Nothing
tests/testthat/_snaps/survival_duration_subgroups.md
In tern: Create Common TLGs Used in Clinical Trials
extract_survival_subgroups functions as expected with valid input and default arguments
Code
res
Output
$survtime
arm n n_events median subgroup var
1 B: Placebo 73 57 727.8043 All Patients ALL
2 A: Drug X 69 44 974.6402 All Patients ALL
3 B: Placebo 40 31 599.1772 F SEX
4 A: Drug X 38 24 1016.2982 F SEX
5 B: Placebo 33 26 888.4916 M SEX
6 A: Drug X 31 20 974.6402 M SEX
7 B: Placebo 24 21 735.4722 LOW BMRKR2
8 A: Drug X 26 15 974.6402 LOW BMRKR2
9 B: Placebo 23 14 731.8352 MEDIUM BMRKR2
10 A: Drug X 26 17 964.2197 MEDIUM BMRKR2
11 B: Placebo 26 22 654.8245 HIGH BMRKR2
12 A: Drug X 17 12 1016.2982 HIGH BMRKR2
var_label row_type
1 All Patients content
2 All Patients content
3 Sex analysis
4 Sex analysis
5 Sex analysis
6 Sex analysis
7 Continuous Level Biomarker 2 analysis
8 Continuous Level Biomarker 2 analysis
9 Continuous Level Biomarker 2 analysis
10 Continuous Level Biomarker 2 analysis
11 Continuous Level Biomarker 2 analysis
12 Continuous Level Biomarker 2 analysis
$hr
arm n_tot n_tot_events hr lcl ucl conf_level pval
1 142 101 0.7108557 0.4779138 1.0573368 0.95 0.09049511
2 78 55 0.5595391 0.3246658 0.9643271 0.95 0.03411759
3 64 46 0.9102874 0.5032732 1.6464678 0.95 0.75582028
4 50 36 0.7617717 0.3854349 1.5055617 0.95 0.43236030
5 49 31 0.7651261 0.3641277 1.6077269 0.95 0.47860004
6 43 34 0.6662356 0.3257413 1.3626456 0.95 0.26285846
pval_label subgroup var var_label row_type
1 p-value (log-rank) All Patients ALL All Patients content
2 p-value (log-rank) F SEX Sex analysis
3 p-value (log-rank) M SEX Sex analysis
4 p-value (log-rank) LOW BMRKR2 Continuous Level Biomarker 2 analysis
5 p-value (log-rank) MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis
6 p-value (log-rank) HIGH BMRKR2 Continuous Level Biomarker 2 analysis
extract_survival_subgroups works as expected with groups_lists
Code
res
Output
[1] "low" "low" "low/medium" "low/medium"
[5] "low/medium/high" "low/medium/high"
Code
res
Output
[1] "low" "low/medium" "low/medium/high"
extract_survival_subgroups functions as expected with NULL subgroups
Code
res
Output
$survtime
arm n n_events median subgroup var var_label row_type
1 B: Placebo 73 57 727.8043 All Patients ALL All Patients content
2 A: Drug X 69 44 974.6402 All Patients ALL All Patients content
$hr
arm n_tot n_tot_events hr lcl ucl conf_level pval
1 142 101 0.7108557 0.4779138 1.057337 0.95 0.09049511
pval_label subgroup var var_label row_type
1 p-value (log-rank) All Patients ALL All Patients content
a_survival_subgroups functions as expected with valid input
Code
res
Output
hr pval
——————————————————
M 0.12 <0.0001
F 0.57 1.3023
tabulate_survival_subgroups functions as expected with valid input
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36)
tabulate_survival_subgroups functions as expected with NULL subgroups
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
tabulate_survival_subgroups functions as expected with extreme values in subgroups
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 18 10 859.0 8 954.2 0.60 (0.23, 1.59)
Geographic Region 1
Asia 9 4 1244.7 5 796.9 0.97 (0.26, 3.64)
North America 2 2 1066.9 NA NA NA NA
South America 7 4 859.0 3 1759.9 0.39 (0.07, 2.17)
tabulate_survival_subgroups functions as expected when one arm has 0 records
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events n Events Median (DAYS) n Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (log-rank)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 73 57 727.8 69 44 974.6 0.71 (0.48, 1.06) 0.0905
Race
ASIAN 51 43 31 731.8 38 20 1500.8 0.52 (0.29, 0.92) 0.0235
BLACK OR AFRICAN AMERICAN 24 13 11 888.5 15 13 685.2 0.84 (0.35, 1.99) 0.6842
WHITE 20 12 11 589.4 11 9 796.9 1.15 (0.45, 2.92) 0.7719
AMERICAN INDIAN OR ALASKA NATIVE 3 3 2 2009.3 4 1 373.5 >999.99 (0.00, >999.99) 0.2207
MULTIPLE 2 1 1 202.4 1 1 660.7 <0.01 (0.00, >999.99) 0.3173
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1 1 1 370.4 0 NA NA NA NA NA
tabulate_survival_subgroups works correctly with both n_tot and n_tot_events in vars
Code
res
Output
$col_x
[1] 1
$col_ci
[1] 2
$col_symbol_size
[1] 3
Code
res
Output
