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691 Update ttet01 snapshot (#692)
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#691

close #691 

thank you for the review

Co-authored-by: benoit <[email protected]>
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@BFalquet
BFalquet and benoit authored Nov 1, 2023
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64 changes: 32 additions & 32 deletions tests/testthat/_snaps/rspt01.md
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Original file line number Diff line number Diff line change
Expand Up @@ -163,49 +163,49 @@
Code
cat(export_as_txt(res, lpp = 100))
Output
B: Placebo A: Drug X C: Combination
(N=134) (N=134) (N=132)
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————————————————
Responders 127 (94.8%) 133 (99.3%) 131 (99.2%)
95% CI (Wald, with correction) (90.6, 98.9) (97.4, 100.0) (97.4, 100.0)
Responders 133 (99.3%) 127 (94.8%) 131 (99.2%)
95% CI (Wald, with correction) (97.4, 100.0) (90.6, 98.9) (97.4, 100.0)
Unstratified Analysis
Difference in Response rate (%) 4.5 4.5
95% CI (Wald, with correction) (-0.3, 9.3) (-0.3, 9.3)
p-value (Fisher's Exact Test) 0.0662 0.0663
Odds Ratio (95% CI) 7.33 (0.89 - 60.42) 7.22 (0.88 - 59.52)
Complete Response (CR) 97 (72.4%) 119 (88.8%) 120 (90.9%)
95% CI (Wald, with correction) (64.45, 80.33) (83.09, 94.52) (85.63, 96.19)
Partial Response (PR) 30 (22.4%) 14 (10.4%) 11 (8.3%)
95% CI (Wald, with correction) (14.96, 29.82) (4.90, 16.00) (3.24, 13.43)
Stable Disease (SD) 7 (5.2%) 1 (0.7%) 1 (0.8%)
95% CI (Wald, with correction) (1.08, 9.36) (0.00, 2.58) (0.00, 2.62)
Difference in Response rate (%) 4.5 4.5
95% CI (Wald, with correction) (-0.3, 9.3) (-0.3, 9.3)
p-value (Fisher's Exact Test) 0.0662 0.0663
Odds Ratio (95% CI) 7.33 (0.89 - 60.42) 7.22 (0.88 - 59.52)
Complete Response (CR) 119 (88.8%) 97 (72.4%) 120 (90.9%)
95% CI (Wald, with correction) (83.09, 94.52) (64.45, 80.33) (85.63, 96.19)
Partial Response (PR) 14 (10.4%) 30 (22.4%) 11 (8.3%)
95% CI (Wald, with correction) (4.90, 16.00) (14.96, 29.82) (3.24, 13.43)
Stable Disease (SD) 1 (0.7%) 7 (5.2%) 1 (0.8%)
95% CI (Wald, with correction) (0.00, 2.58) (1.08, 9.36) (0.00, 2.62)

