def test_ajf_plotting_with_add_count_at_risk(self, block):
E = [0, 1, 1, 2, 2, 0]
T = [1, 2, 3, 4, 5, 6]
ajf = AalenJohansenFitter().fit(T, E, event_of_interest=1)
ajf.plot(at_risk_counts=True)
self.plt.title("test_ajf_plotting_with_add_count_at_risk")
self.plt.show(block=block)
return
def test_ajf_plotting(self, block):
E = [0, 1, 1, 2, 2, 0]
T = [1, 2, 3, 4, 5, 6]
ajf = AalenJohansenFitter().fit(T, E, event_of_interest=1)
ajf.plot()
self.plt.title("test_ajf_plotting")
self.plt.show(block=block)
return
def test_ajf_plotting_no_confidence_intervals(self, block):
E = [0, 1, 1, 2, 2, 0]
T = [1, 2, 3, 4, 5, 6]
ajf = AalenJohansenFitter(calculate_variance=False).fit(T, E, event_of_interest=1)
ajf.plot(ci_show=False)
self.plt.title("test_ajf_plotting_no_confidence_intervals")
self.plt.show(block=block)
return
status2 = 'death_wl' # options: 'death_ld', 'death_dec', 'death_wl'
wl_rows = ['WL_profit', 'Death_profit', 'WL_nonprofit', 'Death_nonprofit']
dec_rows = ['DDKT_profit', 'Death_profit', 'DDKT_nonprofit', 'Death_nonprofit']
ld_rows = ['LDKT_profit', 'Death_profit', 'LDKT_nonprofit', 'Death_nonprofit']
rows = wl_rows
title = 'Cumulative incidence of waitlisting \n by facility profit status'
output = 'output\\cif_wl.png'
cif = pd.read_csv('Data\\Fortable3mi_ld_dec_censored.csv')
cif.loc[cif['death_wl'] == 1, 'wlist'] = 2
cif.loc[cif['death_dec'] == 1, 'dec'] = 2
cif.loc[cif['death_ld'] == 1, 'ldtx'] = 2
cif_p = cif[cif.for_profit == 1]
cif_np = cif[cif.for_profit == 0]
ajf1 = AalenJohansenFitter(calculate_variance=False)
ajf1.fit(cif_p[time] / 12, cif_p[status1], 1)
ajf2 = AalenJohansenFitter(calculate_variance=False)
ajf2.fit(cif_np[time] / 12, cif_np[status1], 1)
ajf3 = AalenJohansenFitter(calculate_variance=False)
ajf3.fit(cif_p[time] / 12, cif_p[status2], 1)
ajf4 = AalenJohansenFitter(calculate_variance=False)
ajf4.fit(cif_np[time] / 12, cif_np[status2], 1)
status1_p = [
float(ajf1.cumulative_density_.loc[slice(2 * i)].tail(1).values.round(3))
for i in range(0, 6)
]
status1_np = [
float(ajf2.cumulative_density_.loc[slice(2 * i)].tail(1).values.round(3))
for i in range(0, 6)
]