response=False,
max_P=2.0,
)
results = batch.run(n_days=1)[0]
k_results.append({
"month": month,
"growth": results["growth"][0],
"k": k
})
for w in np.linspace(0.01, 200, 15):
batch = Model(
w,
daphnia,
temp_fn,
bathymetry,
daylengths[month],
k,
day_light=39350,
allow_dvm=True,
allow_functional_response=False,
max_P=2.0,
)
results = batch.run(n_days=1)[0]
w_results.append({
"month": month,
"growth": results["growth"][0],
"starting_mass": w,
})
for ld in np.geomspace(0.1, 4, 15):
daphnia = get_daphnia_dist(site, month, year, daphnia_density, ld)
batch = Model(
starting_mass,
daphnia,
temp_fn,
bathymetry,
daylengths[month],
light_extinction,
day_light=39350,
allow_dvm=True,
allow_functional_response=False,
max_P=2.0,
)
results = batch.run(n_days=1)[0]
ld_results.append({
"month": month,
"growth": results["growth"][0],
"daphnia_size": ld,
})
for ad in np.geomspace(1, 50000, 15):
daphnia = get_daphnia_dist(site, month, year, ad, daphnia_size)
batch = Model(
starting_mass,
daphnia,
temp_fn,
bathymetry,
daylengths[month],
light_extinction,
day_light=39350,
allow_dvm=True,
allow_functional_response=False,
max_P=2.0,
)
results = batch.run(n_days=1)[0]
ad_results.append({
"month": month,
"growth": results["growth"][0],
"daphnia_density": ad,
})
write_csv(k_results, "k_sensitivity.csv")
write_csv(w_results, "starting_mass_sensitivity.csv")
write_csv(ld_results, "daphnia_size_sensitivity.csv")
write_csv(ad_results, "daphnia_density_sensitivity.csv")
def get_temp_fn(site, month, year):
depths, temps = util.select_rows("tests/data/temperatures.csv", "depth",
"temperature", site, month, year)
return InterpolatedFunction(depths, temps)
def get_daphnia_dist(site, month, year, daphnia_density, daphnia_size):
depths, total = util.select_rows("tests/data/daphnia-vd.csv", "depth",
"total daphnia", site, month, year)
return DaphniaData(daphnia_density, depths, total, size=daphnia_size)
def run(allow_dvm, max_P, write_out=True):
pyplot.close("all")
for site in ["fall creek", "hills creek", "lookout point"]:
elev, area = util.select_rows(
"tests/data/bathymetry.csv",
"elevation (m)",
"2d_area (m2)",
site=site,
)
bathymetry = InterpolatedFunction(elev, area)
for year in ["2015", "2016"]:
starting_mass = 0.3
site_results = {}
for month in [3, 4, 5, 6, 7, 8, 9]:
n_days = days_in_month[month]
values = get_values(site, year, month)
if values is None:
continue
print(site, year, month)
daphnia_density, daphnia_size, light_extinction = values
depths, total = util.select_rows(
"tests/data/daphnia-vd.csv",
"depth",
"total daphnia",
site,
month,
year,
)
daphnia = DaphniaData(daphnia_density,
depths,
total,
size=daphnia_size)
depths, temps = util.select_rows(
"tests/data/temperatures.csv",
"depth",
"temperature",
site,
month,
year,
)
temp_fn = InterpolatedFunction(depths, temps)
start_date = (int(year), month, 1)
batch = Model(
starting_mass,
daphnia,
temp_fn,
bathymetry,
daylengths[month],
light_extinction,
day_light=39350,
allow_dvm=allow_dvm,
max_P=max_P,
)
results = batch.run(n_days=n_days, start_date=start_date)[0]
starting_mass = max(0.3, results["mass"][-1])
site_results = merge_results(site_results, results)
if write_out:
label = ""
if not allow_dvm:
label += "nodvm"
if max_P != 1:
label += "+maxP%d" % max_P
label = label.lstrip("+")
dirname = "experiments/%s/" % (label or "control")
if not os.path.isdir(dirname):
os.makedirs(dirname)
name = name_template % (site, year, label)
name = name.rstrip("_")
extras = {"site": [site] * len(site_results["date"])}
util.export_results(site_results,
dirname + name + ".csv",
extra_columns=extras)
print("final length: %0.3f mm" % results["length"][-1])
def bathymetry():
elev, area = util.select_rows("tests/data/bathymetry.csv",
"elevation (m)",
"2d_area (m2)",
site=site)
return InterpolatedFunction(elev, area)
def daphnia_data():
total_daphnia = 5020.65
daphnia_size = 1.26
depth, counts = util.select_rows("tests/data/daphnia-vd.csv", "depth",
"total daphnia", site, month, year)
return DaphniaData(total_daphnia, depth, counts, size=daphnia_size)