---

Code
cat(export_as_txt(res, lpp = 100))
Output
B: Placebo A: Drug X C: Combination
(N=134) (N=134) (N=132)
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
—————————————————————————————————————————————————————————————————————————————————————————————————————
Responders 127 (94.8%) 133 (99.3%) 131 (99.2%)
95% CI (Wald, with correction) (90.6, 98.9) (97.4, 100.0) (97.4, 100.0)
Responders 133 (99.3%) 127 (94.8%) 131 (99.2%)
95% CI (Wald, with correction) (97.4, 100.0) (90.6, 98.9) (97.4, 100.0)
Unstratified Analysis
Difference in Response rate (%) 4.5 4.5
95% CI (Wald, with correction) (-0.3, 9.3) (-0.3, 9.3)
p-value (Fisher's Exact Test) 0.0662 0.0663
Odds Ratio (95% CI) 7.33 (0.89 - 60.42) 7.22 (0.88 - 59.52)
Difference in Response rate (%) 4.5 4.5
95% CI (Wald, with correction) (-0.3, 9.3) (-0.3, 9.3)
p-value (Fisher's Exact Test) 0.0662 0.0663
Odds Ratio (95% CI) 7.33 (0.89 - 60.42) 7.22 (0.88 - 59.52)
Stratified Analysis
Difference in Response rate (%) 4.4 4.6
95% CI (CMH, without correction) (0.3, 8.5) (0.5, 8.6)
p-value (Cochran-Mantel-Haenszel Test) 0.0344 0.0319
Odds Ratio (95% CI) 7.33 (0.89 - 60.42) 7.22 (0.88 - 59.52)
Complete Response (CR) 97 (72.4%) 119 (88.8%) 120 (90.9%)
95% CI (Wald, with correction) (64.45, 80.33) (83.09, 94.52) (85.63, 96.19)
Partial Response (PR) 30 (22.4%) 14 (10.4%) 11 (8.3%)
95% CI (Wald, with correction) (14.96, 29.82) (4.90, 16.00) (3.24, 13.43)
Stable Disease (SD) 7 (5.2%) 1 (0.7%) 1 (0.8%)
95% CI (Wald, with correction) (1.08, 9.36) (0.00, 2.58) (0.00, 2.62)
Difference in Response rate (%) 4.4 4.6
95% CI (CMH, without correction) (0.3, 8.5) (0.5, 8.6)
p-value (Cochran-Mantel-Haenszel Test) 0.0344 0.0319
Odds Ratio (95% CI) 7.33 (0.89 - 60.42) 7.22 (0.88 - 59.52)
Complete Response (CR) 119 (88.8%) 97 (72.4%) 120 (90.9%)
95% CI (Wald, with correction) (83.09, 94.52) (64.45, 80.33) (85.63, 96.19)
Partial Response (PR) 14 (10.4%) 30 (22.4%) 11 (8.3%)
95% CI (Wald, with correction) (4.90, 16.00) (14.96, 29.82) (3.24, 13.43)
Stable Disease (SD) 1 (0.7%) 7 (5.2%) 1 (0.8%)
95% CI (Wald, with correction) (0.00, 2.58) (1.08, 9.36) (0.00, 2.62)

# rspt01 works if change statistic methods

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106 changes: 53 additions & 53 deletions tests/testthat/_snaps/ttet01.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -194,75 +194,75 @@
Code
cat(export_as_txt(res, lpp = 100))
Output
B: Placebo A: Drug X C: Combination
(N=134) (N=134) (N=132)
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————
Patients with event (%) 90 (67.2%) 86 (64.2%) 92 (69.7%)
Patients without event (%) 44 (32.8%) 48 (35.8%) 40 (30.3%)
Patients with event (%) 86 (64.2%) 90 (67.2%) 92 (69.7%)
Patients without event (%) 48 (35.8%) 44 (32.8%) 40 (30.3%)
Time to Event (MONTHS)
Median 19.7 16.9 12.3
95% CI (13.2, 25.2) (12.8, 19.0) (8.4, 14.9)
25% and 75%-ile 7.2, 34.1 7.7, 30.0 4.5, 25.3
Range (censored) 0.4 to 83.0 0.3 to 65.9 1.0 to 81.8
Range (event) 0.1 to 58.7 0.5 to 85.8 0.2 to 77.8
Median 16.9 19.7 12.3
95% CI (12.8, 19.0) (13.2, 25.2) (8.4, 14.9)
25% and 75%-ile 7.7, 30.0 7.2, 34.1 4.5, 25.3
Range (censored) 0.3 to 65.9 0.4 to 83.0 1.0 to 81.8
Range (event) 0.5 to 85.8 0.1 to 58.7 0.2 to 77.8
Unstratified Analysis
p-value (log-rank) 0.4808 0.0123
Hazard Ratio 1.11 1.45
95% CI (0.83, 1.50) (1.08, 1.95)
p-value (log-rank) 0.4808 0.0123
Hazard Ratio 1.11 1.45
95% CI (0.83, 1.50) (1.08, 1.95)
6 MONTHS
Patients remaining at risk 92 87 77
Event Free Rate (%) 77.85 77.27 67.70
95% CI (69.53, 84.15) (68.76, 83.74) (58.64, 75.20)
Difference in Event Free Rate -0.57 -10.14
95% CI (-10.97, 9.82) (-21.15, 0.87)
p-value (Z-test) 0.9137 0.0710
Patients remaining at risk 87 92 77
Event Free Rate (%) 77.27 77.85 67.70
95% CI (68.76, 83.74) (69.53, 84.15) (58.64, 75.20)
Difference in Event Free Rate -0.57 -10.14
95% CI (-10.97, 9.82) (-21.15, 0.87)
p-value (Z-test) 0.9137 0.0710
12 MONTHS
Patients remaining at risk 68 65 51
Event Free Rate (%) 62.69 62.83 50.16
95% CI (53.31, 70.71) (53.36, 70.91) (40.69, 58.89)
Difference in Event Free Rate 0.14 -12.53
95% CI (-12.25, 12.53) (-25.19, 0.12)
p-value (Z-test) 0.9822 0.0522
Patients remaining at risk 65 68 51
Event Free Rate (%) 62.83 62.69 50.16
95% CI (53.36, 70.91) (53.31, 70.71) (40.69, 58.89)
Difference in Event Free Rate 0.14 -12.53
95% CI (-12.25, 12.53) (-25.19, 0.12)
p-value (Z-test) 0.9822 0.0522

