def plot_residuals_analysis(residuals: TimeSeries,
num_bins: int = 20,
fill_nan: bool = True) -> None:
"""Plots data relevant to residuals.
This function takes a univariate TimeSeries instance of residuals and plots their values,
their distribution and their ACF.
Please note that if the residual TimeSeries instance contains NaN values, the plots
might be displayed incorrectly. If `fill_nan` is set to True, the missing values will
be interpolated.
Parameters
----------
residuals
Univariate TimeSeries instance representing residuals.
num_bins
Optionally, an integer value determining the number of bins in the histogram.
fill_nan
A boolean value indicating whether NaN values should be filled in the residuals.
"""
residuals._assert_univariate()
fig = plt.figure(constrained_layout=True, figsize=(8, 6))
gs = fig.add_gridspec(2, 2)
if fill_nan:
residuals = fill_missing_values(residuals)
# plot values
ax1 = fig.add_subplot(gs[:1, :])
residuals.plot(ax=ax1)
ax1.set_ylabel("value")
ax1.set_title("Residual values")
# plot histogram and distribution
res_mean, res_std = np.mean(residuals.univariate_values()), np.std(
residuals.univariate_values())
res_min, res_max = min(residuals.univariate_values()), max(
residuals.univariate_values())
x = np.linspace(res_min, res_max, 100)
ax2 = fig.add_subplot(gs[1:, 1:])
plot_hist(residuals, bins=num_bins, ax=ax2)
ax2.plot(
x,
norm(res_mean, res_std).pdf(x) * len(residuals) * (res_max - res_min) /
num_bins,
)
ax2.yaxis.set_major_locator(plt.MaxNLocator(integer=True))
ax2.set_title("Distribution")
ax2.set_ylabel("count")
ax2.set_xlabel("value")
# plot ACF
ax3 = fig.add_subplot(gs[1:, :1])
plot_acf(residuals, axis=ax3)
ax3.set_ylabel("ACF value")
ax3.set_xlabel("lag")
ax3.set_title("ACF")
def _fit(self,
series: TimeSeries,
future_covariates: Optional[TimeSeries] = None):
super()._fit(series, future_covariates)
series._assert_univariate()
series = self.training_series
self.model.fit(
series.values(copy=False).flatten(),
X=future_covariates.values(
copy=False) if future_covariates else None,
)
return self
def remove_seasonality(
ts: TimeSeries,
freq: int = None,
model: SeasonalityMode = SeasonalityMode.MULTIPLICATIVE,
method: str = "naive",
**kwargs,
) -> TimeSeries:
"""
Adjusts the TimeSeries `ts` for a seasonality of order `frequency` using the `model` decomposition.
Parameters
----------
ts
The TimeSeries to adjust.
freq
The seasonality period to use.
model
The type of decomposition to use.
Must be a `from darts import SeasonalityMode` Enum member.
Either SeasonalityMode.MULTIPLICATIVE or SeasonalityMode.ADDITIVE.
Defaults SeasonalityMode.MULTIPLICATIVE.
method
The method to be used to decompose the series.
- "naive" : Seasonal decomposition using moving averages [1]_.
- "STL" : Season-Trend decomposition using LOESS [2]_. Only compatible with ``ADDITIVE`` model type.
Defaults to "naive"
kwargs
Other keyword arguments are passed down to the decomposition method.
Returns
-------
TimeSeries
A new TimeSeries instance that corresponds to the seasonality-adjusted 'ts'.
References
-------
.. [1] https://www.statsmodels.org/devel/generated/statsmodels.tsa.seasonal.seasonal_decompose.html
.. [2] https://www.statsmodels.org/devel/generated/statsmodels.tsa.seasonal.STL.html
"""
ts._assert_univariate()
raise_if_not(
model is not SeasonalityMode.NONE,
"The model must be either MULTIPLICATIVE or ADDITIVE.",
)
raise_if(
model not in [SeasonalityMode.ADDITIVE, ModelMode.ADDITIVE]
and method == "STL",
f"Only ADDITIVE seasonality is compatible with the STL method. Current model is {model}.",
logger,
)
_, seasonality = extract_trend_and_seasonality(ts, freq, model, method,
**kwargs)
new_ts = remove_from_series(ts, seasonality, model)
return new_ts
def stationarity_test_adf(
ts: TimeSeries,
maxlag: Union[None, int] = None,
regression: str = "c",
autolag: Union[None, str] = "AIC",
) -> set:
"""
Provides Augmented Dickey-Fuller unit root test for a time series,
using :func:`statsmodels.tsa.stattools.adfuller`. See [1]_.
