def fit(self, durations, event_observed=None, timeline=None, entry=None, label='KM_estimate',
alpha=None, left_censorship=False, ci_labels=None):
"""
Parameters:
duration: an array, or pd.Series, of length n -- duration subject was observed for
timeline: return the best estimate at the values in timelines (postively increasing)
event_observed: an array, or pd.Series, of length n -- True if the the death was observed, False if the event
was lost (right-censored). Defaults all True if event_observed==None
entry: an array, or pd.Series, of length n -- relative time when a subject entered the study. This is
useful for left-truncated (not left-censored) observations. If None, all members of the population
were born at time 0.
label: a string to name the column of the estimate.
alpha: the alpha value in the confidence intervals. Overrides the initializing
alpha for this call to fit only.
left_censorship: True if durations and event_observed refer to left censorship events. Default False
ci_labels: add custom column names to the generated confidence intervals
as a length-2 list: [<lower-bound name>, <upper-bound name>]. Default: <label>_lower_<alpha>
Returns:
self, with new properties like 'survival_function_'.
"""
# if the user is interested in left-censorship, we return the cumulative_density_, no survival_function_,
estimate_name = 'survival_function_' if not left_censorship else 'cumulative_density_'
v = _preprocess_inputs(durations, event_observed, timeline, entry)
self.durations, self.event_observed, self.timeline, self.entry, self.event_table = v
self._label = label
alpha = alpha if alpha else self.alpha
log_survival_function, cumulative_sq_ = _additive_estimate(self.event_table, self.timeline,
self._additive_f, self._additive_var,
left_censorship)
if entry is not None:
# a serious problem with KM is that when the sample size is small and there are too few early
# truncation times, it may happen that is the number of patients at risk and the number of deaths is the same.
# we adjust for this using the Breslow-Fleming-Harrington estimator
n = self.event_table.shape[0]
net_population = (self.event_table['entrance'] - self.event_table['removed']).cumsum()
if net_population.iloc[:int(n / 2)].min() == 0:
ix = net_population.iloc[:int(n / 2)].argmin()
raise StatError("""There are too few early truncation times and too many events. S(t)==0 for all t>%.1f. Recommend BreslowFlemingHarringtonFitter.""" % ix)
# estimation
setattr(self, estimate_name, pd.DataFrame(np.exp(log_survival_function), columns=[self._label]))
self.__estimate = getattr(self, estimate_name)
self.confidence_interval_ = self._bounds(cumulative_sq_[:, None], alpha, ci_labels)
self.median_ = median_survival_times(self.__estimate)
# estimation methods
self.predict = self._predict(estimate_name, label)
self.subtract = self._subtract(estimate_name)
self.divide = self._divide(estimate_name)
# plotting functions
self.plot = self._plot_estimate(estimate_name)
setattr(self, "plot_" + estimate_name, self.plot)
self.plot_loglogs = plot_loglogs(self)
return self
def fit(self,
durations,
event_observed=None,
timeline=None,
entry=None,
label='KM_estimate',
alpha=None,
left_censorship=False,
ci_labels=None):
"""
Parameters:
duration: an array, or pd.Series, of length n -- duration subject was observed for
timeline: return the best estimate at the values in timelines (postively increasing)
event_observed: an array, or pd.Series, of length n -- True if the the death was observed, False if the event
was lost (right-censored). Defaults all True if event_observed==None
entry: an array, or pd.Series, of length n -- relative time when a subject entered the study. This is
useful for left-truncated (not left-censored) observations. If None, all members of the population
were born at time 0.
label: a string to name the column of the estimate.
alpha: the alpha value in the confidence intervals. Overrides the initializing
alpha for this call to fit only.
left_censorship: True if durations and event_observed refer to left censorship events. Default False
ci_labels: add custom column names to the generated confidence intervals
as a length-2 list: [<lower-bound name>, <upper-bound name>]. Default: <label>_lower_<alpha>
Returns:
self, with new properties like 'survival_function_'.
"""
# if the user is interested in left-censorship, we return the cumulative_density_, no survival_function_,
estimate_name = 'survival_function_' if not left_censorship else 'cumulative_density_'
v = _preprocess_inputs(durations, event_observed, timeline, entry)
self.durations, self.event_observed, self.timeline, self.entry, self.event_table = v
self._label = label
alpha = alpha if alpha else self.alpha
log_survival_function, cumulative_sq_ = _additive_estimate(
self.event_table, self.timeline, self._additive_f,
self._additive_var, left_censorship)
if entry is not None:
# a serious problem with KM is that when the sample size is small and there are too few early
# truncation times, it may happen that is the number of patients at risk and the number of deaths is the same.
# we adjust for this using the Breslow-Fleming-Harrington estimator
n = self.event_table.shape[0]
net_population = (self.event_table['entrance'] -
self.event_table['removed']).cumsum()
if net_population.iloc[:int(n / 2)].min() == 0:
ix = net_population.iloc[:int(n / 2)].idxmin()
raise StatError(
"""There are too few early truncation times and too many events. S(t)==0 for all t>%.1f. Recommend BreslowFlemingHarringtonFitter."""
% ix)
# estimation
setattr(
self, estimate_name,
pd.DataFrame(np.exp(log_survival_function), columns=[self._label]))
self.__estimate = getattr(self, estimate_name)
self.confidence_interval_ = self._bounds(cumulative_sq_[:, None],
alpha, ci_labels)
self.median_ = median_survival_times(self.__estimate,
left_censorship=left_censorship)
# estimation methods
self.predict = self._predict(estimate_name, label)
self.subtract = self._subtract(estimate_name)
self.divide = self._divide(estimate_name)
# plotting functions
self.plot = self._plot_estimate(estimate_name)
setattr(self, "plot_" + estimate_name, self.plot)
self.plot_loglogs = plot_loglogs(self)
return self
def plot_loglogs(self, *args, **kwargs):
r"""
Plot :math:`\log(S(t))` against :math:`\log(t)`
"""
return plot_loglogs(self, *args, **kwargs)
def plot_loglogs(self, *args, **kwargs):
return plot_loglogs(self, *args, **kwargs)
def plot_loglogs(self, *args, **kwargs):
r"""
Plot :math:`\log(S(t))` against :math:`\log(t)`. Same arguments as ``.plot``.
"""
return plot_loglogs(self, *args, **kwargs)
def plot_loglogs(self, *args, **kwargs):
r"""
Plot :math:`\log(S(t))` against :math:`\log(t)`
"""
return plot_loglogs(self, *args, **kwargs)