---

Code
cat(export_as_txt(res, lpp = 100))
Output
B: Placebo A: Drug X C: Combination
(N=134) (N=134) (N=132)
A: Drug X B: Placebo C: Combination
(N=134) (N=134) (N=132)
———————————————————————————————————————————————————————————————————————————————————
Patients with event (%) 90 (67.2%) 86 (64.2%) 92 (69.7%)
Patients with event (%) 86 (64.2%) 90 (67.2%) 92 (69.7%)
Earliest contributing event
Death 48 38 41
Disease Progression 42 48 51
Patients without event (%) 44 (32.8%) 48 (35.8%) 40 (30.3%)
Death 38 48 41
Disease Progression 48 42 51
Patients without event (%) 48 (35.8%) 44 (32.8%) 40 (30.3%)
Time to Event (MONTHS)
Median 19.7 16.9 12.3
95% CI (13.2, 25.2) (12.8, 19.0) (8.4, 14.9)
25% and 75%-ile 7.2, 34.1 7.7, 30.0 4.5, 25.3
Range (censored) 0.4 to 83.0 0.3 to 65.9 1.0 to 81.8
Range (event) 0.1 to 58.7 0.5 to 85.8 0.2 to 77.8
Median 16.9 19.7 12.3
95% CI (12.8, 19.0) (13.2, 25.2) (8.4, 14.9)
25% and 75%-ile 7.7, 30.0 7.2, 34.1 4.5, 25.3
Range (censored) 0.3 to 65.9 0.4 to 83.0 1.0 to 81.8
Range (event) 0.5 to 85.8 0.1 to 58.7 0.2 to 77.8
Stratified Analysis
p-value (log-rank) 0.8068 0.0239
Hazard Ratio 1.04 1.42
95% CI (0.77, 1.41) (1.05, 1.93)
p-value (log-rank) 0.8068 0.0239
Hazard Ratio 1.04 1.42
95% CI (0.77, 1.41) (1.05, 1.93)
Unstratified Analysis
p-value (log-rank) 0.4808 0.0123
Hazard Ratio 1.11 1.45
95% CI (0.83, 1.50) (1.08, 1.95)
p-value (log-rank) 0.4808 0.0123
Hazard Ratio 1.11 1.45
95% CI (0.83, 1.50) (1.08, 1.95)
6 MONTHS
Patients remaining at risk 92 87 77
Event Free Rate (%) 77.85 77.27 67.70
95% CI (69.53, 84.15) (68.76, 83.74) (58.64, 75.20)
Difference in Event Free Rate -0.57 -10.14
95% CI (-10.97, 9.82) (-21.15, 0.87)
p-value (Z-test) 0.9137 0.0710
Patients remaining at risk 87 92 77
Event Free Rate (%) 77.27 77.85 67.70
95% CI (68.76, 83.74) (69.53, 84.15) (58.64, 75.20)
Difference in Event Free Rate -0.57 -10.14
95% CI (-10.97, 9.82) (-21.15, 0.87)
p-value (Z-test) 0.9137 0.0710
12 MONTHS
Patients remaining at risk 68 65 51
Event Free Rate (%) 62.69 62.83 50.16
95% CI (53.31, 70.71) (53.36, 70.91) (40.69, 58.89)
Difference in Event Free Rate 0.14 -12.53
95% CI (-12.25, 12.53) (-25.19, 0.12)
p-value (Z-test) 0.9822 0.0522
Patients remaining at risk 65 68 51
Event Free Rate (%) 62.83 62.69 50.16
95% CI (53.36, 70.91) (53.31, 70.71) (40.69, 58.89)
Difference in Event Free Rate 0.14 -12.53
95% CI (-12.25, 12.53) (-25.19, 0.12)
p-value (Z-test) 0.9822 0.0522

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