def plot_fits(generator, prediction_times, sharex, sharey, draw_space, plot_obs=None, plot_uncertainty=False):
"""
Plot the result and draws from a model generator at some prediction times.
Args:
generator: (curvefit.model_generator.ModelPipeline) that has some draws
prediction_times: (np.array) of prediction times
sharex: (bool) fix the x axes
sharey: (bool) fix the y axes
draw_space: (callable) which curvefit.functions space to plot the draws in
plot_obs: (optional str) column of observations to plot
plot_uncertainty: (optional bool) plot the uncertainty intervals
"""
fig, ax = plt.subplots(len(generator.groups), 1, figsize=(8, 4 * len(generator.groups)),
sharex=sharex, sharey=sharey)
if len(generator.groups) == 1:
ax = [ax]
for i, group in enumerate(generator.groups):
draws = generator.draws[group].copy()
draws = data_translator(
data=draws,
input_space=generator.predict_space,
output_space=draw_space
)
mean_fit = generator.mean_predictions[group].copy()
mean_fit = data_translator(
data=mean_fit,
input_space=generator.predict_space,
output_space=draw_space
)
mean = draws.mean(axis=0)
ax[i].plot(prediction_times, mean, c='red', linestyle=':')
ax[i].plot(prediction_times, mean_fit, c='black')
if plot_uncertainty:
lower = np.quantile(draws, axis=0, q=0.025)
upper = np.quantile(draws, axis=0, q=0.975)
ax[i].plot(prediction_times, lower, c='red', linestyle=':')
ax[i].plot(prediction_times, upper, c='red', linestyle=':')
if plot_obs is not None:
df_data = generator.all_data.loc[generator.all_data[generator.col_group] == group].copy()
ax[i].scatter(df_data[generator.col_t], df_data[plot_obs])
ax[i].set_title(f"{group} predictions")
def summarize_result(self, print_summary=True):
"""
Prints a table which characterizes fit quality. It has four columns:
Location, RMSE ERF, RMSE DERF, RMSE LNR
Where
- RMSE ERF: residual squares for the fit in ERF space
- RMSE DERF: residual squares for the fit in DERF space
- RMSE LNR: residual squares for the exponential fit in DERF space, corresponds to the linear fit in ln(DERF) space,
The table is sorted by -ln(RMSE DERF) + ln(RMSE LNR), which means that the fits where a simple exponential
model works better than the CurveFit (which means the fit went badly) will go first.
Returns:
Dataframe with the data.
"""
models = self.models
summary = []
df_summary = pd.DataFrame(
{}, columns=['Location', 'RMSE ERF', 'RMSE DERF', 'RMSE LNR'])
location_list = []
rmse_gaussian_cdf_list = []
rmse_gaussian_pdf_list = []
rmse_gaussian_pdf_linear_list = []
for i, (location, model) in enumerate(models.items()):
gaussian_cdf_pred = model.fun(model.t, model.params[:, 0])
rmse_gaussian_cdf = np.linalg.norm(gaussian_cdf_pred -
model.obs)**2
gaussian_pdf_obs = data_translator(model.obs,
self.basic_model_dict['fun'],
'gaussian_pdf')
gaussian_pdf_pred = gaussian_pdf(model.t, model.params[:, 0])
rmse_gaussian_pdf = np.linalg.norm(gaussian_pdf_obs -
gaussian_pdf_pred)**2
rmse_gaussian_pdf_linear = self.preconditioner._statistics[
"linear_rmse"].get(location, 1e10)
summary.append([
location, rmse_gaussian_cdf, rmse_gaussian_pdf,
rmse_gaussian_pdf_linear
])
location_list.append(location)
rmse_gaussian_cdf_list.append(rmse_gaussian_cdf)
rmse_gaussian_pdf_list.append(rmse_gaussian_pdf)
rmse_gaussian_pdf_linear_list.append(rmse_gaussian_pdf_linear)
df_summary['Location'] = location_list
df_summary['RMSE ERF'] = rmse_gaussian_cdf_list
df_summary['RMSE DERF'] = rmse_gaussian_pdf_list
df_summary['RMSE LNR'] = rmse_gaussian_pdf_linear_list
return df_summary
def simulate(self,
mp,
num_simulations,
prediction_times,
group,
epsilon=1e-2,
theta=1):
"""
Simulate the residuals based on the mean and standard deviation of predicting
into the future.
Args:
mp: (curvefit.model_generator.ModelPipeline) model pipeline
prediction_times: (np.array) times to create predictions at
num_simulations: number of simulations
group: (str) the group to make the simulations for
epsilon: (epsilon) the floor for standard deviation moving out into the future
theta: (theta) scaling of residuals to do relative to prediction magnitude
Returns:
List[pd.DataFrame] list of data frames for each simulation
"""
data = mp.all_data.loc[mp.all_data[mp.col_group] == group].copy()
max_t = int(np.round(data[mp.col_t].max()))
num_obs = data.loc[~data[mp.col_obs_compare].isnull()][
mp.col_group].count()
predictions = mp.mean_predictions[group]
add_noise = prediction_times > max_t
no_noise = prediction_times <= max_t
forecast_out_times = prediction_times[add_noise] - max_t
error = self.create_residual_samples(
num_simulations=num_simulations,
forecast_out_times=forecast_out_times,
num_data=num_obs,
epsilon=epsilon)
no_error = np.zeros(shape=(num_simulations, sum(no_noise)))
all_error = np.hstack([no_error, error])
noisy_forecast = predictions - (predictions**theta) * all_error
noisy_forecast = data_translator(data=noisy_forecast,
input_space=mp.predict_space,
output_space=mp.predict_space)
return noisy_forecast
def test_data_translator_exp(data, input_space, output_space):
result = utils.data_translator(data, input_space, output_space)
assert np.allclose(data, result)
def test_data_translator_diff(data, input_space, output_space):
result = utils.data_translator(data, input_space, output_space)
if 'log' in input_space:
assert np.allclose(np.exp(data), np.cumsum(np.exp(result), axis=1))
else:
assert np.allclose(data, np.cumsum(result, axis=1))