Parameters
----------
ts
The time series to test.
maxlag
Maximum lag which is included in test, default value of 12*(nobs/100)^{1/4} is used when None.
regression
Constant and trend order to include in regression.
"c" : constant only (default).
"ct" : constant and trend.
"ctt" : constant, and linear and quadratic trend.
"n" : no constant, no trend.
autolag
Method to use when automatically determining the lag length among the values 0, 1, …, maxlag.
If "AIC" (default) or "BIC", then the number of lags is chosen to minimize the corresponding
information criterion. "t-stat" based choice of maxlag. Starts with maxlag and drops a lag
until the t-statistic on the last lag length is significant using a 5%-sized test.
If None, then the number of included lags is set to maxlag.
Returns
-------
set
| adf: The test statistic.
| pvalue: MacKinnon's approximate p-value based on [2]_.
| usedlag: The number of lags used.
| nobs: The number of observations used for the ADF regression and calculation of the critical values.
| critical: Critical values for the test statistic at the 1 %, 5 %, and 10 % levels. Based on [2]_.
| icbest: The maximized information criterion if autolag is not None.
References
----------
.. [1] https://www.statsmodels.org/dev/generated/statsmodels.tsa.stattools.adfuller.html
.. [2] MacKinnon (1994, 2010)
"""
ts._assert_univariate()
ts._assert_deterministic()
return adfuller(ts.values(copy=False), maxlag, regression, autolag)
def remove_trend(
ts: TimeSeries,
model: ModelMode = ModelMode.MULTIPLICATIVE,
method: str = "naive",
**kwargs,
) -> TimeSeries:
"""
Adjusts the TimeSeries `ts` for a trend using the `model` decomposition.
Parameters
----------
ts
The TimeSeries to adjust.
model
The type of decomposition to use.
Must be a `from darts import ModelMode` Enum member.
Either ModelMode.MULTIPLICATIVE or ModelMode.ADDITIVE.
Defaults ModelMode.MULTIPLICATIVE.
method
The method to be used to decompose the series.
- "naive" : Seasonal decomposition using moving averages [1]_.
- "STL" : Season-Trend decomposition using LOESS [2]_. Only compatible with ``ADDITIVE`` model type.
Defaults to "naive"
kwargs
Other keyword arguments are passed down to the decomposition method.
Returns
-------
TimeSeries
A new TimeSeries instance that corresponds to the trend-adjusted 'ts'.
"""
ts._assert_univariate()
raise_if(
model not in [SeasonalityMode.ADDITIVE, ModelMode.ADDITIVE]
and method == "STL",
f"Only ADDITIVE seasonality is compatible with the STL method. Current model is {model}.",
logger,
)
trend, _ = extract_trend_and_seasonality(ts,
model=model,
method=method,
**kwargs)
new_ts = remove_from_series(ts, trend, model)
return new_ts
def stationarity_test_kpss(ts: TimeSeries,
regression: str = "c",
nlags: Union[str, int] = "auto") -> set:
"""
Provides Kwiatkowski-Phillips-Schmidt-Shin test for stationarity for a time series,
using :func:`statsmodels.tsa.stattools.kpss`. See [1]_.
Parameters
----------
ts
The time series to test.
regression
The null hypothesis for the KPSS test.
'c' : The data is stationary around a constant (default).
'ct' : The data is stationary around a trend.
nlags
Indicates the number of lags to be used. If 'auto' (default), lags is calculated using the data-dependent method
of Hobijn et al. (1998). See also Andrews (1991), Newey & West (1994), and Schwert (1989). If set to 'legacy',
uses int(12 * (n / 100)**(1 / 4)) , as outlined in Schwert (1989).
Returns
-------
set
| kpss_stat: The test statistic.
| pvalue: The p-value of the test. The p-value is interpolated from Table 1 in [2]_,
| and a boundary point is returned if the test statistic is outside the table of critical values,
| that is, if the p-value is outside the interval (0.01, 0.1).
| lags: The truncation lag parameter.
| crit: The critical values at 10%, 5%, 2.5% and 1%. Based on [2]_.
