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Addressing issue #182 : scipy.integrate.simps deprecated #186

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Addressing issue #182 : scipy.integrate.simps deprecated #186

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15 changes: 9 additions & 6 deletions pycox/evaluation/ipcw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ def _inv_cens_score_single(func, ts, durations, events, surv, censor_surv, idx_t
g_ts = max(g_ts, min_g)
g_tt = max(g_tt, min_g)
score, w = func(ts, tt, s, g_ts, g_tt, d)
#w = min(w, max_weight)
# w = min(w, max_weight)
scores[i] = score * w
weights[i] = w

Expand All @@ -44,11 +44,14 @@ def metric(time_grid, durations, events, surv, censor_surv, index_surv, index_ce
n_indiv = len(durations)
scores = np.zeros((n_times, n_indiv))
weights = np.zeros((n_times, n_indiv))
idx_ts_surv = utils.idx_at_times(index_surv, time_grid, steps_surv, assert_sorted=True)
idx_ts_censor = utils.idx_at_times(index_censor, time_grid, steps_censor, assert_sorted=True)
idx_tt_censor = utils.idx_at_times(index_censor, durations, 'pre', assert_sorted=True)
idx_ts_surv = utils.idx_at_times(
index_surv, time_grid, steps_surv, assert_sorted=True)
idx_ts_censor = utils.idx_at_times(
index_censor, time_grid, steps_censor, assert_sorted=True)
idx_tt_censor = utils.idx_at_times(
index_censor, durations, 'pre', assert_sorted=True)
if steps_censor == 'post':
idx_tt_censor = (idx_tt_censor - 1).clip(0)
idx_tt_censor = (idx_tt_censor - 1).clip(0)
# This ensures that we get G(tt-)
_inv_cens_scores(func, time_grid, durations, events, surv, censor_surv, idx_ts_surv, idx_ts_censor,
idx_tt_censor, scores, weights, n_times, n_indiv, max_weight)
Expand Down Expand Up @@ -83,7 +86,7 @@ def metric(time_grid, durations, events, surv, censor_surv, index_surv, index_ce
max_weight=np.inf, steps_surv='post', steps_censor='post'):
scores = func(time_grid, durations, events, surv, censor_surv, index_surv, index_censor,
max_weight, True, steps_surv, steps_censor)
integral = scipy.integrate.simps(scores, time_grid)
integral = scipy.integrate.simpson(y=scores, x=time_grid)
return integral / (time_grid[-1] - time_grid[0])
return metric

Expand Down