$col_x
[1] 9
$col_ci
[1] 10
$col_symbol_size
[1] 1
Code
res
Output
[1] "Baseline Risk Factors" "Total Events" "Total n"
[4] "Median (DAYS)" "Events" "n"
[7] "Median (DAYS)" "Events" "n"
[10] "Hazard Ratio" "95% Wald CI" "p-value (log-rank)"
d_survival_subgroups_colvars functions as expected with valid input
Code
res
Output
$vars
[1] "n" "n_events" "median" "n_tot_events" "hr"
[6] "lcl" "pval"
$labels
n n_events median
"n" "Events" "Median (Months)"
n_tot_events hr ci
"Total Events" "Hazard Ratio" "90% Wald CI"
pval
"p-value (log-rank)"
tabulate_survival_subgroups .formats argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101.00 57 727.8 44 974.6 0.71 0.5 to 1.1
Sex
F 55.00 31 599.2 24 1016.3 0.56 0.3 to 1.0
M 46.00 26 888.5 20 974.6 0.91 0.5 to 1.6
Continuous Level Biomarker 2
LOW 36.00 21 735.5 15 974.6 0.76 0.4 to 1.5
MEDIUM 31.00 14 731.8 17 964.2 0.77 0.4 to 1.6
HIGH 34.00 22 654.8 12 1016.3 0.67 0.3 to 1.4
tabulate_survival_subgroups na_str argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
Sex
F 55 31 599.2 24 1016.3 <No data> (0.32, 0.96)
M 46 26 888.5 20 974.6 <No data> (0.50, 1.65)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 <No data> (0.39, 1.51)
MEDIUM 31 14 731.8 17 964.2 <No data> (0.36, 1.61)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36)
label_all argument to extract_survival_subgroups works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Full Analysis Set 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36)
tabulate_survival_subgroups riskdiff argument works as expected
Code
res
Output
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI (95% CI)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06) 14.3 (-0.5 - 29.1)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96) 14.3 (-5.7 - 34.4)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65) 14.3 (-7.6 - 36.1)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51) 29.8 (6.7 - 53.0)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61) -4.5 (-31.6 - 22.5)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36) 14.0 (-11.7 - 39.7)
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extract_survival_subgroups functions as expected with valid input and default arguments
Code
res
Output
$survtime
arm n n_events median subgroup var
1 B: Placebo 73 57 727.8043 All Patients ALL
2 A: Drug X 69 44 974.6402 All Patients ALL
3 B: Placebo 40 31 599.1772 F SEX
4 A: Drug X 38 24 1016.2982 F SEX
5 B: Placebo 33 26 888.4916 M SEX
6 A: Drug X 31 20 974.6402 M SEX
7 B: Placebo 24 21 735.4722 LOW BMRKR2
8 A: Drug X 26 15 974.6402 LOW BMRKR2
9 B: Placebo 23 14 731.8352 MEDIUM BMRKR2
10 A: Drug X 26 17 964.2197 MEDIUM BMRKR2
11 B: Placebo 26 22 654.8245 HIGH BMRKR2
12 A: Drug X 17 12 1016.2982 HIGH BMRKR2
var_label row_type
1 All Patients content
2 All Patients content
3 Sex analysis
4 Sex analysis
5 Sex analysis
6 Sex analysis
7 Continuous Level Biomarker 2 analysis
8 Continuous Level Biomarker 2 analysis
9 Continuous Level Biomarker 2 analysis
10 Continuous Level Biomarker 2 analysis
11 Continuous Level Biomarker 2 analysis
12 Continuous Level Biomarker 2 analysis
$hr
arm n_tot n_tot_events hr lcl ucl conf_level pval
1 142 101 0.7108557 0.4779138 1.0573368 0.95 0.09049511
2 78 55 0.5595391 0.3246658 0.9643271 0.95 0.03411759
3 64 46 0.9102874 0.5032732 1.6464678 0.95 0.75582028
4 50 36 0.7617717 0.3854349 1.5055617 0.95 0.43236030
5 49 31 0.7651261 0.3641277 1.6077269 0.95 0.47860004
6 43 34 0.6662356 0.3257413 1.3626456 0.95 0.26285846
pval_label subgroup var var_label row_type
1 p-value (log-rank) All Patients ALL All Patients content
2 p-value (log-rank) F SEX Sex analysis
3 p-value (log-rank) M SEX Sex analysis
4 p-value (log-rank) LOW BMRKR2 Continuous Level Biomarker 2 analysis
5 p-value (log-rank) MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis
6 p-value (log-rank) HIGH BMRKR2 Continuous Level Biomarker 2 analysis
extract_survival_subgroups works as expected with groups_lists
Code
res
Output
[1] "low" "low" "low/medium" "low/medium"
[5] "low/medium/high" "low/medium/high"
Code
res
Output
[1] "low" "low/medium" "low/medium/high"
extract_survival_subgroups functions as expected with NULL subgroups
Code
res
Output
$survtime