References
----------
.. [1] https://www.statsmodels.org/dev/generated/statsmodels.tsa.stattools.kpss.html
.. [2] Kwiatkowski et al. (1992)
"""
ts._assert_univariate()
ts._assert_deterministic()
return kpss(ts.values(copy=False), regression, nlags)
def remove_from_series(ts: TimeSeries, other: TimeSeries,
model: Union[SeasonalityMode, ModelMode]) -> TimeSeries:
"""
Removes the TimeSeries `other` from the TimeSeries `ts` as specified by `model`.
Use e.g. to remove an additive or multiplicative trend from a series.
Parameters
----------
ts
The TimeSeries to be modified.
other
The TimeSeries to remove.
model
The type of model considered.
Must be `from darts import ModelMode, SeasonalityMode` Enums member.
Either MULTIPLICATIVE or ADDITIVE.
Returns
-------
TimeSeries
A TimeSeries defined by removing `other` from `ts`.
"""
ts._assert_univariate()
raise_if_not(
model in ModelMode or model in SeasonalityMode,
f"Unknown value for model_mode: {model}.",
logger,
)
if model.value == "multiplicative":
new_ts = ts / other
elif model.value == "additive":
new_ts = ts - other
else:
raise_log(
ValueError(
"Invalid parameter; must be either ADDITIVE or MULTIPLICATIVE. Was: {}"
.format(model)))
return new_ts
def plot_pacf(
ts: TimeSeries,
m: Optional[int] = None,
max_lag: int = 24,
method: str = "ywadjusted",
alpha: float = 0.05,
fig_size: Tuple[int, int] = (10, 5),
axis: Optional[plt.axis] = None,
) -> None:
"""
Plots the Partial ACF of `ts`, highlighting it at lag `m`, with corresponding significance interval.
Uses :func:`statsmodels.tsa.stattools.pacf` [1]_
Parameters
----------
ts
The TimeSeries whose ACF should be plotted.
m
Optionally, a time lag to highlight on the plot.
max_lag
The maximal lag order to consider.
method
The method to be used for the PACF calculation.
- | "yw" or "ywadjusted" : Yule-Walker with sample-size adjustment in
| denominator for acovf. Default.
- "ywm" or "ywmle" : Yule-Walker without adjustment.
- "ols" : regression of time series on lags of it and on constant.
- "ols-inefficient" : regression of time series on lags using a single
common sample to estimate all pacf coefficients.
- "ols-adjusted" : regression of time series on lags with a bias
adjustment.
- "ld" or "ldadjusted" : Levinson-Durbin recursion with bias
correction.
- "ldb" or "ldbiased" : Levinson-Durbin recursion without bias
correction.
alpha
The confidence interval to display.
fig_size
The size of the figure to be displayed.
axis
Optionally, an axis object to plot the ACF on.
References
----------
.. [1] https://www.statsmodels.org/dev/generated/statsmodels.tsa.stattools.pacf.html
"""
ts._assert_univariate()
raise_if(
max_lag is None or not (1 <= max_lag < len(ts) // 2),
"max_lag must be greater than or equal to 1 and less than len(ts)//2.",
)
raise_if(
m is not None and not (0 <= m <= max_lag),
"m must be greater than or equal to 0 and less than or equal to max_lag.",
)
raise_if(
alpha is None or not (0 < alpha < 1),
"alpha must be greater than 0 and less than 1.",
)
r, confint = pacf(ts.values(), nlags=max_lag, method=method, alpha=alpha)
if axis is None:
plt.figure(figsize=fig_size)
axis = plt
for i in range(len(r)):
axis.plot(
(i, i),
(0, r[i]),
color=("#b512b8" if m is not None and i == m else "black"),
lw=(1 if m is not None and i == m else 0.5),
)
# Adjusts the upper band of the confidence interval to center it on the x axis.
upp_band = [confint[lag][1] - r[lag] for lag in range(1, max_lag + 1)]
axis.fill_between(
np.arange(1, max_lag + 1),
upp_band,
[-x for x in upp_band],
color="#003DFD",
alpha=0.25,
)
axis.plot((0, max_lag + 1), (0, 0), color="black")
def plot_acf(
ts: TimeSeries,
m: Optional[int] = None,
max_lag: int = 24,
alpha: float = 0.05,
bartlett_confint: bool = True,
fig_size: Tuple[int, int] = (10, 5),
axis: Optional[plt.axis] = None,
) -> None:
"""
Plots the ACF of `ts`, highlighting it at lag `m`, with corresponding significance interval.
