Bring yli.turnbull up to date with hpstat 82f4a54
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@ -135,7 +135,7 @@ def calc_survfunc_kaplanmeier(time, status, ci, transform_x=None, transform_y=No
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return xpoints, ypoints, None, None
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def turnbull(df, time_left, time_right, by=None, *, ci=True, step_loc=0.5, maxiter=None, fail_prob_tolerance=None, se_method=None, zero_tolerance=None, transform_x=None, transform_y=None, nan_policy='warn', fig=None, ax=None):
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def turnbull(df, time_left, time_right, by=None, *, ci=True, step_loc=0.5, maxiter=None, ll_tolerance=None, se_method=None, zero_tolerance=None, ci_precision=None, transform_x=None, transform_y=None, nan_policy='warn', fig=None, ax=None):
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"""
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Generate a Turnbull estimator plot, which extends the Kaplan–Meier estimator to interval-censored observations
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@ -159,12 +159,14 @@ def turnbull(df, time_left, time_right, by=None, *, ci=True, step_loc=0.5, maxit
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:type step_loc: float
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:param maxiter: Maximum number of iterations to attempt
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:type maxiter: int
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:param fail_prob_tolerance: Terminate algorithm when the absolute change in failure probability in each interval is less than this tolerance
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:type fail_prob_tolerance: float
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:param ll_tolerance: Terminate algorithm when the absolute change in log-likelihood is less than this tolerance
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:type ll_tolerance: float
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:param se_method: Method for computing standard error or survival probabilities (see hpstat *turnbull* documentation)
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:type se_method: str
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:param zero_tolerance: Threshold for dropping failure probability when se_method is "oim-drop-zeros"
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:type zero_tolerance: float
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:param ci_precision: Desired precision of confidence limits when se-method is "likelihood-ratio"
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:type ci_precision: float
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:param transform_x: Function to transform x axis by
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:type transform_x: callable
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:param transform_y: Function to transform y axis by
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@ -195,11 +197,17 @@ def turnbull(df, time_left, time_right, by=None, *, ci=True, step_loc=0.5, maxit
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for group in groups.groups:
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subset = groups.get_group(group)
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handle = plot_survfunc_turnbull(ax, subset[time_left], subset[time_right], ci, step_loc, maxiter, fail_prob_tolerance, se_method, zero_tolerance, transform_x, transform_y)
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handle = plot_survfunc_turnbull(
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ax, subset[time_left], subset[time_right],
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ci=ci, step_loc=step_loc, maxiter=maxiter, ll_tolerance=ll_tolerance, se_method=se_method, zero_tolerance=zero_tolerance, ci_precision=ci_precision, transform_x=transform_x, transform_y=transform_y
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)
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handle.set_label('{} = {}'.format(by, group))
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else:
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# No grouping
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plot_survfunc_turnbull(ax, df[time_left], df[time_right], ci, step_loc, maxiter, fail_prob_tolerance, se_method, zero_tolerance, transform_x, transform_y)
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plot_survfunc_turnbull(
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ax, df[time_left], df[time_right],
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ci=ci, step_loc=step_loc, maxiter=maxiter, ll_tolerance=ll_tolerance, se_method=se_method, zero_tolerance=zero_tolerance, ci_precision=ci_precision, transform_x=transform_x, transform_y=transform_y
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)
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if time_units:
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ax.set_xlabel('{} + {} ({})'.format(time_left, time_right, time_units))
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@ -214,8 +222,11 @@ def turnbull(df, time_left, time_right, by=None, *, ci=True, step_loc=0.5, maxit
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return fig, ax
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def plot_survfunc_turnbull(ax, time_left, time_right, ci, step_loc=0.5, maxiter=None, fail_prob_tolerance=None, se_method=None, zero_tolerance=None, transform_x=None, transform_y=None):
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xpoints, ypoints, ypoints0, ypoints1 = calc_survfunc_turnbull(time_left, time_right, ci, step_loc, maxiter, fail_prob_tolerance, se_method, zero_tolerance, transform_x, transform_y)
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def plot_survfunc_turnbull(ax, time_left, time_right, *, ci=True, step_loc=0.5, maxiter=None, ll_tolerance=None, se_method=None, zero_tolerance=None, ci_precision=None, transform_x=None, transform_y=None):
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xpoints, ypoints, ypoints0, ypoints1 = calc_survfunc_turnbull(
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time_left, time_right,
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ci=ci, step_loc=step_loc, maxiter=maxiter, ll_tolerance=ll_tolerance, se_method=se_method, zero_tolerance=zero_tolerance, ci_precision=ci_precision, transform_x=transform_x, transform_y=transform_y
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)
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handle = ax.plot(xpoints, ypoints)[0]
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@ -224,7 +235,7 @@ def plot_survfunc_turnbull(ax, time_left, time_right, ci, step_loc=0.5, maxiter=
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return handle
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def calc_survfunc_turnbull(time_left, time_right, ci, step_loc=0.5, maxiter=None, ll_tolerance=None, se_method=None, zero_tolerance=None, transform_x=None, transform_y=None):
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def calc_survfunc_turnbull(time_left, time_right, *, ci=True, step_loc=0.5, maxiter=None, ll_tolerance=None, se_method=None, zero_tolerance=None, ci_precision=None, transform_x=None, transform_y=None):
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# Estimate the survival function
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# Prepare arguments
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@ -241,6 +252,9 @@ def calc_survfunc_turnbull(time_left, time_right, ci, step_loc=0.5, maxiter=None
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if zero_tolerance:
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hpstat_args.append('--zero-tolerance')
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hpstat_args.append(str(zero_tolerance))
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if ci_precision:
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hpstat_args.append('--ci-precision')
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hpstat_args.append(str(ci_precision))
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# Export data to CSV
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csv_buf = io.StringIO()
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