arm n n_events median subgroup var var_label row_type
1 B: Placebo 73 57 727.8043 All Patients ALL All Patients content
2 A: Drug X 69 44 974.6402 All Patients ALL All Patients content
$hr
arm n_tot n_tot_events hr lcl ucl conf_level pval
1 142 101 0.7108557 0.4779138 1.057337 0.95 0.09049511
pval_label subgroup var var_label row_type
1 p-value (log-rank) All Patients ALL All Patients content
a_survival_subgroups functions as expected with valid input
Code
res
Output
hr pval
——————————————————
M 0.12 <0.0001
F 0.57 1.3023
tabulate_survival_subgroups functions as expected with valid input
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36)
tabulate_survival_subgroups functions as expected with NULL subgroups
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
tabulate_survival_subgroups functions as expected with extreme values in subgroups
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 18 10 859.0 8 954.2 0.60 (0.23, 1.59)
Geographic Region 1
Asia 9 4 1244.7 5 796.9 0.97 (0.26, 3.64)
North America 2 2 1066.9 NA NA NA NA
South America 7 4 859.0 3 1759.9 0.39 (0.07, 2.17)
tabulate_survival_subgroups functions as expected when one arm has 0 records
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events n Events Median (DAYS) n Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (log-rank)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 73 57 727.8 69 44 974.6 0.71 (0.48, 1.06) 0.0905
Race
ASIAN 51 43 31 731.8 38 20 1500.8 0.52 (0.29, 0.92) 0.0235
BLACK OR AFRICAN AMERICAN 24 13 11 888.5 15 13 685.2 0.84 (0.35, 1.99) 0.6842
WHITE 20 12 11 589.4 11 9 796.9 1.15 (0.45, 2.92) 0.7719
AMERICAN INDIAN OR ALASKA NATIVE 3 3 2 2009.3 4 1 373.5 >999.99 (0.00, >999.99) 0.2207
MULTIPLE 2 1 1 202.4 1 1 660.7 <0.01 (0.00, >999.99) 0.3173
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1 1 1 370.4 0 NA NA NA NA NA
tabulate_survival_subgroups works correctly with both n_tot and n_tot_events in vars
Code
res
Output
$col_x
[1] 1
$col_ci
[1] 2
$col_symbol_size
[1] 3
Code
res
Output
$col_x
[1] 9
$col_ci
[1] 10
$col_symbol_size
[1] 1
Code
res
Output
[1] "Baseline Risk Factors" "Total Events" "Total n"
[4] "Median (DAYS)" "Events" "n"
[7] "Median (DAYS)" "Events" "n"
[10] "Hazard Ratio" "95% Wald CI" "p-value (log-rank)"
d_survival_subgroups_colvars functions as expected with valid input
Code
res
Output
$vars
[1] "n" "n_events" "median" "n_tot_events" "hr"
[6] "lcl" "pval"
$labels
n n_events median
"n" "Events" "Median (Months)"
n_tot_events hr ci
"Total Events" "Hazard Ratio" "90% Wald CI"
pval
"p-value (log-rank)"
tabulate_survival_subgroups .formats argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101.00 57 727.8 44 974.6 0.71 0.5 to 1.1
Sex
F 55.00 31 599.2 24 1016.3 0.56 0.3 to 1.0
M 46.00 26 888.5 20 974.6 0.91 0.5 to 1.6
Continuous Level Biomarker 2
LOW 36.00 21 735.5 15 974.6 0.76 0.4 to 1.5
MEDIUM 31.00 14 731.8 17 964.2 0.77 0.4 to 1.6
HIGH 34.00 22 654.8 12 1016.3 0.67 0.3 to 1.4
tabulate_survival_subgroups na_str argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
Sex
F 55 31 599.2 24 1016.3 <No data> (0.32, 0.96)
M 46 26 888.5 20 974.6 <No data> (0.50, 1.65)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 <No data> (0.39, 1.51)
MEDIUM 31 14 731.8 17 964.2 <No data> (0.36, 1.61)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36)
label_all argument to extract_survival_subgroups works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Full Analysis Set 101 57 727.8 44 974.6 0.71 (0.48, 1.06)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36)
tabulate_survival_subgroups riskdiff argument works as expected
Code
res
Output
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI (95% CI)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 101 57 727.8 44 974.6 0.71 (0.48, 1.06) 14.3 (-0.5 - 29.1)
Sex
F 55 31 599.2 24 1016.3 0.56 (0.32, 0.96) 14.3 (-5.7 - 34.4)
M 46 26 888.5 20 974.6 0.91 (0.50, 1.65) 14.3 (-7.6 - 36.1)
Continuous Level Biomarker 2
LOW 36 21 735.5 15 974.6 0.76 (0.39, 1.51) 29.8 (6.7 - 53.0)
MEDIUM 31 14 731.8 17 964.2 0.77 (0.36, 1.61) -4.5 (-31.6 - 22.5)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36) 14.0 (-11.7 - 39.7)
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