Uses :func:`statsmodels.tsa.stattools.acf` [1]_
Parameters
----------
ts
The TimeSeries whose ACF should be plotted.
m
Optionally, a time lag to highlight on the plot.
max_lag
The maximal lag order to consider.
alpha
The confidence interval to display.
bartlett_confint
The boolean value indicating whether the confidence interval should be
calculated using Bartlett's formula. If set to True, the confidence interval
can be used in the model identification stage for fitting ARIMA models.
If set to False, the confidence interval can be used to test for randomness
(i.e. there is no time dependence in the data) of the data.
fig_size
The size of the figure to be displayed.
axis
Optionally, an axis object to plot the ACF on.
References
----------
.. [1] https://www.statsmodels.org/dev/generated/statsmodels.tsa.stattools.acf.html
"""
ts._assert_univariate()
raise_if(
max_lag is None or not (1 <= max_lag < len(ts)),
"max_lag must be greater than or equal to 1 and less than len(ts).",
)
raise_if(
m is not None and not (0 <= m <= max_lag),
"m must be greater than or equal to 0 and less than or equal to max_lag.",
)
raise_if(
alpha is None or not (0 < alpha < 1),
"alpha must be greater than 0 and less than 1.",
)
r, confint = acf(
ts.values(),
nlags=max_lag,
fft=False,
alpha=alpha,
bartlett_confint=bartlett_confint,
)
if axis is None:
plt.figure(figsize=fig_size)
axis = plt
for i in range(len(r)):
axis.plot(
(i, i),
(0, r[i]),
color=("#b512b8" if m is not None and i == m else "black"),
lw=(1 if m is not None and i == m else 0.5),
)
# Adjusts the upper band of the confidence interval to center it on the x axis.
upp_band = [confint[lag][1] - r[lag] for lag in range(1, max_lag + 1)]
axis.fill_between(
np.arange(1, max_lag + 1),
upp_band,
[-x for x in upp_band],
color="#003DFD",
alpha=0.25,
)
axis.plot((0, max_lag + 1), (0, 0), color="black")
def granger_causality_tests(
ts_cause: TimeSeries,
ts_effect: TimeSeries,
maxlag: int,
addconst: bool = True,
verbose: bool = True,
) -> None:
"""
Provides four tests for granger non causality of 2 time series using
:func:`statsmodels.tsa.stattools.grangercausalitytests`.
See [1]_.
Parameters
----------
ts_cause
A univariate deterministic time series. The statistical test determines if this time series
'Granger causes' the time series ts_effect (second parameter). Missing values are not supported.
if H_0 (non causality) is rejected (p near 0), then there is a 'granger causality'.
ts_effect
Univariate time series 'Granger caused' by ts_cause.
maxlag
If an integer, computes the test for all lags up to maxlag.
If an iterable, computes the tests only for the lags in maxlag.
addconst
Include a constant in the model.
verbose
Print results.
Returns
-------
Dict
All test results, dictionary keys are the number of lags. For each lag the values are a tuple,
with the first element a dictionary with test statistic, pvalues, degrees of freedom, the second element are
the OLS estimation results for the restricted model, the unrestricted model and the restriction (contrast)
matrix for the parameter f_test.
References
----------
.. [1] https://www.statsmodels.org/dev/generated/statsmodels.tsa.stattools.grangercausalitytests.html
"""
ts_cause._assert_univariate()
ts_effect._assert_univariate()
ts_cause._assert_deterministic()
ts_effect._assert_deterministic()
raise_if_not(
ts_cause.freq == ts_effect.freq,
"ts_cause and ts_effect must have the same frequency.",
)
if not ts_cause.has_same_time_as(ts_effect):
logger.warning(
"ts_cause and ts_effect time series have different time index. "
"We will slice-intersect ts_cause with ts_effect.")
ts_cause = ts_cause.slice_intersect(ts_effect)
ts_effect = ts_effect.slice_intersect(ts_cause)
if not stationarity_tests(ts_cause):
logger.warning(
"ts_cause doesn't seem to be stationary. Please review granger causality validity in your problem context."
)
if not stationarity_tests(ts_effect):
logger.warning(
"ts_effect doesn't seem to be stationary. Please review granger causality validity in your problem context."
)
return grangercausalitytests(
np.concatenate(
(ts_effect.values(copy=False), ts_cause.values(copy=False)),
axis=1),
maxlag,
addconst,
verbose,
)
def check_seasonality(ts: TimeSeries,
m: Optional[int] = None,
max_lag: int = 24,
alpha: float = 0.05):
"""
Checks whether the TimeSeries `ts` is seasonal with period `m` or not.
If `m` is None, we work under the assumption that there is a unique seasonality period, which is inferred
from the Auto-correlation Function (ACF).
Parameters
----------
ts
The time series to check for seasonality.
m
The seasonality period to check.
max_lag
The maximal lag allowed in the ACF.
alpha
The desired confidence level (default 5%).
Returns
-------
Tuple[bool, int]
A tuple `(season, m)`, where season is a boolean indicating whether the series has seasonality or not
and `m` is the seasonality period.
"""
ts._assert_univariate()
if m is not None and (m < 2 or not isinstance(m, int)):
raise_log(ValueError("m must be an integer greater than 1."), logger)
if m is not None and m > max_lag:
raise_log(ValueError("max_lag must be greater than or equal to m."),
logger)
n_unique = np.unique(ts.values()).shape[0]
if n_unique == 1: # Check for non-constant TimeSeries
return False, 0
r = acf(
ts.values(), nlags=max_lag, fft=False
) # In case user wants to check for seasonality higher than 24 steps.
# Finds local maxima of Auto-Correlation Function
candidates = argrelmax(r)[0]
if len(candidates) == 0:
return False, 0
if m is not None:
# Check for local maximum when m is user defined.
test = m not in candidates
if test:
return False, m
candidates = [m]
# Remove r[0], the auto-correlation at lag order 0, that introduces bias.
r = r[1:]
# The non-adjusted upper limit of the significance interval.
band_upper = r.mean() + norm.ppf(1 - alpha / 2) * r.var()
# Significance test, stops at first admissible value. The two '-1' below
# compensate for the index change due to the restriction of the original r to r[1:].
for candidate in candidates:
stat = _bartlett_formula(r, candidate - 1, len(ts))
if r[candidate - 1] > stat * band_upper:
return True, candidate
return False, 0
def extract_trend_and_seasonality(
ts: TimeSeries,
freq: int = None,
model: Union[SeasonalityMode, ModelMode] = ModelMode.MULTIPLICATIVE,
method: str = "naive",
**kwargs,
) -> Tuple[TimeSeries, TimeSeries]:
"""
Extracts trend and seasonality from a TimeSeries instance using `statsmodels.tsa`.
Parameters
----------
ts
The series to decompose
freq
The seasonality period to use.
model
The type of decomposition to use.
Must be ``from darts import ModelMode, SeasonalityMode`` Enum member.
Either ``MULTIPLICATIVE`` or ``ADDITIVE``.
Defaults ``ModelMode.MULTIPLICATIVE``.
method
The method to be used to decompose the series.
- "naive" : Seasonal decomposition using moving averages [1]_.
- "STL" : Season-Trend decomposition using LOESS [2]_. Only compatible with ``ADDITIVE`` model type.
kwargs
Other keyword arguments are passed down to the decomposition method.
Returns
-------
Tuple[TimeSeries, TimeSeries]
A tuple of (trend, seasonal) time series.
References
-------
.. [1] https://www.statsmodels.org/devel/generated/statsmodels.tsa.seasonal.seasonal_decompose.html
.. [2] https://www.statsmodels.org/devel/generated/statsmodels.tsa.seasonal.STL.html
"""
ts._assert_univariate()
raise_if_not(
model in ModelMode or model in SeasonalityMode,
f"Unknown value for model_mode: {model}.",
logger,
)
raise_if_not(
model is not SeasonalityMode.NONE,
"The model must be either MULTIPLICATIVE or ADDITIVE.",
)
if method == "naive":
decomp = seasonal_decompose(ts.pd_series(),
period=freq,
model=model.value,
extrapolate_trend="freq")
elif method == "STL":
raise_if_not(
model in [SeasonalityMode.ADDITIVE, ModelMode.ADDITIVE],
f"Only ADDITIVE model is compatible with the STL method. Current model is {model}.",
logger,
)
decomp = STL(
endog=ts.pd_series(),
period=freq,
**kwargs,
).fit()
else:
raise_log(ValueError(f"Unknown value for method: {method}"), logger)
season = TimeSeries.from_times_and_values(
ts.time_index,
decomp.seasonal,
static_covariates=ts.static_covariates,
hierarchy=ts.hierarchy,
)
trend = TimeSeries.from_times_and_values(
ts.time_index,
decomp.trend,
static_covariates=ts.static_covariates,
hierarchy=ts.hierarchy,
)
return trend, season